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Unit 1: Ecology

The word ecology was coined in the last century from the Greek oikos (meaning³house´) to designate the study of organisms in their natural homes. Specifically, means the study of the interactions of organisms with one another and with the physical and chemical environment. Although it includes the study of environmental problems such pollution, the science of ecology also encompassesresearch on the natural world from many viewpoints, using many techniques.Modern ecology relies heavily on experiments, both in the laboratory and in fieldsettings, and on mathermatical ± models. These techniques have proven helpful intesting ecological theories and in arriving at practical decisions in the managemenof natural resources.

Organisms live in nature in association with other organisms, in assemblageswhich we call populations. A population is a group of individuals of the samespecies occupying a given area. The place where a population (or an individual)lives is called its habitat.In nature, populations rarely live alone. Rather, populations live in association wiother populations, in assemblages which are called communities. Frequently,

populations in communities interact, either in beneficial ways or in harmful waysIf two populations interact in a beneficial way, these populations will then maintathemselves better when together than when separate. In such cases we speak of thcooperative nature of the populations.



classified more than 1.5 milion different kinds of organisms. All these organismslive in a region of the Earth that stretches from the ocean floor to about 8 km intothe atmosphere. The region of Earth that supports all living things is called the

biosphere. This global ecosystem is comprised of the hydrosphere, the lithospherand the atmosphere. The biosphere maintains or creates the conditions of temperature, light, gases, moisture, and mineral required for the life processes. Th biosphere may be naturally subdivided into terrestrial and aquatic realms. Theterrestrial realm is usually distributed into particular climatic regions called biomes, each of which is characterized by a dominant plant form, altitude, andlatitude. Particular biomes include grassland, desert, mountain and tropical rainforest. The aquatic biosphere is generally divisible into freshwater and marinerealms. Ecosystems are generally balanced, with each organism existing in its particular habitat and niche. The habitat is the physical location in the environmeto which an organism has adapted. The niche is the overall role that a species (or population) serves in a community. This includes such activities as nutritionalintake (what it eats), position in the community structure (what eats it) and rate o population growth. A niche can be broad (such as scavengers that feed on nearlyany organic food source) or narrow (microbes that decompose cellulose in forestlitter).

All living things must obtains nutrients and a usable form of energy from theabiotic and biotic environments. The energy and nutritional relationships in

ecosystems may be described in a number of convenient ways. A food chain or energy pyramid provides a simple summary of the general trophic (feeding) leveldesignated as producers, consumers, and decomposers, and traces the flow andquantity of available energy from one level to another. It is worth noting thatmicroorganisms are the only living things that exist at all three major trophic



levels.

Life would not be possible without producers, because they provide the

fundamental energy source for all levels of the trophic pyramid. Producers are theonly organism in an ecosystem that can produce organic carbon compounds likeglucose by assimilating (fixing) inorganic carbon (CO2) from the atmosphere.Such organisms may also be termed autotrophs. Most producers are photosynthetorganisms such as plants and cyanobacteria that convert the sun¶s energy into thethe energy of chemical bonds. A small but important amount of CO2 assimilationis brought about by unusual bacteria called chemolithotrophs. The metabolism ofthese organisms derives energy from oxidation-reduction reactions of simpleinorganic compounds such as sulfides and hydrogen.

Consumers eat the bodies of other living organisms and obtain energy from bond present in the organic substrates they contain. The category includes animals, protozoa, and a few bacteria and fungi. A pyramid usually has several levels of consumers, raging from primary consumers (grazers), which consume producers;to secondary consumers (carnivoers), which feed on secondary consumers; and uto quaterary consumers (usually the last level), which feed on tertiary consumers.Decomposers, primarily microbes inhabiting soil and water, break down andabsorb the organic matter of dead organisms, including plants, animals, and othermicroorganisms. Because of their biological function, decomposers are active at a

levels of the food pyramid. Without this important nutritional class of saprobes, th biosphere would stagnate and die. The work of decomposers is to reduce organicmatter into an inorganic form such as minerals and gases that can be cycled back into the ecosystem, especially for the use of primary producers. This process istermed mineralization.



Unit 2: The diversity of life can be arranged into three domains Rain forests abound with the sights, sounds, and scents of living things. Ants,

mosquitoes, beetles, and other insects are literally everywhere ± flying, crawling, jumping ± and you hear them day and night. In a tropical rain forest, the sweetfragrance of showy orchids often hangs in the air, and the loud calls of parrots,toucans, and other colorful birds compete with the hoots and howls of monkeys.

The richness of life in a rain forest ± the vast diversity of species ± can be almostoverwhelming. To make diversity somewhat more comprehensible, scientists havdevised ways of grouping (classigying) organisms. Today, biologists generallyfavor classification schemes with at least eight kingdoms, which are themselves,classified into three higher groups called domains.

The organisms representing the three domains could all be found in one small areof a tropical rain forest. The microscopic organisms are called prokaryotes. Foundliterally everywhere there is life, from rain forests and polar oceans to your ownskin and intestines, prokaryotes are the most widespread of all living organisms.Prokaryotes are distinguished from all other forms of life by their structure. Everyliving being is composed of cells, but only prokaryotes have cells without anucleus, a discrete internal structure that controls cellular activities. There are twovery different groups of prokaryotes, which make up two of the three domains:

Bacteria and Archaea. All organisms except prokaryotes are members of a thirddomain, the Eukarya, organisms made of cells with a nucleus and discrete internastructures called organelles.

Most pools of water containing prokaryotes would also support members of



Domain Eukarya commonly called protists. One group of protists, commonlycalled algae, make their own food molecules by the process of photosynthesis.Another group, commonly called protozoan, are single celled and are animal ± lik

in that they eat other organisms, including algae and prokaryotes.

The large, irregular, bluish cell is an amoeba (a protozoan) and the smaller cells amostly single-celled algae. Also present are considered algae (the long rodlikefilaments), protists because of their similarities to single-celled algae. Untilrecently, protists were classified in a single kingdom, but evidence from moleculastudies now indicates that they are more diverse than any other group of eukaryotes. As we will see when we study them in more detail, protists compriseseveral kingdoms within the domain Eukarya.

Organisms in the remaining three groups (kingdoms) of the Eukarya are allmulticellular. Kimdom Plantae, the plants, are photosynthetic and consist of cellswith strong walls made of cellulose. Kingdom Fungi is a diverse group thatincludes the molds, yeasts, and mushrooms. Fungi decompose the remains of deaorganisms and absorb nutrients from the leftovers.

Representing the kingdom Animalia (animals), the sloth resides in tropical rainforest canopies. Animals eat other organisms and are made of cells that lack rigidwalls. Most animals are motile. The sloth is a slow0moving animal that spends

most of its time hanging upside down eating leaves.

There are actually members of three major groups. The sloth is clinging to one ofthe tall trees (kingdom Plantae) dominating the rain forest. And the greenish tingein the animal¶s hair is a luxuriant growth of photosynthetic prokaryotes (Domain



Bacteria). The sloth depends on trees for food and shelter, the prokaryotes gainaccess to the sunlight necessary for photosynthesis by living on the sloth, and thetree uses some chemical nutrients supplied mainly by prokaryotes.

Life¶s diversity and its interconnectedness are evident almost everywhere. You cafind representatives of the major group on may city streets. There the most obvioexamples of Animalia are likely to be people, with trees, shrubs, and grassrepresenting Plantae. With the help of a microscope, you can find prokaryotes,fungi and protists in any puddle of water or patch of molst soil. Less obsious, but just as significant, are signs of the baisc similarities shared by all organisms. Lifegreat paradox is the unity in its diversity ± the fact that the million of species of organisms are all variations on a relatively small set of basic features.

Unit three: Life¶s levels of organization define the scope of biology

A forest researcher mentions the dialogue between trees and the atmosphere. Whdoes this mean? The word ³dialogue´ refers to interactions between livingorganisms and nonliving matters the gases in the atmosphere. Such interactions aa fundamental property of ecosystems, the highest of several structural levels intowhich life is organized. An ecosystem (for example, a rain forest) consists of allthe organisms living in a particular area, as well as all the nonliving, physicalcomponents of the enviroment that affect the organisms, such as air, soil, and

sunlight. The ecosystem and the structural levels below its form a hierarchy, witheach level building on the ones below it. Below the ecosystem level, all theorganisms in a rain forest are collectively called a community. Below thecommunity, an interacting group of individuals of one species, flying squirrels inour example, is called a population. Below population in the hierarchy is the



organism, an individual living thing.

Below the organism level, life¶s hierarchy unfolds within the individual organism

The flying squirrels¶s body consists of several organ systems, such as a circulatorexcretory system, and a nervous system, shown here. Each organ system consistsof organs. For instance, the main organs of the nervous system are the brain, thespinal cord, and the nerves, which transmit messages between the spinal cord andother parts of the body.

As we continue downward through the hierarchy, each organ is made up of severdifferent tissues, each of which consists of a group of similar cells. A cell is a uniof living matter separated from its environment by a boundary called a membraneEach tissue has a specific function, which is performed by the cells that composeit. The nervous tissue that akes up most of the brain, for example, consists of nervcells. The nervous tissue in the squirrels¶s brain has millions of microscopic nervcells organized into a communication network of spectacular complexity. Thenerve cells transmit signals that coordinate the squirrel¶s body parts, such as themuscles that strtch out its legs during a glide.

Finally, we reach the molecular level in the hierarchy. We show as our exampleDNA (deoxyribonucleic acid). DNA molecules provide the blueprints for constructing the organism¶s other important molecules and transmit this

information, as genes, from parents to offspring. A molecule is acluster of atoms, the smallest particles of ordinary matter. Each of the spheres represents anatom. Each DNA molecule is a very long double helix, two chains coiled aroundeach other.



As we discuss life¶s hierarchy builds from molecules to ecosystems. It takes manmolecules to make a cell, many cells to make a tissue, several kins of tissues tomake an organ, and so on. Most biologists specialize in the sudy of life at a

particular level. For instance, a researcher analyzing the body postures of agliding squirrel focuses on the organism level. However, understanding gliding posture may require studying, at the organ system level the interaction betweenmuscles and bones, so the same researcher often works at more than one level. Thfull spectrum of life¶s hierarchy, from molecules to ecosystems, encompasses thescope of biology. With this in mind, let¶s see how biological scientists go about

their work. Although we focus on examples of outdoor research inforestecosystems, the same scientific approach is used in all types of biological researc

Unit four: Acid precipitation threatens the environment

Imagine arriving for a long-awaited vacation at a mountain lake only to discover that, since your last visit a few years ago, all fish and other forms of life in the lakhave perished bcause of increased acidity of the water. Over the past two decadesthousands of lakes in North America, Europe, and Asia have suffered that fate,

primarily as a result of acid precipitation, usually defined as rain or snow with a pH below 5.6. About 4% of the lakes in the U.S are now dangerously acidic, withthe number close to 10% in the eastern part of the country.

Effects of acid precipitation are also felt on land. There are dead spruce and fir trees on Mount Mitchell in North Carolina, where acid precipitation and acid foghave greatly reduced the numbers of these high mountain trees. In cities, acid inthe air eats away the surfaces of buildings and contributes to smog.



Acid precipitation resuls mainly from the presence in the air of sulfur oxides andnitrogen oxides, air polluting compounds composed of oxygen combined withsulfur or nitrogen. These oxides react with water vapor in the air to form sulfuric

and nitric acids, which fall to the earth in rain or snow. Rain with a pH between 2and 3 ± more acidic than vinegar 0 have been recorded in the eastern U.S. Acid foof pH 1.7, approaching that of the digestive juices in the human stomach, has benrecorded downwind from Los Angeles.

Sulfur and nitrogen oxides arise mostly from the burning of fossil fuels (coal, oil,and gas) in factories and automobiles. Electrical power plants that burn coal produce more of these pollutnats than any other single source. Itonically, the tallsmokestacks built to reduce local pollution by dispersing factory exhaust helpspread airborn acids. Winds carry the pollutants away, and acid rain may fallthousands of miles away from industrial centers.

The effect of acid in lakes and streams is motst pronounced in the spring, as snow begins to melt. The surface snow melts first, drains down, and sends much of theacid that has accumulated over the winter into lakes and streams all at once. Earlymeltwater often has a pH as low as 3, and this acid surge hits when fish and otherforms of aquatic life are producing eggs and young, which are especially vunerabto acidic conditions. Strong acidity can break down the molecules of livingorganisms. And even if the molecules remain intact, they may not be able to carry

out the essential chemical processes of life at very low pH.

While acid precipitation can clearly damage lakes and streams, its effects onforests and other land life are controversial. The damage to the forest on MountMitchell, on one hand, almost certainly results from acid fog and precipitation. Th



acid apparently causes changes in the soil that lead to mineral imbalances, loweretolerance to cold, and general weakness in the trees. On the other hand, carefulstudies over the past decade seem to show that the vast majority of North

American forests are not suffering substantially from acid precipitation.

Many questions remain. We do not know for sure what the long-term effects of acid precipitation may be on plants and soils. Nor do we know much about theeffects of air-borne acid on terrestrial animals, including humans. Perhaps mostimportantly, we do not know how much we must reduce fossil-fuel emission inorder to prevent more damage.

As with most environmental issues, there are no easy solutions to the acid precipitation problem. There is some hopeful news, however. In the united StatesCanada, and Europe, emissions of sulfur oxides have declined signficantly inrecent decades, causing a decrease in acid precipitation. Laws that requirereductions in emissions are thus already helping to alleviate the problem. But justas important is energy conservation. We all need to realize that unless we decreasour consumption of electricity and our dependence on gasoline-poweredautomobiles, we will continue to contribute to acid precipitation and other threatsto the environment.

Rearrangements of atoms

The basic chemistry of life has an overriding theme: the structure of atoms andmolecules determines the way they behave. As we have seen, the chemical properties of an atom are determined by the number and arrangement of itssubatomic paricles, particularly its electrons. Other properties emerge when atom



combine to form more complex substances, such as liquid water. Water is goodexample, because its unusual properties form the foundation of life.

Water can be made from hydrogen and oxygen:2H2 + O2 2 H2O

This is a chemical reaction, a process leading to chemical changes in matter. In th particular case, two molecules of hydrogen (2H2) react with one molecule of oxygen (O2) to give two molecules of water (2H20). The arrow indicates the

conversion of the starting materials, calls reactants (H2 and O2) to the resulting product (H2O)

Notice that the same numbers of hydrogen and oxygen atoms appear on the rightand left sides of the arrow, although they are grouped differently. Chemicalreactions do not create or destroy matter; they only rearrange it in various ways.Chemical reactions involve the making and breaking of chmical bonds. In theexample above, the bonds holding hydrogen atoms together in H2 and thoseholding oxygen atoms together in O2 are broken, and new bonds are formed tovield the H2O product molecules.

Organisms can not make water from H2 and O2 but they do carry out a greatnumber of chemical reactions that rearrange matter in significant ways. Let¶s

examine one that relates to the chapter¶s opening essay. Much of the yellow coloin autumn leaves is from molucules of [igments called carotenoids. These organicmolecules are important in photosynthesis, absorbing solar energy as chlorophylldoes. One of the most common carotenoids is beta-carotene. Beta-carotene is alsoabundant in carrots and many green vegetables and is sold in concentrated form a



a food supplement. This substance can be important in our diet as a source of vitamin A, which is essential for normal vision and healthy skin. Our cells canmake vitamin A from beta-carotene in the following way:

C40H56 + O2 + 4 H 2C20H30O

Beta-carotene Vitamin A

Although there are many atoms in beta-carotene and vitamin A, the chemicalreaction that converts one to the other is essentially a simple one. Two molecules

of vitamin A are made from each beta-caotene molecule by spliting the beta-carotene molecule in half. Notice that beta-carotene has 40 carbon (C) atoms,where as each vitamin A molecule has 20 carbons. The other reactants are amolecule of O2 and 5H atoms contributed by other molecules in the cell. If youcount up all the atims, you will see that the same number of each type appears oneach side of the reaction.

The conversion of beta-carotene to vitamin A is only one example of the thousanof chemical reactions routinely crried out in living cells. Like most of thesereactions, our example involved compounds of the element carbon. We look at thcarbon compunds of cells in more detail in Chapter 3.

Unit 5: The carbon cycle

I. Text1. introduction

Ecosystem are open with regard to energy because the sun is constantly infusing



them with a renewable source. In contrast, the bioelements and nutrients that areessential components of protoplasm are supplied exclusively by sourcessomewhere in the biosphere and are not being continuallly replenished from outd

the Earth. In fact, the lack of a required nutrient in the immediate habitat is one othe chief factors limiting organismic and population growth. Because of the finitesource of life¶s building blacks, the long-terms sustenance of the biosphere requicontinous recycling of elements and nutrients. Essential elements such as carbon,nitrogen, sulfur, phosphorus, oxygen, and iron are cycled through biologic,geologic, and chemical machanisms called biogeochemical cycles.

2. The carbon cycle

Because carbon is the fundamental atom in all biomolecules and accounts for atleast one-half of the dry weight of protoplasm, some form of carbon must beconstantly available to living things. As a result, the carbon cycle is moreintimately associalted with the energy transfers and trophic pattern in the biosphethan are other elements. Besides the enormous organic reservoir in the bodies of organisms, carbon also exitsts in the gaseous state as carbon dioxide (CO2) andmethane (CH4) and in the mineral state as carbonate (CO3 2-). In general, carbonis recycled through ecosystems via photosynthesis (carbon fixation), respirationand fermentation of organic molecules, limestone decomposition, andmethaneproduction. Aconvenient starting point from which to trace the movemen

of carbon is with carbon dioxide, which occupies a central position in the cycle anrepresents a large common pool that diffuses into all parts of the ecosystem. As ageneral rule, the cycles of oxygen and hydrogen are closely allied to the carboncycle.



The principal users of the atmospheric car bon dioxide pool are photosyntheticautotrophs (phototrophs) such as plants, algae, and cyanobacteria. An estimated165 bilion tons of orgnic material per year are produced by terrestrial and aquatic

photosynthesis. A smaller amount of CO2 is used by chemosynthetic autotrophssuch as methane bacteria. A review of the general equation for photosynthesis:

CO2 + H2O =Glucose + O2

Will reveal that phototrophs use energy from the sun to fix Co2 into organic

compunds such as glucose that can be used in synthesis and compounds such asglucose that can be used in synthesis and respiration. Photosynthesis is also the primary means by which the atmospheric supply of O2 is regenerated.

Just as photosynthesis removes CO2 from the atmosphere, other modes of generating energy, such as respiration and fermentation, return it. Recall in thegeneral equation for aerobic repiration that, in the presence of O2, organiccompounds such as glucose are degraded completely to CO2 and H2O, with therelease of energy. Carbondioxide is also released by anaerobic respiration andcertain types of fermentation reactions. Heterotrophic organisms, includingconsumers and decomposers, released Co2 as do most phototrophs, which mustrespire in the absence of light.

A small but important phase of the carbon cycle involves certain limestonedeposits composed primarily of calcium carbonate (CaCO2). Limestone is produced when marine organism like molluscs, corals, protozoans, and algae formhardened sheels by combining carbon dioxide and calcium ions from thesurrounding water. When these organisms die, the durable skeletal components



accumulate in marine deposits. As these immense deposits are gradually exposed by geologic upheaval or receding ocean levels, various decomposing agentsliberate CO2 and return it to the CO2 pool of the water and atmosphere.

The complementary actions of photosynthesis and respiration along with other narural CO2- releasing processes such as limestone erosion and volcanic activityhave maintaned a relatively stable atmospheric pool of carbon dioxide. Recentfigures show that this balance is being disturbed as humans burn fossil fuels andother organic carbon sources. Fossil fuels, including coal, oil, and natural gas, weformed over millions of years through the combined actions of microbes andgeologic forces, and so are actually apart of the carbon cycle. Humans are sodependent upon this energy source that within the past 25 years, the propotion of CO2 in the atmosphere has steadily increased from 0.032% to 0.035%. Althoughthis increase may seem slight and insignificant, many experts now feel it has the potetial to profoundly disrupt the delicate temporature balance of the biosphere.

Compared to carbon dioxide, methane (CH4) plays a secondary part in the carboncycle, though it can be a significant product in anaerobic ecosystems dominated bmethanogens (methan producers). In general, when methanogens reduce CO2 bymeans of variuos oxidizable substrates, they give off CH4. Lithotrophicmethanogens use H2 as an oxidizing agent, and heterotrophic ones use organicacids such as formate or acetate. Typical habitats for methanogens are black mud

marshes sewage sludge and gastrointestinal sites of various animals.

3. The greenhouse effect

The sun¶s radiant energy does more than drive photosyntheisis, it also helps



maintain the stability of the earth¶s temperature and climatic conditions. Asradiation impinges on the earth¶s surface much of it absorbed, but a large amountof the infrared (heat) radiation bounces back into the upper levelas of the

atmosphere. For billions of years, the atmosphere has been insulated by a layer ofgases (primarily CO2, CH4, watervapor, and nitrous oxide) formed by natural processes such as respiration, decomposition, and biogeochemical cycles. Thislayer traps a certain amount of the reflected heat, yet also allows some of its toescape into space. As long as the amounts of heat entering and leaving are balanced, the mean temperature of the earth will not rise or fall in an erratic or lifthreatening way. Although this phenonmenon, called the green house effect, is popularly viewed in a negative light, it must be emphasized that its function for eons has been primarily to foster file.

The greenhouse effect had recently been a matter of concern because greenhousegases appear to be increasing at a rate that could disrupt the temporature balance.In effect, a denser insulation layer will trap more heat energy and gradually heatthe earth. In recent times, 3.5.10 11 tons per year of CO2 have been releasedcollectively by respiration, anaerobic microbial activity, fuel combustion, andvolcanic activity. By far the greatest increase in CO2 production results fromhuman activities such as combustion of fossil fuels, burning forest to clear agricultural land, and manufaturing. Deforestation has the added impact of removing large area of photosynthesizing plants that would otherwise use some o

the CO2.

Originally experts on the greenhouse effect were concerned primarily aboutincreasing CO2 levels, but it now appears that the other greenhouse gasescombined may have a slightly greater contribution than CO2 and they, too, are



increasing. One of these gases CH4 is released from the gastrointestinal track of ruminant animals such as cattle, goats and sheep. Anaerobic bacteria in a part of the stomach called the tumen produce large amounts of this gas as they

sequentially digest cellulose, a major component of the animal¶s diet. The gult oftermites also harbors wood-digest cellulose, a major component of the animal¶sdiet. The gult of termites also harbors wood-digesting and methane-producing bacteria. Although humans can not digest cellulose, intestinal microenvironmentsalso support methanogens. Other greenhouse gases such as nirous oxide (N2O) asulfur dioxide (SO2) are also increasin through automobile and industrial pollutio

So far there is no complete agreement as to the extent and effects of globalwarning. It has been documented that the mean temperature of the earth hasincreased by 0.5 o C since the beginning of the centure. In one proposed senario, by the next century, a rise in the average temperature of 4 to 5 o C will begin tomelt the polar ice caps and raise the level of the ocean 2 to 3 feet, but some exper predict more seriou effect, including massive flooding of coastal regions, changesin rainfall patterns, expansion of deserts, and long term climatic discruptions.

Unit 6: Chemical reactions either store or release energy

Chemical reactions, including those that occur in cells, are of two types. One typecalled endergonic reactions, requires a net input of energy (endergonic means

³energy in´). Endergonic reactions yield products that are rich in potential energy.As you can see, an endergonic reaction starts out with reactant molecules thatcontain relatively little potential energy. Energy is absorbed from the surroundingas the reaction occurs, so that the products of an endergonic reaction store moreenergy than the reactants did. The energy is actually stored in the covalent bonds



the product molecules. And the amount of additional energy stored in the productequals the difference in potential energy between the reactants and the products.

Photosynthesis, the process whereby plant cells make sugar, is one example of astrongly endergonic process. Photosynthesis starts with energy-poor reactants(carbon dioxide and water molecules) and using energy absorbed from sinlight, produces energy rich sugar mlecules.

Some other chemical processes are exergonic. An exergonic reaction is a chemicareaction that releases energy (exergonic means ³energy out´)

An xergonic reaction begins with reactants whose covalent bonds contain moreenergy than those in the products. The reaction releases to the surroundings anamount of energy equal to the difference in potential energy between the reactantand products.

As an example of an exergonic reaction, consider what happens when wood burnOne of the major components of wood is cellulose, a large carbonhydratecomposed of many glucose monomers. Each glucose monomer is rich in potentiaenergy. When wood burns, the potential energy is released as heat and light.Carbon dioxide and water are the products of the reaction.

Burning is one way to release energy from chemicals. Cells release energy bymeans of a different exergonic process, called cellular respiration. Cellular respiration is the energy ± releasing chemical breakdown of glucose molecules anthe storeage of the energy in a form that the cell can use to perform work. Burninand cellular respiration are alike in being exergonic. They differ in that burning is



essentially a one - step process that releases all of a substance¶s energy at once.Cellular respiration, on the other hand, involves many steps, each a separetechemical reaction; you could think of it as a ³slow burn´. Some of the energy

released from glucose by cellular respiration escapes as heat, but a substantialamount of released energy is converted to the chemical energy of molecules of ATP, which we discuss in the next module. Cellls use ATP as an immediate sourcof fuel.

Every working cell in every organism carries out thousands of endergonic andexergonic reactions, the sums of which in known as cellular metabolism. In afirefly, for in stance, the light display discussed earlier is exergonic. In this case,light energy is released when reactants are converted to product molecules withless energy than the reactants. In addition to generating light, fireflies, like allanimals, must find, eat and digest food; escape predatoer; repair damage to the body; grow; and reproduce; All these activities require energy, which is obtainedfrom sugar and other food molecules by the exergonic reactions of cellular respiration. Cells then use that energy in endergonic reactions to make moleculesthat pervform specific tasks. To digest food, for instance, an animal¶s cells usechemical energy to synthesize digestive enzymes. To repair damaged tissues, cellmake other proteins that seal up wounds. In the next module, we see that theconnection between exergonic and endergonic reactions in cellular metabolism ismade by ATP molecules.

Unit 7: Soil factors

Soil is a thin layer of material that lies over rocks, covering most of the land. Itmay be only a few centimeters deep, or it may extend several meters down to the



rock below. Soil forms the link between the abiotic and biotic parts of a terrestriaecosystem. Plant roots grow through it and take in water, minerals and oxygen. Ithas four main components: mineral particles (which may account for up to 60

percent), organic matter (about 10 percent) water (up to 35 percent) and air (up to25 percent). The mineral particles of soil are derived from underlying rock as itundergoes weathring.

Physical weathering can be caused by changes in temperature that cause the rock expand and contract, weakening it so that it eventually shatters. Plants such asmosses and lichens may grow through the cracks, loosening the rock material.Further breakdown occurs in chemical weathering as the rock is exposed to oxygfrom the atmosphere or to acid in rainwater. Bacteria, fungi and lichens alsocontribute acids for chemical weathering.

The mineral particles in soil are distinguished by size: and is the largest, then silt,and the smallest are clay. The proportions of each of these components give a soiits particular characteristics. A soil with a lot of sand and little clay is lightweightwith many air spaces and drains easily, but it is poor in nutrients.

A soil with mostly clay particles is much heavier, holds more water and is slowerto drain. A loamy soil, with balanced amounts of sand, silt and clay, is best suitedfor agricultural use.

The character of a soil also depends on its chemical composition, is formed. Asandy soil may also carry layers of iron or aluminum oxides (this is known as pidsol); salty soilds, wth a high proportion of sodium and a clay ± rich subsoil(solonetz), are frequently found in arid regions.



The organic matter that accumulates as the top layers comes from humus-deadmaterial such as fallen leaves and the remains of animal. Humus give soil its dark

color and nutrients, and improves water retention (insandy soils) and drainage(inclay soils). Bacteria in the murmus play an important role in fixing atmospherinitrogen and making it available to plants. New soil contains no humus. Maturesoil takes as long as 10,000 years to develop, while plant cover grows to allownutrients to circulate between the soil and vegetation. If it is not overexploited, thsoil remains fertile for millions of years. Without plant cover, the soil becomes badly eroded within decades and cannot be replenished.

Acid and alkaline soils

The varying levels of minerals and acidity in the soil have a considerable effect othe types of plants that are able to grow. An acid sandy soil, low in nutrients, isfavored by coniferous trees and by plants such as healthers, which cannot toleratemuch calcium; these are called calcifuges. If calcifuges are grown in alkaline soilthey suffer from poor iron metabolism. In contrast, calcicoles (calcium ± seekers)grow in calcium ± rich alkaline soils often found in grasslands. Typical calcicolesare the grassland plants growing on thin chalky downs.

Calcium and other alkaline compounds may accumulate in the arid climates. The

may be leached (washed) away by irrigation as long as drainage is adequate to prevent waterlogging.

Water factors



All forms of life need water in order to survive. The human body is about 70 percent water, other animals and plants range from 50 to 97 percent water. Livingcells comprise a number of organelles and chemicals within a liquid, the

cytoplasm, and the cell¶s survival may be threatened by changes to the proportionof water in the cytoplasm through evaporation (desiccation), oversupply, of theloss of either water or nutrients to the environment ± a result, for example, of placing a cell designed for a freshwater environment into salt water.

Water is available very widely on the earth, although in some desert areas thesupply is limited, perhaps confined to a single rain shower annually. Water isnaturally of variable quality, and the variation affect the type of organism thatoccupies a particular habitat. Apart from availability, the major natural variationsin water quality are salinity, acidity, temperature, oxygen content and mineralcontent.

Because aquatic organisms are wholly surrounded by water, supply is not a problem. The suitability of the water depends on its teperature, oxygen content ansalinity. Neither the salinity nor the temperature, of the water in the oceans varygreatly; for this reason it is not surprising that the earliest life was found in theoceans rather than on land. In oceans, and large lakes, the temperature of the wateunder the surface layer remains approximately 4 o C in spite of the huge amount solar energy absorbed during the summer.

In the oceans, however, differences do occur which affect the life within them.Currents, both cold and warm, move masses of water around the globe. Cold watholds more oxygen than warm water, and therefore supports a greater quantity of plankton and other life forms that feed off it.



In a smaller body of water such as a lake or inland sea, with little water movementhere are distinct layers of water which do not mix. The top layer tends to warm u

quickly and can be much warmer than the layers below. However, in winter, thislayer cools rapidly and may freeze, whereas the lower layers do not. The lower layers may have little oxygen.

On land, the availability of a regular supply of water is one of the most importantfactors affecting the presence ± or absence ± of plants and animals. The mostspecies are found in the regions with the most abundant water. Few land organismcan drink salt water, as too much salt causes their cells to dry out. The temperaturof the water is less important. It may be quite warm, as is the rain that falls in a

tropical forest, or it may be cold or even frozen: some animals ³drink´ snow,and many rivers that are the main water supply for whole regions are fed by meltsnow.

Most lakes contain fresh water, but in warm areas where there are high rates of evaporation, the water contains a higher ± than ± usual concentration of dissolvedminerals washed from the surrounding rocks, forming a salt lake. These include tGreat Salt lake of the United States and the Dead Sea, between Israel and Jordan,as well as many of the lakes of the rift Valley of Africa. Their community of planand animals is adapted to the abnormally high levels of salt.

The more regularly an animal needs to take in water, the closer it must live to thewater source. Many birds can live far from water because their metabolisms areadapted to survive on only small amounts of liquid. In contrast, large animals tento congregate around common watering holes. If rain is not abundant year ± roun



a regular seasonal supply makes an otherwise arid region more hospitable. Thenatural acidity or mineral content of the water reflects that of the surrounding soil

Because they have so little water, deserts are occupied by fewer species than othe biomes. However, occational supplies of water from rainfall and flash floods may be sufficient for plants and animals adapted to a limited or irregular water supply

Unit 8: Chromosome determine sex in many species

Many animals including fruit flies and humans, have a pair of sex chromosomes,designated X and Y, that determine an individual¶s sex. You learned in Chapter 9about sex determination in humans. Individuals with one X chromosome and oneY chromosome are males; XX individuals are females. Human males and female both have 44 autosomes (nonsex chromosomes). As a result of chromosomesegregation during meiosis, each gamete contains one sex chromosome and ahaploid set of autosomes (22 in humans). All eggs contain a single X chromosomOf the sperm cells, half contain an X chromosome and half contain a Ychromosome. An offspring¶s sex depends on whether the sperm cell that fertilizethe egg bears an X or a Y.

The genetic basis of sex determination in humans is not yet completely understoo

but one gene on the Y chromosome plays a crucial role. This gene, discovered byBritish research team in 1990, is called SRY and triggers testis development. In thabsence of a functioning version of SRY, an individual develops ovaries rather than testes. Other genes on the Y chromosome are also necessary for normal sper production. The X-Y system in other mammals is similar to that in humans. In th



fruit fly¶s X-Y system, however, some genetic details are different, although a Ychromosome is still essential for sperm formation.

The X-Y system is only one of several sex ± determining sys tems. Grasshopperscrickets, and roaches, for example, have an X ± O system, in which O stands for the absence of a sex chromosome. Females have two X chromosome (XX); malehave only one sex chromosome, giving them genotype XO. Males produce twoclasses of sperm (X-bearing and lacking sex chromosome), and sperm cellsdetermine the sex of the offspring at fertilization.

In contrast to the X-Y and X-O systems, eggs determine sex in certain fishes, buterflies, and birds. The sex chromosome in these animals are designated Z andW. Males have the genotype ZZ, females are ZW. Sex is determined by whether the egg carries a Z or a W.

Some organisms lack sex chromosome altogether. In most ants and bees, sex isdetermined by chromosome number, rather than by sex chromosomes.

Females develop from fertilized eggs and thus are diploid. Males develop fromunfertilized eggs ± they fatherless ± and are haploid.

Most animals have two separate sexes; that is individuals are either male or fema

Many plants also have separate sexes, with male and female flowers borne ondifferent individuals. Some plants with separate sexes, such as date palms, spinacand marijuana, have the X ± Y system of sex determination; others, such as thewild strawberry, have the X ± W system



But not all organisms have separate sexes. Most plant species and some animalspecies have individuals that produce both sperm and eggs. Plants of this type ± corn, for example ± are to be monoecious ( from the Greek monos, one, and oiko

house). Animals of this type, such as earthworms and garden snails, are said to behermaphroditic (from the names of the Greed god Hermes and goddess AphroditIn monoectious plants and hermaphroditic animals, all individuals of a specieshave the same complement of chromosome.

Unit 9: The nitrogen cycle

Nitrogen is an essential element that all organisms need to function properly.Plants grown on nitrogen ± deficient soils suffer stunted growth and early death. animals, nitrogen is a component of crucial organic molecules such as DNA and proteins. Although 79 percent of the atmosphere is nitrogen gas, it is relativelyinert and therefore cannot be used directly by most living organisms until it has been converted into nitrates or other nitrogen compounds. Certain bacteria in thesoil, and cyanobacteria in the oceans, are among the few organisms that are able tcarry out this conversion. Nitrogen can be added to the soil as a result of electricadischarge during thunderstorms. The energy from lighting causes oxygen andnitrogen gases to combine with water vapor, forming weak nitric acid. This iswased down in rain and contributes to the nitrogen content of the soil.

Nitrogen is fixed by special nitrogen ± fixing bacteria found in soil and water.These bacteria have the ability to take nitrogen gas from the air and convert it tonitrate. This is called nitrogen fixation. Some of these bacteria occur as free ± living organisms in the soil. Others live in a symbiotic relationship with plants.



Legumes such as clover, peas and beans have nitrogen ± fixing bacteria in their roots which enable them to grow in nitrogen ± deficient soil.

Nitrates taken in by plant roots are incorporated into large organic molecules,which are transferred to animals when they eat the plants. The wastes and remainof both plants and animals contain organic nitrogen compounds which are brokendown by decomposers and converted into inorganic compounds such asammonium ions. Nitrifying bacteria convert these compounds back into nitrates ithe soil, which can be taken in again by plants and cycled through the ecosystemonce more.

In denitrification, nitrates are converted back to nitrogen gas. Denitrifying bacteriare found in waterlogged soils where they release nitrogen gas, causing the soil tolose its nitrogen. Farmers normally try to prevent their fields from becomingwaterlogged.

Because they are not readily available from the atmosphere, nitrates have been inshort supply for most of the Earth¶s history. Nitrogen in artificially ± producedcompunds ± the basic ingredient of fertilizers ± is now more abundant thannitrogen from natural sources, and agricultural yields have improved dramaticallyBut nitrogen cycle is easily unbalanced; even a small change can cause problems

Modern crops, such as wheat and rice, require high levels of nitrogen to sustaintheir fast growth rates. The plants are harvested at the end of the growing season.The nitrogen within the crop is not returned to the soil, whose nitrogen levelquickly becomes depleted. Farmers then have to add artificial sources of nitrogenfertilizers ± to the soil. The most common fertilizers are inorganic substances suc



as ammonium nitrate. Organic fertilizers, such as sewage sludge, manure and bonare a good source of nitrate, but they can be expensive and are less convenient toapply.

Too much nitrogen can cause plants to become too lush and tall, so that they aremore susceptible to damage from wind and disease. If a famer applies too muchnitrate fertilizer, particularly during wet weather, the water-soluble nitrate canleach out of the soil. It passes into water courses or soaks down to the water tablethe supply below the earth¶s surface. Eventually, the fertilizer ends up in a river o pond where it stimulates the growth of freshwater algae, which grow rapidly toform a green blanket over the surface of the water, called algal bloom. It can blocthe light to plants in the water, inhibiting their growth..

Unit 10: The uranium cycle

Like carbon, nitrogen and other naturally ± occuring chemicals, uranium is anelement found in the Earth¶s crust. However, unlike them it plays no part in biological processes, and in large quantities or concentrated form it is dangerous living organisms. This is because uranium, which is the heaviest naturally ± occuring element, undergoes radioactive decay, giving off radiation that caninonize the atoms of substances through which it passes. This can cause metabolidisorders in living cells, causing radiation sickness and in may instances, cancero

growth.

The radioactivity of uranium was discovered in the late 19th century, and by the1940s scientists had learned how to cause the uranium atom to split intoapproximately equal parts (fission) when bombarded by a neutron. This fission se



up a chain reaction which released huge quantities of energy and if the uraniumwere paked sufficiently densely it would create a nuclear explosion

Alternatively, if the chain reaction is controlled, the heat can be released slowlyand used to create steam for driving a turbine: this made possible the developmenof the modern nuclear power industry

Nuclear energy is costly and involves complex technology, but it requires onlysmall amounts of fuel: half a kilogram of uranium can give off as much heat as1400 tonnes of coal. A proportion of that fuel can be recycyled for reuse. Theuranium cycle, although a technological cycle, is therefore an importantcomponent in considering the effects of industrial activity on the Earth¶s naturalcycles.

Uranium ore is mined in Australia, France, North America and southern Africa.Less than one percent of the ore is urnium; the rest is left as spoil at the quarry.Uranium is found in two forms (isotopes): uranium 235 and uranium ± 238.Uranium 235 is more fissionalbe and is therefore better fuel; but natural uraniumcontains less than one percent uranium 235. The mined uranium thereforeundergoes a process of enrichment to increase the proportion, by converting it intgaseous form, then separating the isotopes by centrifuge and diffusion, or by laseseparation.

Enriched uranium is made into fuel in the form of rods which are placed in the coof a reactor, where they generate heat for about seven years, becoming increasingless efficient as a porportion of the uranium decays into other elements, many of them (such as plutonium and strontium) highly radioactive and poisonous. The



spent fuel rod¶s may be taken to a reprocessing plant where they are dissolved instrong acid and up to 96 percent of the remaining uranium is reclaimed for furtheuse.

Nuclear power itself is a ralatively clean source of energy; nuclear power stationsdo not emit air pollutants such as carbon dioxide, nitrogen oxide or sulfur dioxideHowever, they produce a great deal of highly, contaminating wastes. ³Low level´or slightly radioactive wast may be stored in drums and buried in shallow pits, bumuch of the waste from the fuel rods, as well as equipment in the reactor itself,may remain gighly radioactive, dangeous and hot for hundreds or even thousandsof years. This material must be sealed and stoed so that there is no danger of radiation seeping into the ecosystem. It is often place in stainless steel containerssurrounded with a concrete jacket, or made into glass pellets and stored in steeldrums. The nuclear industries are looking for geologically stable sites in which thdrums of waste can be safely entombed for thousands of years. Equally,reprocessing is expensive and hazardous, and transport of spent fuel rods is alsoenvironmentally dangerous.

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