A_Molecular_Approach_B_L_U_E_V_E_R_S_I_O_N.pdf

8B L U E V E R S I O N

8th edition

BSCS BiologyA Molecular ApproachBSCS Biology

A Molecular Approach

E V E R Y D A Y L E A R N I N G C O R P O R A T I O NE V E R Y D A Y L E A R N I N G C O R P O R A T I O N

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New Features of the 8th Edition

Chemistry Tips give chemistrybackground information in themargins on an as-needed basis.

Word Etymologies provide themeanings of word roots that studentswill encounter in repeated contexts.

Theory Boxes appear in each of the six units todescribe a theory that has been important in theresearch and development of that area of biology.

Web Resources direct students tokey sites on the Internet for furtherexplanation and individual research.

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8B L U E V E R S I O N

8th edition

BSCS BiologyA Molecular Appro a c hBSCS Biology

A Molecular Appro a c h

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Credits: viii: © M. I. Walker / Photo Researchers, Inc.; 2 and 28: © Gregory Ochocki / Photo Researchers, Inc.; 4: CORBIS / WolfgangKaehler; 6: Dr. Lewis K. Shumway, College of Eastern Utah; 7: BSCS by Carlye Calvin; 9: © Image copyright 2000, PhotoDisc, Inc.; 11:BSCS; 12: (a) This image was made with VMD at the NIH Resource for Macromolecular Modeling and Bioinformatics, University ofIllinois at C-U based on a structure provided in “X-ray Structure of Bacteriorhodopsin at 2.5 Angstroms from Microcrystals Grown inLipidic Cubic Phases” by E. Pebay-Peyroula, G. Rummel, J.P. Rosenbusch, and E.M. Landau in Science, V. 277, p. 1676, 1997; (b) Thisimage was made with VMD at the NIH Resource for Macromolecular Modeling and Bioinformatics, University of Illinois at C-U; 16: © Charles D. Winters / Photo Researchers, Inc.; 22: BSCS by Doug Sokell; 27: (top) Simon Fraser / Science Photo Library / PhotoResearchers, Inc.; (right): Charles Fisher, National Undersea Research Program.

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vii

BRIEF CONTENTSPrologue Biology and the Molecular Perspective

Unit 1: Energy, Matter, and Organization

Chapter 1 The Chemistry of Life2 Energy, Life, and the Biosphere3 Exchanging Materials with the Environment4 Autotrophy: Collecting Energy from the Nonliving

Environment5 Cell Respiration: Releasing Chemical Energy

Unit 2: The Cell: Homeostasis and Development

Chapter 6 Cell Structures and Their Functions7 Transport Systems8 The Cell Cycle9 Expressing Genetic Information

10 Animal Growth and Development11 Plant Growth and Development

Unit 3: Heredity: Continuity of Life

Chapter 12 Reproduction13 Patterns of Inheritance14 Other Forms of Inheritance15 Advances in Molecular Genetics16 Population Genetics

Unit 4: Evolution

Chapter 17 The Origin of Life18 Diversity and Variation19 Changes in Species20 Human Evolution

Unit 5: Responding to the Environment

Chapter 21 Nervous Systems22 Behavior23 Immune Systems

Unit 6: Interactions and Interdependence

Chapter 24 Ecosystem Structure and Function25 Change in Ecosystems

oles

oles

oles

C H A P T E R S

1 The Chemistry of Life

2 Energy, Life, and the Biosphere

3 Exchanging Materials with the Environment

4 Autotrophy: Collecting Energy from theNonliving Environment

5 Cell Respiration: Releasing Chemical Energy


1

U N I T

1

Nonliving things are passive; they cannot control how the environment affects them. Living things, in contrast, select whatthey absorb and what they retain or release. How do they do this?

This is an important question that biologists, scientists who study livingthings, try to answer. In this unit, you will learn some important ideas thatscientists use to understand life. In particular, you will learn about themolecular approach to biology. This approach seeks to answer thesequestions by using the laws of chemistry and physics that describe allthings, not just living ones.

This unit is your introduction to the molecular approach. Here you will learn about the substances that make up living things and how energydrives their activities. You will find out how living things selectively take in some substances from their environment, while rejecting or releasingothers. Finally, this unit will explain how living things collect energy fromthe environment and use it to survive.

How do these tiny living things benefit from

living inside their glass shells?

Can scientists explain the structure of glass

made by living things in the same way that

they explain the structure of glass made in a

factory from sand?

Energy, Matter, and Organization

Energy, Matter, and Organization

Glass shells protect these diatoms, microscopic single-celled algae, from predators. Diatomsform their shells from minerals they absorb from water, not by melting sand as manufacturersdo. However, chemists can analyze and explain the structure of all glass in the same way.Living things obey the laws of physics and chemistry just as nonliving matter does.


Giant kelp (Macrocystis pyrifera) and associated animals in the underwater giant kelp forest off the California coast

C O N T E N T S

AUTOTROPHY AND PHOTOSYNTHESIS

4.1 What Are Autotrophs?4.2 Overview of Photosynthesis4.3 The Light Reactions4.4 The Calvin Cycle

PHOTOSYNTHESIS AND THE ENVIRONMENT

4.5 Rate of Photosynthesis4.6 Photorespiration and Special Adaptations4.7 Photosynthesis and the Atmosphere

CHEMOAUTOTROPHY

4.8 Varieties of Chemoautotrophs4.9 Chemoautotrophs and the Environment


3

P hotosynthesis can be compared to a “living bridge”—connecting the Sun with the organisms on Earth by providing the energy needed forlife. Plants and other photosynthetic organisms harvest solar energy

and use it to combine molecules of carbon dioxide into complex, energy-rich organic compounds. In a sense, plants are the “supermarket” that feedsmuch of the living world. But some environments are too dark or harsh forplants. In these places, bacteria that obtain energy from minerals such asiron or sulfur take their place. In this chapter, you will learn how organismsuse the nonliving energy sources in their environment.

Autotrophy: Collecting Energy from the

Nonliving Environment

Autotrophy: Collecting Energy from the

Nonliving EnvironmentHow do these organisms obtain energy from

their environment?

How could animals survive without plants?

C H A P T E R

4

Plants and other photosynthetic organisms collect energy from sunlight. Other organismsobtain energy from these photoautotrophs. In environments where photosynthesis is notpossible, animals depend on bacteria that obtain energy from chemical reactions of nonliving minerals.


Organic compounds are compoundsthat contain carbon. Organisms arecomposed almost entirely of waterand organic compounds.

CHEMISTRY TIPCHEMISTRY TIP

4 UNIT 1 Energy, Matter, and Organization

A u t o t rophy and Photosynthesis4.1 What Are Autotrophs?

In Chapter 2, you learned the difference between autotrophs, whichobtain energy from nonliving sources, and heterotrophs, which obtainenergy from other organisms. All organisms need a source of energy and asource of carbon compounds for making sugars, amino acids, and othercompounds necessary for life. Photosynthesis, performed by plants, somebacteria, and other small organisms called algae, uses the energy of sunlightto convert carbon dioxide to sugars. Enzymes convert the sugars to aminoacids and other compounds. Autotrophs such as plants that depend onphotosynthesis for both energy and carbon compounds are known asphotoautotrophs. In most environments, photosynthesis supplies theenergy and carbon compounds that photoautotrophs and the heterotrophsthat depend on them need to survive and grow.

We depend on photosynthesis for the production of cotton and otherfibers, wood, grains, vegetables, and fruits, as well as the animal feedsneeded to produce meat, wool, and dairy products. We even rely on theproducts of ancient photosynthesis—petroleum and coal—to power carsand factories and to heat our homes. The oil and coal deposits we useformed millions of years ago from the partly decayed bodies of plants andthe animals that fed on them.

But deep in the ground and under the ocean, there is not enough light for photosynthesis to occur. And some places, such as hot springs, are toohot, salty, or acidic for photoautotrophs to survive. Still, life exists in theseextreme environments. Bacteria called chemoautotrophs obtain energy byoxidizing inorganic substances such as iron, sulfur, or other minerals, just asphotoautotrophs obtain energy from sunlight. They use this energy to formsugars from carbon dioxide. These bacteria replace plants as the basis offood chains in many environments where photosynthesis is not possible(Figure 4.1).

FIGURE 4.1 The upper geyser basin atYellowstone National Park. Note the steam rising from the water. The water is too hot to supportphotoautotrophs. The colors are due to chemoautotrophic bacteriathat can tolerate these extremeconditions.


TABLE 4.1Nutritional Classification of Organisms

Source of Energy Source of Carbon

CO2 (auto-) organic compounds made by other organisms (hetero-)

Light (photo-) photoautotrophs (plants, algae, photoheterotrophs (some bacteria)some bacteria)

Chemicals* (chemo-) chemoautotrophs (some bacteria) chemoheterotrophs (animals, fungi, some bacteria and other one-celled organisms)

CHAPTER 4 Autotrophy: Collecting Energy from the Nonliving Environment 5

Table 4.1 summarizes the major types of autotrophs and heterotrophs.These categories are not absolute. For example, some algae and bacteria canobtain energy from either light or organic compounds, depending on whichis more plentiful in their environment. These organisms are heterotrophspart of the time, and photoautotrophs at other times.

4.2 Overview of Photosynthesis

Photoautotrophs have adapted to take advantage of an energy source that they can never exhaust: sunlight. Light consists of a vibratingelectric and magnetic field. The vibration of this field is like a wave (Figure 4.2). The length of the waves determines the light’s color and energy; the shorter the wave, the greater its energy. Visible light waves have a certain range of energies. They have enough energy to cause small,reversible changes in the molecules that absorb them. When this occurs inour eyes, a chemical signal is generated that allows us to see. When it occursin cells of a photoautotroph, the organism can capture the energy and use it.Photoautotrophic cells contain light-absorbing substances, or pigments,

that absorb visible light. Although ultraviolet waves provide more energy

*This category can be further divided according to whether organic or inorganic chemicals are used as asource of energy.

FIGURE 4.2 The electromagneticspectrum. Energy thatradiates from the Sunforms a continuous series of waves called aspectrum. The range ofwavelengths that animalscan detect with theireyes—visible light—isroughly the same range plants use inphotosynthesis. Shorterwavelengths (blue light)have more energy thanlonger wavelengths (red light).

Use a prism, diffraction grating, orspectroscope to demonstrate thevisible spectrum. Ask studentswhich color of light has the mostenergy. Explain that the color of anobject is due to the light that ittransmits or reflects, not the lightthat is absorbed. Ask studentswhich colors of light leaves absorbmost strongly.


chloro- = green (Greek)-plast = form (Greek, Latin)-phyll = leaf (Greek)granum = grain (Latin)

A chloroplast is a green form.Chloroplasts contain chlorophyll,the pigment that gives leaves theirgreen color. Grana were namedwhen they were first seen with thelight microscope and appeared to besmall grains.

E T Y M O L O G Y


than visible light, few organisms have evolved the ability to absorb and make use of these high-energy waves without being damaged by them.

The light-absorbing pigments that function in photosynthesis areembedded in membranes within cells. These membranes, called thylakoids,form closed sacs. Some of the enzymes involved in photosynthesis are alsoembedded in the thylakoids. In the simple cells of bacteria, the thylakoidssimply float inside the cell. In the cells of plants and algae, each thylakoidsac is part of an organized structure called a chloroplast. An outerchloroplast membrane separates the thylakoid from the cytoplasm andregulates the flow of materials into and out of the chloroplast. Chloroplastmembranes have the same basic structure as other cellular membranes(see Section 1.8).

Figure 4.3 shows a chloroplast from a corn-plant leaf (Zea mays). Thethylakoid membrane inside consists mostly of a series of flattened sacs,which increase the amount of membrane surface area that the chloroplastcan hold. Many of the sacs are stacked like pancakes. These stacks arecalled grana (singular: granum).

The space surrounding the thylakoids is called the stroma. Enzymes inthe stroma catalyze the formation of sugar from carbon dioxide and water,using the light energy captured in the thylakoids. Chloroplasts make a few of

FIGURE 4.3 Electron micrograph of a chloroplast in a leaf of corn, Zea mays, 324,000. The darker areasare stacks of thylakoids called grana; the drawing shows the structure of one enlarged granum.Photosynthetic pigments are embedded in the thylakoid membranes; DNA, RNA, and Calvin-cycle enzymes are in the stroma.

C O N N E C T I O N SC O N N E C T I O N SLight absorption by rhodopsin inboth animal vision and bacterialphotosynthesis is an example ofsimilar adaptations to the samephysical and chemical task inthese unrelated organisms.



their proteins under the direction of their own DNA. The stroma contains the chloroplast’s DNA, as well as the RNA and enzymes needed to makeproteins encoded in the chloroplast DNA. Figure 1.33 summarizes theimportance of DNA.

Most photosynthesis depends on the green pigment chlorophyll,

found in the thylakoids. Plants contain two forms of chlorophyll, a and b,

(Figure 4.4). Chlorophylls a and b absorb light in the violet/blue andorange/red ranges, but not in the green range (Figure 4.5). The green lightthat is not absorbed gives leaves their color. Other, accessory pigmentsabsorb additional wavelengths of light; their absorbed light energy istransferred to a special type of chlorophyll a for use in photosynthesis. Asthe chlorophyll content of leaves declines in the fall, the accessory pigmentsbecome more visible (Figure 4.6). Some photosynthetic bacteria contain aform of a light-absorbing protein called rhodopsin instead of chlorophyll.Another form of rhodopsin occurs in the eyes of animals, where it isinvolved in vision.

The process of photosynthesis involves three energy conversions:

1. absorption of light energy,2. conversion of light energy into chemical energy, and3. storage of chemical energy in the form of sugars.

FIGURE 4.4 The structure of chlorophyll a.Chlorophyll b differs only in having aCHO—group in place of the circledCH3—. Other forms of chlorophylloccur in algae and photosyntheticbacteria. The part of the moleculeshown in green absorbs light; thehydrophobic tail helps to keep themolecule anchored in the lipid-richthylakoid membrane.

FIGURE 4.5 Absorption spectra for chlorophyll a and b. What wavelengths do these chlorophylls absorbmost? least?

FIGURE 4.6 Autumn leaves. The colors are due to accessorypigments that become visible as chlorophyll isbroken down.

You may need to explain that a nanometer, used in Figure 4.5 to describe wavelength, is equal to 10-9 m. Chlorophyll absorbs most light in the blue and red ends of the visiblespectrum, and least in the green region.

Leaves are green because they absorb almost all colors except green light. Askstudents whether a plant would grow better in green light or red light.



These events occur in two groups of reactions, summarized in Figure 4.7.In the light reactions, pigment molecules in the thylakoids absorb light(step 1) and convert it to chemical energy carried by short-lived, energy-richmolecules (step 2). In step 3, the energy of these molecules is used to make3-carbon sugars from carbon dioxide in a series of reactions known as theCalvin cycle. The chemical energy and carbon skeletons of the sugars areavailable to the plant for future growth.

The following equation summarizes the overall reactions ofphotosynthesis.

3 CO2 + 3 H2O light energy C3H6O3 + 3 O2

chlorophyll

carbon water 3-carbon oxygendioxide sugar gas

Note that, in this process, carbon dioxide is reduced and water isoxidized. This equation indicates only the major raw materials and finalproducts of photosynthesis. The many steps and substances involved areexplained in Sections 4.3 and 4.4. As you read the details that follow, keep inmind the overall process as it is described in this section. Remember that theproducts of the light reactions are used in the Calvin cycle. The two groupsof reactions together accomplish the changes described by the previousequation.

4.3 The Light Reactions

The light reactions of photosynthesis convert visible light into thechemical energy that powers sugar production in the Calvin cycle. In thesereactions, chlorophyll and other pigments in the thylakoid absorb lightenergy, water molecules are split into hydrogen and oxygen, and light energy is converted to chemical energy. Refer to Figure 4.9 as you read.

The light-absorbing pigments form two types of clusters, calledphotosystems (PS) I and II. The chlorophyll and other pigments in each

FIGURE 4.7 An overview of photosynthesis. Solar energy is converted to chemical energy in the thylakoidmembranes. Enzymes of the Calvin cycle use this energy to reduce carbon dioxide, formingsugars.

In explaining photosynthesis, first make certain that studentsunderstand the overall processdescribed here; then work downfrom this general description to the details. Refer frequently to the general process.

Ask students howphotosynthesis is important to their own lives. Students oftenrecognize the importance of plantsas a source of food, but neglect the fact that photosynthesis alsoproduces the oxygen we breathe.Ask students what would happen to our air supply withoutphotosynthesis.

The Calvin cycle is also known asthe Calvin-Benson cycle and thephotosynthetic carbon reductioncycle. It was also formerly known asthe photosynthetic dark reactions,but this name is inaccurate becauseit does not occur in the dark.

Try Investigation 4A Photosynthesis.



D I S C O V E R I E S

The Secret of Vegetation

People have long known that they and all otheranimals grow and develop by eating plants or byeating other animals that feed on plants. What is the“food” that plants eat, and how do they increase insize? In the seventeenth century, a physician namedJan Baptista van Helmont tried to answer thesequestions. He reached an amazing conclusion bydoing something completely new. He did not justobserve plants, but performed a quantitativescientific experiment on plant growth (Figure 4.8).In van Helmont’s own words,

Van Helmont performed a beautifully simpleexperiment and tried to measure carefully, but hedid not take into account the air. Neither vanHelmont nor anyone else for another 100 years hadany reason to suspect that the “food” that madeplants grow was made in the leaves from carbondioxide and water.

In 1772, Joseph Priestley discovered that plantsaffect air. In one experiment, he noted that when aburning candle is covered with a jar, its flamequickly goes out. However, when a sprig of mint is

placed in the jar for a few days, and then the candleis covered, the candle burns for a short time.

By 1804, it had been shown that plants must beexposed to light for results such as Priestley’s tooccur. Plants had also been found to release oxygenand absorb carbon dioxide. Nicolas de Saussureshowed that when a plant is exposed to sunlight, itsweight increases by more than the weight of thecarbon dioxide it absorbs. He concluded from thisthat plant growth results from the intake of bothcarbon dioxide and water.

Julius Robert von Mayer proposed in 1845 thatplants absorb light energy and convert it intochemical energy, which is then stored incompounds. These compounds account for morethan 90% of all plant substance.

FIGURE 4.8Van Helmont’s experiment on plant growth in the late 1600s.Over the next 200 years, scientists learned that plantsmanufacture energy from water, sunlight, and carbon dioxide.

I took an earthenware pot, placed in it 200 lbs of earth dried in an oven, soaked thiswith water, and planted in it a willow shootweighing about 5 lbs. After five years hadpassed, the tree grown therefrom weighed169 lbs and about 3 oz. But the earthenwarepot was constantly wet only with rain or(when necessary) distilled water . . . and, to prevent dust flying around from mixingwith the earth, the rim of the pot was keptcovered with an iron plate coated with tinand pierced with many holes. . . . Finally, Iagain dried the earth of the pot, and found itto be the same 200 lbs minus 2 oz. Therefore,164 lbs of wood, bark, and root had arisen

from the water alone.



photosystem absorb light energy and transfer it from one molecule to thenext. All this energy is funneled to a specific chlorophyll a molecule calledthe reaction center (Figure 4.10).

The reaction-center molecules accumulate so much energy that some of their electrons jump to other molecules, known as electron carriers.These molecules form an electron transport system between the twophotosystems. The proteins and other molecules that serve as electroncarriers are embedded in the thylakoid membrane and are organized in away that allows easy movement of electrons from one carrier to the next.Some of them move through the membrane as they transport electrons tothe next carrier in the system. Electrons from photosystem II move throughthe system to replace electrons lost from photosystem I. PSII receivesreplacements for these electrons from an enzyme near its reaction centerthat oxidizes water. This enzyme splits water molecules into protons,electrons, and oxygen.

2 H2O 4 H+ + 4 e– + O2

Recall from Chapter 1 that a hydrogen atom consists of a single proton inthe nucleus and a single electron. Thus a hydrogen ion, H+, is a single proton.When the enzyme oxidizes a water molecule, the oxygen is released as a gas,and the protons accumulate inside the thylakoid sac. The electrons reduce

Stress to students the value ofdiagrams as an aid to u n d e r s t a n d i n gmetabolic pathways such asphotosynthesis. Many studentsignore them and do not realize whata tremendous help they can be. Inorder to follow the diagrams withyour students, it may be helpful tobreak them up into steps, usingworksheets or transparencies.

FIGURE 4.9 The light reactions of photosynthesis. In the thylakoid membrane, pigment molecules in eachphotosystem (PSI and PSII, green) absorb light and transfer its energy to the reaction center,which loses energy-rich electrons (a). At the reaction center of PSII (b), water (blue) is split,freeing electrons (e–), protons (H+), and oxygen (O2). As electrons flow along an electrontransport system (c, yellow), protons are transported to the inside of the thylakoid (d). ATPforms as the membrane enzyme ATP synthetase (e, gray) allows protons to diffuse back out ofthe thylakoid. The electrons and protons finally join with the hydrogen carrier NADP+ (f).



the PSII reaction center, replacing electrons that have already traveled toPSI. You might think of the transfer of electrons from water through PSII to PSI as a flow of reducing power.

Some photosynthetic bacteria obtain electrons from hydrogen sulfide gas(H2S) instead of water. If you replace water in the above equation with H2S,you can figure out what these bacteria produce instead of oxygen—solidsulfur. Bright yellow sulfur particles are visible in these cells under themicroscope (Figure 4.11). The sulfur accumulates in quantities large enoughthat it can be profitably mined.

When electrons from water reach PSI, they receive an energy boost fromthe reaction center there. This gives them enough energy to reduce amolecule known as NADP+ (nicotinamide adenine dinucleotide phosphate).The electrons, along with protons from water, combine with NADP+ toconvert it to its reduced form, NADPH. This is the end of the electron flow inthe light reactions. NADPH then provides the protons and electrons neededto reduce carbon dioxide in the Calvin cycle.

As electrons flow from carrier to carrier along the electron transportsystem, some of the solar energy they received from PSII powers the activetransport of protons across the thylakoid membrane. A high concentrationof positively charged protons accumulates inside the thylakoid. Thedifference in concentration and charge between the inside and outside of thethylakoid creates a difference in potential energy across the membrane,similar to the potential energy of a battery, with its positive and negativeends. And like a battery, this potential energy can do useful work. Theconcentrated protons diffuse out of the thylakoid through an enzymecomplex in the membrane. As they do so, they transfer energy to the enzymecomplex ATP synthetase. The enzyme then uses this energy to synthesizeATP from ADP and phosphate. Appendix 4A, “ATP Synthesis in Chloroplastsand Mitochondria,” explains how the movement of electrons and protonsresults in ATP synthesis.

In summary, you can think of the energy from light as forcing electrons to flow from water to NADP+ in the chloroplast. The electrons retain thisenergy in NADPH. Some of the NADPH is used to synthesize ATP. Thus,photosynthesis converts light energy into the chemical energy of ATP andNADPH. This energy is used later to make sugars from carbon dioxide. ATPand NADPH, along with oxygen gas, are the products of the light reactions of photosynthesis.

FIGURE 4.10 Structure of a photosystem. Eachphotosystem consists of severalhundred molecules of chlorophyll(green) and accessory pigments(orange and yellow) that absorblight energy and transfer it to aspecial chlorophyll a molecule, thereaction center. The reaction centeris the only pigment molecule thatcan participate directly in electronflow in the light reactions.

FIGURE 4.11 Photosynthesis without watersplitting. The photosyntheticbacterium Chromatium oxidizeshydrogen sulfide gas instead of water, producing the yellow sulfur globules visible in its cells.Compare the water-splitting reaction (2 H2O O2 + 4 e– + 4 H+) to the oxidation of hydrogen sulfide(2 H2S 2 So + 4 e– + 4 H+).

During the oxidation of water,positively charged protons areseparated from negatively chargedelectrons. Because these oppositelycharged particles are attracted toeach other, energy is required toseparate them. This reactionconverts solar energy into electricpotential energy that helps to drivethe flow of electrons.


C O N N E C T I O N SC O N N E C T I O N SThe use of solar energy andoxidation-reduction reactions inthe light reactions demonstratehow successful evolutionaryadaptations are shaped by thelaws of chemistry and physics.


Protein Structure and Function

On the shores of San Francisco Bay, evaporationcauses sea salt to accumulate in the wet, sandy soil. A pink scum on the sand reveals the presence ofHalobacterium. This photosynthetic bacterium relies ona purple protein called bacteriorhodopsin, in place ofchlorophyll and the light reactions of thylakoids, tocarry out photosynthesis. Because bacteriorhodopsin isa fairly small protein molecule and its structure andaction are similar to the rhodopsin that absorbs light inour eyes, biochemists have studied it intensively.

Biochemists have found that the bacteriorhodopsinmolecule has seven sections that spiral across thebacterial cell membrane (Figure 4.12a). These sevencoils cluster together to form a channel through themembrane (Figure 4.12b). Amino acids on the outsideof this channel have hydrophobic (nonpolar) sidechains, which associate with the membrane lipids. Thishelps to hold the protein in the membrane. Amino acidson the inside of the channel have hydrophilic (polar)side chains. Water and ions can pass through the polarinterior of the channel between the inside and outside ofthe cell.

A molecule of retinal (a compound related tovitamin A) is weakly bound to one of the amino-acidside chains inside the channel, near the opening to theinterior of the cell. When the retinal molecule absorbslight, it detaches from the protein and binds to ahydrogen ion. Retinal then binds to another amino acidat the outer end of the channel, releasing the hydrogenion. As this cycle is repeated, light powers the transportof hydrogen ions out through the bacterial membrane.ATP synthetase then uses the difference in hydrogen-ion concentration between the inside and outside of thecell to power ATP production, just as it does in thylakoidmembranes. The structure of bacteriorhodopsin ishighly adapted to its function in photosynthesis.

FIGURE 4.12 Bacteriorhodopsin, a photosynthetic pigment. Bacteriorhodopsinand its attached retinal molecule (purple) ( a ) form an ionchannel, shown here in green ( b ) , through the cell membraneof H a l o b a c t e ri u m.

(a)

(b)

Why does photosynthesis not stop with the synthesis of ATP andNADPH? There are two reasons. First, ATP and NADPH are not particularlystable compounds. A plant cannot conveniently store or transport energy in this form. Second, the light reactions do not produce any new carboncompounds that the organism can use to grow. Instead, the Calvin cycle usesthe energy of ATP and NADPH to convert carbon dioxide into stable, easilytransported sugars that provide energy and carbon skeletons for buildingnew cells.

12 UNIT 1 Energy, Matter, and Organization Sample Chapter: Copyrighted Material—Do Not Copy


FIGURE 4.13 Reduction of carbon dioxide tosugars in the Calvin cycle. Enzymesin the stroma of the chloroplastcatalyze each step of the cycle.Rubisco, the enzyme at a, catalyzescarbon dioxide fixation. Thereactions require ATP and NADPHfrom the light reactions at b and d.ADPand NADP+ return to the lightreactions. Aseries of enzymes (c)catalyzes the recombination of five3-carbon molecules of PGALtoform three 5-carbon molecules ofRuBP.

The term bisphosphate describes a molecule such as RuBP with two phosphate groups attached to different carbon atoms (P—C—C—P). Diphosphate is the term for a molecule with a chain of two phosphates attached to each other, as in ADP (C—P—P).

Three turns of the Calvin cycle eachbegin with one molecule of RuBP,for a total of 15 carbons (3 3 5 =15). Each turn adds one carbonatom from CO2, for a total of 18.This is equivalent to six 3-carbonmolecules of PGAL(6 3 3 = 18).Five of these 3-carbon moleculesare needed to regenerate theoriginal 15 carbons in threemolecules of RuBP.

A sugar-phosphate consists of asugar molecule with one or morephosphate groups attached.


4.4 The Calvin Cycle

The Calvin cycle conserves the chemical energy produced in the lightreactions in the form of sugars that the organism can use for growth. Thiscompletes the process of photosynthesis. Figure 4.13 summarizes theenzyme-catalyzed steps of the Calvin cycle as they occur in the stroma of a chloroplast. Follow these steps as you read the description.

At a, the beginning of the cycle, a molecule of carbon dioxide combineswith the 5-carbon sugar-phosphate, ribulose bisphosphate (RuBP). Thisreaction is known as carbon dioxide fixation because it “fixes” carbondioxide gas into an organic molecule. This produces an unstable 6-carbonmolecule that immediately splits into two molecules of the 3-carbon acid,phosphoglyceric acid (PGA). At b, two enzymatic steps reduce eachmolecule of PGA to the 3-carbon sugar-phosphate, phosphoglyceraldehyde(PGAL). This requires one molecule each of ATP and the reducing agentNADPH from the light reactions.

As the Calvin cycle continues, a series of enzymatic reactions, (c),

combines and rearranges molecules of PGAL, eventually producing a 5-carbon sugar-phosphate. The final step, d, uses an ATP molecule from thelight reactions to add a second phosphate group to the 5-carbon sugar-phosphate. This produces a molecule of the starting material, RuBP, thuscompleting the cycle. Three turns of the cycle, each turn incorporating onemolecule of carbon dioxide, result in the formation of six molecules ofPGAL. Of these, five molecules are required to regenerate RuBP. The sixthone is available for the organism to use for maintenance and growth.



Sugar-phosphates such as PGAL are removed from the Calvin cycle foruse in other cellular functions, as shown in Figure 4.14. From these sugar-phosphates, plants can synthesize other compounds they need, such ascarbohydrate polymers and amino acids. In plants, much of the sugarproduced in photosynthesis is converted in the cytoplasm of leaf cells to the12-carbon disaccharide sucrose. Leaf cells can consume sucrose or export itthrough the veins to supply the rest of the plant with energy and carbonskeletons. Chloroplast enzymes can also convert sugars to starch. Manyplants accumulate starch in their chloroplasts during daylight. Whenphotosynthesis shuts down at night, the chloroplasts break the starch down to supply the plant with energy and carbon skeletons.

An enzyme called rubisco catalyzes the reaction that incorporates (fixes)carbon dioxide into the Calvin cycle (Figure 4.13, step a). Because theproduct of this reaction is the 3-carbon acid PGA, plants that use only theCalvin cycle to fix carbon dioxide are called C3 plants. In addition toproviding energy for the synthesis of ATP and NADPH, light activatesrubisco and several other enzymes of the cycle. For these reasons, and alsobecause sufficient carbon dioxide is unavailable when the stomates areclosed, the Calvin cycle cannot operate in the dark.

PGAL and other sugar-phosphates from the Calvin cycle are food for theplant. They supply energy and carbon skeletons to the entire plant, as shownin Figure 4.14. Some of the sugar-phosphates are made into lipids and othersinto amino acids and then proteins. (Chapter 5 discusses how these processeso c c u r.) These changes can happen right in the chloroplast, elsewhere in theplant, or even in other organisms: Humans and other animals consume plants, using the products of photosynthesis as a source of carbon skeletons and energy.

FIGURE 4.14 Fates of sugar produced inphotosynthesis. Plants use thesugars produced in photosynthesisto supply energy and carbonskeletons for growth and other cellwork. Much of this sugar isconverted to sucrose or starch.

The equation for photosynthesis isoften written as

light6 CO2 + 6 H2O — ——>C6H12O6 + 6 O2

This is incorrect—the 6-carbonsugar glucose is not a major product of photosynthesis—but isoften used to summarize the wholeprocess. This equation shows thatthe result of photosynthesis is thereverse of the result of respiration:Photosynthesis captures energy,fixes carbon dioxide, and releasesoxygen gas; respiration releasesenergy and carbon dioxide andconsumes oxygen gas.

Rubisco is short for ribulosebisphosphate carboxylaseoxygenase. This enzyme is themost abundant protein in nature,and may make up 25% or more ofthe total protein in the leaves ofsome plants.

Try Investigation 4B Rate ofPhotosynthesis.



Photosynthesis and theEnvironment 4.5 Rate of Photosynthesis

Environmental conditions strongly affect photosynthesis. Therefore, they also affect the growth of photoautotrophs and the animals and otherheterotrophs that depend on them. An understanding of environmentalinfluences can help people protect and make more efficient use of Earth’sresources. Environmental effects on organisms are usually described in terms of how they affect the rate, or activity per unit of time, of a

Pathways and Compartments

Sometimes it is confusing to think about cycles,pathways, and molecules of metabolism in cells.Remember that the diagrams in this book are modelsbased on the best available experimental data aboutcellular processes. Models help us understand howcells and their parts, such as chloroplasts, work, butthere are no arrows, labels, or enclosing boxes in theactual cell. (There are, however, transport channels,preferred directions of reactions, and compartmentswithin cells.)

Pathways and cycles are made of multiple copies ofthe enzymes and other molecules. The enzymes may beattached to a membrane, making the pathway or cyclemore efficient. For example, the enzymes and electron-carrying proteins of the light reactions are embedded in

sequence in the individual thylakoids. Calvin-cycleenzymes in the stroma may also be attached to thechloroplast membranes. The sugar molecules of theCalvin cycle are probably distributed evenly inside thechloroplast. The organization of enzymes andcompartments in living cells is a result of millions of years of evolution that favor the most efficientarrangements.

PSI and PSII occur at many places along thethylakoids and make millions of molecules of ATP andNADPH. Because there are many molecules of eachCalvin-cycle enzyme, many molecules of carbon dioxidecan be fixed at the same time. Likewise, the activities ofphotosynthesis occur simultaneously in the thousandsof chloroplasts in a single leaf. Do not let diagrams andmodels mislead you. They provide a way to representand study biochemical pathways, but do not representthem exactly.

Check and Challenge1. How is photosynthesis essential to life on Earth?

2. Why are photosynthetic organisms called producers in an ecosystem?

3. How is light used in photosynthesis?

4. What are the products of the light reactions, and how are they used?

5. Why does the Calvin cycle not operate at night?

6. What are the products of the Calvin cycle, and how are they used?


T H E O R YMaterialism and Vitalism

Living things seem different from nonlivingthings. The ancient Greek philosopher Aristotleexpressed this idea when he claimed that spermgives a “vital force” to an egg, bringing it to life.Vitalism, the theory that a “life force” makes livingmatter different from nonliving matter, has come in and out of fashion over the centuries. During theMiddle Ages and Renaissance, vitalism lost some of its appeal. Humans were thought to be unique in possessing a soul, but most people believed thatour bodies, like everything else, were made of fourelements (fire, earth, water, and air). Complexobjects such as animals were just at higher levels on the same Great Chain of Being.

During the 1700s, chemists began to analyzeliving things. The materialists, who claimed thatorganisms and their products are composed of thesame elements as nonliving things, began to opposevitalism. In 1824, the German chemist FriedrichWohler synthesized crystals of urea, a component of urine. He isolated urea from urine and thencompared the crystals to it. They were identical! This seemed to contradict the idea of a vital spirit.

Because materialism claims to be able to explainsomething complicated (life) by completely reducingit to simpler ideas (chemical substances), it is calleda reductionist theory. The chemical reductionistapproach to biology gained ground during the 1800s.The major groups of biochemicals—carbohydrates,proteins, lipids, and nucleic acids—were identified.In 1899, Jacques Loeb discovered certain salts couldforce unfertilized sea urchin eggs to start developing.When he varied the salts, Loeb observed changes inthe rate of growth. Loeb’s experiments implied thatchemistry, not a mysterious force, is the key to life.

By the 1950s scientific vitalism was dead. In anattempt to see how life could have originated,Stanley Miller passed electric current through gasessuch as methane and water vapor. Amazingly, the reaction produced amino acids. Around the same

time, James Watson and Francis Crick uncovered thedouble helix structure of DNA. Their discoveryrevealed that the common link among all life is aparticular chemical molecule.

Scientists are confident today in the power ofphysics and chemistry to explain the structure andfunction of living things. Some phenomena, such as consciousness, are too complex to explain easilyin those terms. Scientists call consciousness anemergent property because it emerges from acomplex brain composed of many simpler parts. As long as mysteries such as consciousness remain,vitalism will retain its appeal.

Experiments have demonstrated that everything is composed of chemical substances. Still, vitalistic thinking leads many people to believe that “natural” or “organic” products are safer and superior to “chemical” ones. Do these products containchemicals?

T H E O R Y

16 UNIT 1 Energy, Matter, and Organization Sample Chapter: Copyrighted Material—Do Not Copy


biological process. For example, you can measure photosynthesis by howmuch carbon dioxide is consumed. Suppose you found that a plantconsumed 2.5 g of carbon dioxide. Was it 2.5 g per second, per hour, or perday? These are very different rates of photosynthesis. The value expressedwithout the unit of time is meaningless. By expressing cell functions in termsof a rate, you answer the question, How fast did the process occur?

Light intensity, temperature, and the concentrations of carbon dioxideand oxygen all affect the rate of photosynthesis. You might expect anincrease in light intensity to increase the rate of photosynthesis. Is thatalways the case? Study the graph in Figure 4.15. What happens to the rate of photosynthesis as light intensity increases? Note that before the lightreaches the intensity of full sunlight, the rate of photosynthesis levels off. At this point, the light reactions are saturated with light energy and areproceeding as fast as possible. In still brighter light, chlorophyll accumulatesenergy faster than it can transfer that energy to the electron transportsystem. Some of this extra energy passes to oxygen molecules. The oxygenmay react with water to form hydroxyl ions (OH–) or hydrogen peroxide(H2O2). These substances can damage chloroplasts by reacting withpigments and proteins. The resulting decline in photosynthesis is calledphotoinhibition.

How would light intensity affect the fate of a pine tree growing under amaple tree in a forest? Young pine trees need more light than young broad-leaved trees such as maple, beech, and oak. This gives young broad-leavedtrees an advantage near the ground in a dense, shady pine forest. Eventually,they take over the forest as the pines die off. That, in turn, changes the typesof animals found in the forest (see Chapter 25). This situation is an exampleof how a cellular adaptation can influence an entire ecosystem.

Temperature affects photosynthesis differently from light intensity. Studythe graph in Figure 4.16 and explain the shape of the curve. Look carefully at

FIGURE 4.15 Effect of light intensity on photosynthesis. As light intensity increases, the rate ofphotosynthesis increases, and then declines slightly. Data are generalized to show trends in C3 plants.

Other environmental factors, suchas humidity and soil conditions, alsoaffect photosynthesis indirectly.



each axis of the graph so you understand what the curve means. Develop a hypothesis to explain the changes in the rate of photosynthesis as thetemperature increases.

An increase in carbon dioxide concentration increases the rate ofphotosynthesis to a maximum point, after which the rate levels off. A curveshowing the effect of carbon dioxide on photosynthesis would be similar inshape to the one for light intensity in Figure 4.15, up to the light saturationpoint. Above the carbon dioxide saturation point, further increases in carbondioxide concentration have no effect on photosynthesis.

The effects of light, temperature, and carbon dioxide all interact witheach other. Any of these factors may be at an ideal level when another is far below optimum. In this case, the factors in shortest supply have the most effect on the rate of photosynthesis. This effect is called the principleof limiting factors, illustrated in Figure 4.17. Note that in maximum light, a higher temperature can increase the rate of photosynthesis.

FIGURE 4.16 Effect of temperature on photosynthesis. As temperature increases, the rate of photosynthesisalso increases, and then declines. Data are generalized to show trends in C3 plants that growbest between 20˚C and 30˚C.

FIGURE 4.17 Interaction of limiting factors. At high light intensity, the rate ofphotosynthesis is greater at 25˚Cthan at 15˚C. Thus, temperature canbe a limiting factor when furtherincreases in light intensity no longerstimulate photosynthesis. Data aregeneralized for typical C3 plants.

Photosynthesis is a series ofchemical reactions that speed up as higher temperatures providemore energy. If the temperature gets too high, however, the proteinsinvolved in photosynthesis become denatured. Some of thedecline in net photosynthesis at high temperatures is also due toincreased cell respiration (Chapter 5) and reduced solubility of carbon dioxide gas.



Brighter light will not do this. Thus plants grown in a greenhouse will notgrow at the maximum rate, even in full sunlight, if the greenhouse is cold.In a forest, limiting factors include light, water, temperature, and nutrients. In the oceans, nutrients are the most important limiting factors forphotoautotrophs in surface water. Below the surface, the availability of light limits photosynthesis.

4.6 Photorespiration and Special Adaptations

Figure 4.18 shows the effect of oxygen on photosynthesis by a C3 plant.Normal atmospheric concentrations of oxygen (about 20%) can inhibitphotosynthesis by up to 50%. How does this happen?

Recall from Section 4.4 that the enzyme rubisco incorporates carbondioxide into sugars in the Calvin cycle. The molecular structures of oxygenand carbon dioxide help to explain how oxygen interferes with carbonfixation. Both molecules are held together by double bonds that keep theatoms about the same distance apart (Figure 4.19). This similarity allowsrubisco to bind to either oxygen or carbon dioxide. When carbon dioxidebinds to rubisco and combines with RuBP, two molecules of PGA form. Butwhen oxygen replaces carbon dioxide in this reaction, the products includeonly one molecule of PGA, and one molecule of the 2-carbon acid glycolate(Figure 4.20). Glycolate is transported out of the chloroplast and partlybroken down to carbon dioxide. The result is that the organism loses fixed carbon atoms, instead of gaining them. This pathway is calledphotorespiration. Unlike true cell respiration (see Chapter 5), the benefits of photorespiration are not yet clearly known. Photorespiration enablesorganisms to recover some of the carbon in glycolate. It may also help toreduce photoinhibition by providing a way for chlorophyll to release excesslight energy.

FIGURE 4.18 Effect of oxygen on photosynthesis. Increasing concentrations of oxygen inhibit the rate ofphotosynthesis in C3 plants.

FIGURE 4.19 Comparison of the structures ofcarbon dioxide and oxygen.Similarities in the double bonds ofthese molecules allow rubsico tobind oxygen instead of carbondioxide.

C O N N E C T I O N SC O N N E C T I O N SThe effects of environmentalconditions on photosynthesisand the adaptations of differentplants to various environmentsare examples of how organismsinteract with their environmentas they evolve in it.



The loss of carbon from the Calvin cycle due to photorespiration slowsthe net rate of photosynthesis. Relatively high levels of carbon dioxide favorphotosynthesis. Relatively high levels of oxygen favor photorespiration.

Weather also affects the balance between these two processes. Manyplants reduce water loss during hot, dry weather by partly closing theirstomates. When stomates are closed, however, carbon dioxide levels in the leaves may drop so low that photorespiration is favored overphotosynthesis.

Two groups of plants have evolved adaptations that reducephotorespiration and aid survival in hot, dry environments. One group,including sugarcane, corn, and crabgrass, has evolved a system that first fixes carbon dioxide by incorporating it in a 4-carbon acid. For thisreason, the process is called C4 photosynthesis. C4 plants have two systemsof carbon dioxide fixation that occur in different parts of the leaves.Surrounding each vein in the leaves is a layer of tightly packed cells, thebundle sheath (Figure 4.21). Mesophyll cells surround the bundle sheathand extend into the air spaces in the leaf.

The mesophyll cells do not contain rubsico. Instead, they fix carbondioxide by combining it with a 3-carbon acid. Unlike rubisco, the enzymethat catalyzes this reaction distinguishes well between carbon dioxide andoxygen. The resulting 4-carbon acid is rearranged and then transported tothe bundle-sheath cells, as shown in Figure 4.22. There, carbon dioxide isreleased from the 4-carbon acid and refixed by rubisco, forming PGA by wayof the Calvin cycle (Section 4.4).

C4 photosynthesis occurs in sometropical grass species and a fewother families.

FIGURE 4.20 Comparison of photosynthesis and photorespiration. Photorespiration occurs simultaneouslywith photosynthesis and results in the loss of previously fixed carbon dioxide. Both processesdepend on the enzyme rubisco, which can react with either carbon dioxide or oxygen. Highcarbon dioxide levels favor photosynthesis over photorespiration. High oxygen levels promotephotorespiration.

C O N N E C T I O N SC O N N E C T I O N SThe binding of rubisco to bothcarbon dioxide and oxygen is anexample of how chemicalstructures and reactions limit therange of possible adaptations.



This arrangement delivers carbon dioxide efficiently to the bundle-sheathcells. By concentrating carbon dioxide in the bundle-sheath cells, the systemfavors photosynthesis and inhibits photorespiration. Although hightemperatures raise the rate of photorespiration more than the rate ofphotosynthesis, the high concentration of carbon dioxide around rubisco inC4 plants overcomes photorespiration. Thus C4 plants can functionefficiently at high temperatures while keeping stomates partly closed to reduce water loss.

By contrast, high temperatures can inhibit photosynthesis in C3 plants byas much as 40 or 50%. In general, C4 plants grow more rapidly than C3 plants,especially in warm climates where C4 plants evolve. Many C4 plants can be

FIGURE 4.21 Specialized leaf anatomy in a C4 plant. Notice the tightly packed layers of cells—bundle-sheathcells and mesophyll cells—that surround the vein.

FIGURE 4.22 The C4 photosynthetic pathway. Carbon dioxide first combines with a 3-carbon acid in theoutside mesophyll cells. The resulting 4-carbon acid is then transported into the bundle-sheathcells, where carbon dioxide is released to the Calvin cycle and refixed by rubisco.

The carbon-fixing enzyme in themesophyll cells of C4 plants is moreeffective than rubisco at low carbondioxide concentrations. Rapidcarbon fixation keeps the carbondioxide concentration in C4 leaveslow, which promotes the diffusion of carbon dioxide into the leaf cells,even when the stomates are partlyclosed.

High temperatures reducephotosynthesis by driving carbondioxide gas out of solution. Point out to students that the same thinghappens in a warm open containerof soda pop. Oxygen is moresoluble than carbon dioxide at high temperatures.

C O N N E C T I O N SC O N N E C T I O N SC4 photosynthesis is anadaptation by certain plants to ahot, dry climate. It is an exampleof evolution through naturalselection.


about twice as efficient as C3 plants in converting light energy to sugars.Most of our important food crops, such as soybeans, wheat, and rice, are C3 plants. Photorespiration may be a major factor limiting plant growth and world food production today.

Another specialization for photosynthesis was first discovered in desertplants such as cactus, jade (Figure 4.23), and snake plants. This system iscalled CAM, for crassulacean acid metabolism. CAM plants open theirstomates at night and incorporate carbon dioxide into organic acids, just asC4 plants do in daylight. During the hot, dry, desert days, the stomates close,conserving water. Enzymes then break down the organic acids, releasingcarbon dioxide that enters the Calvin cycle just as it does in C3 and C4 plants.The CAM system is not very efficient. CAM plants can survive intense heat,but they usually grow very slowly.


Biotechnology

One goal of biotechnology is to create moreproductive food crops. The production of C3 crop plantsin which oxygen does not inhibit rubisco has been thesubject of two areas of genetic engineering research.The first was an attempt to change the gene for theenzyme rubisco, so that the enzyme would not bindoxygen. If the genetically engineered enzyme would stillfix carbon dioxide and initiate the Calvin cycle, then wemight greatly enhance photosynthesis and crop

productivity. After unsuccessfully testing thousandsof genetically altered plants for a form of rubisco thatwould bind carbon dioxide, but not oxygen, researchersconcluded that the project was hopeless.

Some plant physiologists are trying to incorporatethe genes for the C4 system into C3 plants, instead. If wecould genetically engineer critical C3 crops, such assoybeans, wheat, and rice, to photosynthesize as C4

plants, food production might be increased, especiallyin hot, dry regions. This is not an easy task. There aremany differences between C3 and C4 plants. Geneticallyaltering photosynthesis will be extremely difficult, evenwith today’s technology.

CAM refers to the Crassulaceae, afamily of succulent desert plants.Perceptive students may notice thesimilarities between CAM plants andC4 plants. Just as C4 plants reducephotorespiration by separatingcarbon fixation and the Calvin cyclein two places—the mesophyll andthe bundle sheath—CAM plantsseparate these functions in time.

FIGURE 4.23 The jade plant (Crassula). This is an example of a CAM plant.



4.7 Photosynthesis and the Atmosphere

Photosynthesis supplies oxygen gas to Earth’s atmosphere and food to Earth’s organisms. Most organisms, including plants, use oxygen andrelease carbon dioxide. Photoautotrophs use the carbon dioxide again inphotosynthesis, completing the cycle. These relationships are shown inFigure 4.24.

Photosynthesis produces enormous amounts of oxygen. Each year plants use as much as 140 billion metric tons of carbon dioxide and 110 billion metric tons of water in photosynthesis. They produce more than 90 billion metric tons each of organic matter and oxygen gas.

Because photosynthesis is the largest single biochemical process onEarth, any disruption of that process may have dramatic effects. The carbondioxide content of the atmosphere has been increasing steadily at least since1800. Each year, it reaches levels higher than any recorded in history. Theincrease is mostly due to large amounts of carbon dioxide released whenpeople burn fossil fuels or clear land by burning rain-forest plants. Shrinkingforests are also able to remove less and less carbon dioxide from the

One metric ton (MT) = 1,000 kg

FIGURE 4.24 Summary of carbon, oxygen, and energy cycles in the biosphere. Note that energy flows in onedirection—from the Sun to organisms—but substances such as carbon and oxygen cyclerepeatedly through the biosphere.


Check and Challenge1. Why is metabolic activity most accurately expressed as a rate?

2. How does increasing light intensity affect the rate of photosynthesis?

3. Describe the process of photorespiration. What is its effect on therate of photosynthesis?

4. Describe the location and function of the two systems of carbondioxide fixation in C4 plants.

5. Which reaction in photosynthesis is inhibited by oxygen? Construct a graph that compares the effect of oxygen on C3 and C4

photosynthesis.

6. Explain the following statement: The C4 pathway separates carbonfixation from the Calvin cycle in space, and the CAM pathwayseparates them in time.


atmosphere through photosynthesis. The rising carbon dioxide level mayalready have begun to heat up Earth’s climates (see Chapter 25). Althoughthe extra carbon dioxide could increase photosynthesis, preserving thebalance of oxygen and carbon dioxide in the atmosphere may be vital to thefuture of all life on Earth.

Early in the history of life, when the Calvin cycle evolved, there was littleoxygen in the air, so the binding of oxygen by rubisco was not a problem.After millions of years of photosynthesis, oxygen levels built up in theatmosphere and photorespiration became important. The C4 and CAMpathways are examples of the adaptation of photosynthesis to an oxygen-rich atmosphere. Since the 1980s, scientists have noticed increased growthof C3 plants in many parts of the world that were previously dominated by C4

plants. Some biologists think this is happening because the increasing levelof carbon dioxide in the atmosphere favors C3 plants in their competitionwith C4 plants.

Chemoautotrophy4.8 Varieties of Chemoautotrophs

Chemoautotrophs are bacteria that obtain energy by performingchemical reactions, and fix their own carbon. The energy comes fromoxidation of some substance in the environment, usually an inorganicmineral such as iron or sulfur. In general, this process does not provide asmuch energy as photosynthesis or heterotrophy. Many chemoautotrophsmust oxidize large quantities of material to obtain enough energy to live. Thismay be one reason that chemoautotrophy occurs only in certain bacteria.

Since 1750, the concentration ofcarbon dioxide in the atmospherehas risen from about 280 parts permillion to more than 360 ppm.

Some chemoautotrophs that oxidizehydrogen gas (H2) also haveenzymes that enable them to usehydrogen to reduce NAD+ directly.Oxidation of other electron donorsdoes not yield enough energy todrive this reaction.


More complex organisms, such as plants, animals, and fungi, are all eitherphotoautotrophs or heterotrophs. Chemoautotrophs do not compete wellwith other organisms. This is why they grow best in environments whereother organisms cannot survive and light and organic compounds are inshort supply.

Three questions are important in studying a chemoautotroph.

1. What is its source of energy?2. What is its source of carbon?3. What is its source of electrons for reducing carbon?

The answers to these questions are simple for most heterotrophs andphotoautotrophs. Heterotrophs obtain electrons and energy by consumingcarbon compounds produced by other organisms. Photoautotrophs obtainenergy from sunlight, and carbon from carbon dioxide. Most of them obtainelectrons by oxidizing water.

Chemoautotrophs fix carbon dioxide, usually with the Calvin cycle. Their sources of energy and electrons vary greatly, however (Table 4.2). Like photoautotrophs, chemoautotrophs have electron transport systems.They pass the electrons they extract from various substances through theirelectron transport systems to generate ATP and reduce NADPH (or a similarcompound, NADH). The more reduced the electron source is, the moreenergy is released when it is oxidized. Chemoautotrophs that oxidize highlyreduced substances such as hydrogen gas or elemental sulfur are able toproduce more energy and grow faster than those that rely on partly oxidizedelectron donors such as ferrous iron and nitrite ions. Many chemoautotrophscan adapt to changing environments by switching electron donors or living heterotrophically when food is plentiful. Like photoautotrophy,chemoautotrophy is often a matter of degree.

Try Investigation 4C Chemoautotrophs.


Type of Bacteria Electron Donor Energy-Yielding Reaction

hydrogen bacteria hydrogen (H2) 2 H2 + O2 2 H2O

sulfur bacteria hydrogen sulfide (H2S) H2S + 2 O2 SO4–2 + 2 H+

sulfur bacteria elemental sulfur (So) 2 So + 3 O2 + 2 H2O 2 SO4–2 + 4 H+

sulfur bacteria thiosulfate ion (S2O3–) S2O3

–2 + H2O + 2 O2 2 SO4–2 + 2 H+

nitrifying bacteria ammonia (NH4+) 2 NH4

+ + 3 O2 2 NO2– + 4 H+ + 2 H2O

nitrifying bacteria nitrite ion (NO2–) 2 NO2

– + O2 2 NO3–

iron bacteria ferrous-iron ion (Fe+2) 4 Fe+2 + 4 H+ + O2 4 Fe+3 + 2 H2O

TABLE 4.2 Some Common Energy-Yielding Oxidations Performed by Chemoautotrophs

C O N N E C T I O N SC O N N E C T I O N SChemoautotrophs that areadapted to oxidize poor energysources such as nitritedemonstrate that competitionamong organisms and variationin available resources bothcontribute to evolution.



Because many chemoautotrophs can use more than one electron source,you might wonder why any of them rely on the reactions that yield lessenergy. Some use different energy sources, depending on what is available.Others avoid competition by specializing in the use of resources that otherorganisms ignore.

4.9 Chemoautotrophs and the Environment

Because chemoautotrophs do not compete well with other organisms,they are not very important in the sun-lit, organic carbon–rich environmentsfamiliar to us. For example, the chemoautotrophic bacterium calledDeinococcus survives on rocks near the South Pole, exposed to high levelsof ultraviolet radiation and dry, frigid winds that would freeze-dry mostorganisms, without organic nutrients. However, underground and deep inthe ocean where sunlight does not penetrate, chemoautotrophic bacteria arethe carbon-fixing organisms on which others depend. Since the 1980s,studies of the deep ocean (below 1,000 m) and deep earth (below 500 m)have shown that chemoautotrophs are so common in these environmentsthat they may make up the majority of life on Earth.

The oxidized end products of chemoautotrophs form important depositsof oxidized mineral ores, especially iron and sulfur. Chemoautotrophicbacteria also form nodules of manganese and other valuable minerals on thesea floor. These nodules may be mined in the future. Iron-oxidizing bacteriain bogs help to form “bog iron” (ferric hydroxide, Fe(OH)3), an importantsource of iron for the early English settlers in New England. Metal-oxidizingbacteria are important in purifying copper metal from ores, and ascontributors to water pollution near coal mines. They oxidize the copper inore, converting it to soluble cupric ions (Cu+2). The mine workers thencollect the copper as metal. However, when the same bacteria attack coalthat is rich in iron sulfide, or pyrite (FeS2), they oxidize the sulfur in thepyrite, forming sulfuric acid (H2SO4). This strong acid dissolves aluminumand iron from the coal and rock. The acid and dissolved metals wash intolocal streams, killing many of the organisms living there (Figure 4.25).

Nitrogen-oxidizing bacteria are also important in the environment.Inorganic nitrogen ions are important plant nutrients. The supply of nitrogenin soil is often a limiting nutrient in plant growth. Chemoautotrophicbacteria contribute to plant growth by oxidizing ammonium ions (NH4

+) tonitrite ions (NO2

–), and nitrite to nitrate ions (NO3–). Most plants absorb and

use nitrate more effectively than ammonium ions. The nitrogen cycle isdiscussed in more detail in Chapter 24.

In the deepest levels of the sea, chemoautotrophs are the primaryproducers that support heterotrophs such as animals. Deeper than 1,000 m,living things are increasingly rare. On most of the deep sea floor, cold water,high pressure, and scarce nutrients prevent the growth of most organisms.Around underwater volcanic vents, however, the hot water dissolvesreduced forms of sulfur, manganese, and iron from rock. These minerals, as well as volcanic gases such as hydrogen, methane (CH4), and carbon

Ammonia (NH3) is potentially toxicto many plants.

Deep-sea chemoautotrophs obtaincarbon from bicarbonate ions(HCO3

2), which are plentiful inseawater.



FIGURE 4.25 Copper-rich, polluted water of the Queen River in Queenstown, Tasmania (Australia).Chemoautotrophic bacteria oxidize copper ions in the acidic waste water that drains fromcopper mines upstream, coloring the water brown.

monoxide (CO), support a variety of chemoautotrophs. Among the animalsthat depend on these bacteria are worms that do not eat (Figure 4.26).Instead, their bodies contain large numbers of sulfur-oxidizing bacteria.Apparently the worms protect the bacteria inside their bodies, and thebacteria provide the worms with organic nutrients.

Hydrogen-oxidizing bacteria support another kind of biologicalcommunity in the pores of rocks as deep as 2,800 m beneath the surface ofthe earth. Heterotrophic bacteria and fungi consume organic compoundsthat these chemoautotrophs produce. Many of these deep-earth dwellers arenot adapted to survive under these conditions: Some are simply washeddown by groundwater. They may grow so slowly in this nutrient-poorenvironment that they reproduce less than once per century. Eventually, theymay die of starvation or be crushed as the pores they occupy fill up withmineral deposits.

Check and Challenge1. What part of the light reactions of photosynthesis is similar to the

oxidation of minerals by chemoautotrophs?

2. Why are chemoautotrophs rare among familiar organisms?

3. How do chemoautotrophs obtain organic nutrients?

4. Some deep-earth bacteria consume petroleum or natural gas. Arethese organisms chemoautotrophs?

5. Some bacteria reduce metal ions or other inorganic substances. Isthis behavior a clue that these organisms are chemoautotrophs?Explain.

FIGURE 4.26 Tube worms and other organismsliving around an underwatervolcanic vent on the Juan de Fucaridge near the coast of Washingtonstate. Minerals dissolved in thesuperheated water from the “blacksmoker” vent in the backgroundform black solid particles when theyreach the cooler ocean water. Allthese organisms depend on carbonfixation by mineral-oxidizing bacteriafor carbon skeletons and energy.



Summary

Photosynthesis, the most common chemicalprocess on Earth, transforms sunlight into thechemical energy that supports much of life on theplanet. It also releases the oxygen that manyorganisms consume.

The cellular processes of photosynthesis includethe production of ATP and NADPH by the combinedactions of photosystems I and II of the lightreactions. NADPH and ATP are used to fix carbondioxide into sugars during the Calvin cycle. Bothautotrophs and heterotrophs use the sugars forenergy and the manufacture of cellular components.In eukaryotes, photosynthesis occurs in, anddepends on, the structure of the chloroplast.

Environmental factors that directly influence the rate of photosynthesis in plants include lightintensity, temperature, and the concentrations ofcarbon dioxide and oxygen. An increase of lightintensity and carbon dioxide concentration tends toincrease the rate of photosynthesis up to the point ofsaturation. After this, further increases do notstimulate the rate of photosynthesis. Increasingtemperatures affect photosynthesis in the same way,except that high temperatures usually cause adecline in the rate of reactions. High concentrationsof oxygen inhibit the rate of photosynthesis byfueling photorespiration. Environmental factors donot act individually but instead interact as limitingfactors.

C4 and CAM plants have evolved specializationsthat enable them to reduce photorespiration andwater loss in hot, dry climates. C4 plants reducephotorespiration by concentrating carbon dioxide atthe Calvin cycle. In CAM plants, the stomates open atnight and close during the day, greatly reducingtranspiration. Both C4 and CAM are effectiveadaptations to hot, dry climates.

Chemoautotrophs are bacteria that fix carbon,often by the Calvin cycle, and obtain energy byoxidizing substances in the environment, especiallyinorganic minerals. In general, this process providesless energy than photosynthesis or heterotrophy.Chemoautotrophs grow best in environments where other organisms cannot survive and light and organic compounds are in short supply. Manychemoautotrophs are able to use more than oneelectron source.

Chemoautotrophs support communities oforganisms around underwater volcanic vents anddeep in the earth. They are also important in theoxidation of ammonia in soil, and in the formationand mining of mineral ores.

Key Concepts

Use the concepts below to build a concept map,linking to as many other concepts from the chapteras you can.

• C3 • oxidation• C4 • photoautotrophs• Calvin cycle • photorespiration• chemical energy • photosynthesis• chemoautotrophs • reduction• chloroplasts • rubisco• light energy • stroma• light reactions • thylakoids

Reviewing Ideas

1. During photosynthesis, how is light energyconserved in ATP and NADPH?

2. Does the Calvin cycle operate in the dark?Explain.

3. In what ways is photosynthesis important tohumans?

HIGHLIGHTSC h a p t e r

HIGHLIGHTS


4. What is the relationship between the lightreactions and the carbon dioxide–fixingreactions of photosynthesis?

5. Describe how the structure of the chloroplastrelates to its function in photosynthesis.

6. What happens to the sugars made during theCalvin cycle?

7. How does the special leaf anatomy of the C4

plant support C4 photosynthesis?8. Compare photosynthesis in C3 and C4 plants.9. Do chemoautotrophs gain energy by oxidizing

or reducing substances in their environment?What step in photosynthesis is this like?

10. In which part of a pond would you look forchemoautotrophs?

Using Concepts

1. C4 and CAM mechanisms of photosynthesis haveevolved in some plants. What are the advantagesof each type of photosynthesis?

2. Develop a concept map showing how theenvironment influences the rate ofphotosynthesis.

3. The curve in Figure 4.16 shows the effectof temperature increase on the rate of

photosynthesis in a typical C3 plant. Constructand explain a curve showing the response of aC4 plant to the same increase in temperature.

4. Are the light reactions necessary in themesophyll cells of C4 plants? Explain thereasons for your answer.

5. Atmospheric levels of carbon dioxide haveincreased from 300 parts per million (ppm) toalmost 355 ppm in recent years. What will be theeffect of this increase on photosynthesis andgrowth in C3 plants? In C4 plants?

6. Why doesn’t photorespiration occur inchemoautotrophs?

7. Could chemoautotrophs survive and grow onthe rocky surface of the Moon, which has noatmosphere? Explain.

Synthesis

The level of carbon dioxide in the atmospherecontinues to increase. How will this affectcompetition between chemoautotrophs andphotoautotrophs? Explain the reasons for youranswer.

Extensions

You have three plants—one C3, one C4, and oneCAM plant. You also have a pH meter and amicroscope. Describe how you could use only yourpH meter and microscope (with the necessarysupplies that go with each instrument) to identifyeach plant as C3, C4, or CAM.


Web Resources

Visit http://www. e v e r y d a y l e a r n i n g . c o m / b s c s b l u efor useful learning resources related to thisc h a p t e r. There you will find links to informationand activities related to photosynthesis,information about chemoautotrophs and otherorganisms that live in extreme environments, andresearch on the possibility of life on other planets.



Investigations for Chapter 4Autotrophy: Collecting Energy from theNonliving Environment

Investigation 4A Photosynthesis

Section 4.2 of your text used the following equation to represent the chemical reactions ofphotosynthesis:

This equation raises several questions—these willact as the basis for the following experiments thatwill help you understand the process:A. Does a plant use carbon dioxide in the light? in

the dark?B. Is light necessary in order for this reaction to

occur?C. Are the materials shown in the equation

involved in any plant process other thanphotosynthesis?

D. Do plants release the oxygen produced duringphotosynthesis?

In this investigation, you are asked to designexperiments to answer these questions. You willneed to consider the following factors beforebeginning.

1. What type of plant could best serve yourpurpose—a water plant or a land plant?

2. What factor affecting photosynthesis could bestbe used to start and stop the process?

3. How can you detect whether photosynthesis hasor has not occurred?

4. How can you identify the substances that areproduced or released during photosynthesis?

5. What type of controls are necessary?

Materials (per team of 2)

2 lab aprons2 pairs of safety goggles4 15-mm 3 125-mm test tubes (at least)2 wrapped drinking straws4 test tube stoppers (at least)carbonated waterbromothymol blue solutionelodea (Anacharis)

Procedure

PART A Use of CO2 in Light

1. Add enough bromothymol blue solution to a test tube to see a light blue color. Using a drinking straw, gently bubble your breaththrough the liquid until you see a color change.CAUTION: Do not suck any liquid through

the straw. Discard the straw after use.2. Add a few drops of carbonated water to a small

amount of bromothymol blue in a test tube.Observe any color change. What do carbonatedwater and your breath have in common thatmight be responsible for the similar result? Whataction would be necessary to restore theoriginal color of the bromothymol blue?

3. Using elodea, bromothymol blue solution, andtest tubes, set up an experiment to answer

30 INVESTIGATIONS

SAFETY Put on your safety goggles andlab apron. Tie back long hair.

3CO2 + 3H2O plants C3H6O3 + 3O2

lightcarbon water sugar oxygendioxide

Test Material Added Expected Indicator Change Actual Indicator Change What the Change ShowsTube (procedure) (hypothesis) (data) (interpretation)

1 Bromothymol blue Yellow bromothymol blue solution, elodea, solution will turn blue.CO2 and light

TABLE 4A1 Sample Data Table


INVESTIGATIONS 31

Question A. (Hint: Bromothymol blue solution isnot poisonous to elodea.)

4. Using Table 4A1 as a guide, prepare a table inyour logbook that lists the test tubes in yourexperiment. Show what you added to each tube,what change you expected in the bromothymolblue solution, and what change actuallyoccurred. Explain the changes. Fill in the firstthree columns of the table on the day theexperiments are set up, and fill in the last twocolumns the next day.

5. Wash your hands before leaving the laboratory.

PART B Light and Photosynthesis

6. Using the same types of materials as in Part A,set up an experiment to answer Question B. Useas many plants and test tubes as necessary to besure of your answer.

7. Prepare and complete a data table as in Part A.

PART C CO2 in Other Plant Processes

8. Using the same types of materials as in Part A,set up an experiment to answer Question C for CO2.

9. Prepare and complete a data table as in Part A.

PART D Oxygen and Photosynthesis

10. Your teacher or a selected group of students canset up a demonstration experiment to answerQuestion D. What observations in Parts A, B, orC indicate that the elodea in light was giving offa gas? How might some of this gas be collectedand tested to determine its identity?

Analysis

1. Do you have evidence from Procedure A toconfirm that light alone does not change thecolor of the bromothymol blue solution?Explain.

2. Which test tubes show that light is necessary for a plant to carry on photosynthesis?

3. Do plants produce or consume CO2 when theyare not carrying on photosynthesis? What testtubes show CO2’s role? What biological processmight account for your findings?

4. Determine why your expected changes disagreewith the actual changes. Are the differences, ifany, due to experimental error or a wronghypothesis? Explain.

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