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of chlorophyll molecules, called the reaction center, which uses the energy to promote an

electron to a higher energy level and transfer it to the electron transport system. The reac-

tions centers of photosystem I and photosystem II are known as P700 and P680, respec-

tively, for the optimum wavelengths at which they operate.

The chlorophyll molecule consists of a hydrocarbon tail connected to a ring system

with a nonionic magnesium atom at its center (Figure 5.10). The ring system has the alter-

nating single and double bonds that often characterize compounds that absorb visible

light. There are two main types of chlorophyll: a and b, but chlorophyll a is most common

in plants. Chlorophyll a absorbs most strongly in the blue (400 to 450 nm) and red (640 to

680 nm) regions of the spectrum, leaving green to please our eyes (Figure 5.11). However,

photosystem antennas contain other pigments, such as carotenoids, which capture green

and yellow light energy and transfer it to the chlorophyll. This is particularly important for

plants that live in deep waters, where the longer wavelengths do not penetrate. Diatoms,

the brown algae, and dinoﬂagellates (including the red tide organism) contain pigments

that absorb strongly in the range 400 to 550 nm. The carotenoids become visible when the

Photosystem II

Photosystem I

ATPase

high [H

]

½O

Thylakoid

membrane

P680

P700

AT P

ADP

NADP

NADPH

Photon

Stroma

(low [H

])

P700

Figure 5.9 Photosynthetic apparatus. (From Fried, 1990. # The McGraw-Hill Companies, Inc.

Used with permission.)

Chlorophyll a : R = CH

Chlorophyll b : R = CHO

Figure 5.10 Structure of chlorophyll a and chlorophyll b.

108

ENERGY AND METABOLISM

chlorophyll degrades in deciduous tree leaves in certain areas in the fall, creating the spec-

tacular fall color displays.

Before examining photosynthesis in plants, it may be useful to consider bacterial

photosynthesis ﬁrst, because it is simpler and because its mechanism is retained in

algae and plants. Bacteria have only one photosystem. Absorption of a photon by the

photosystem starts the process of cyclic photophosphorylati on, which results in the pro-

duction of a single ATP. The photon excites an electron in the chlorophyll, which transfers

to the electron transport chain. As the electron is passed down the chain, two protons are

secreted outside the cell using energy from the electron. At the end of the chain, the low-

energy electron returns to the chlorophyll, ready to start the cycle again. The proton secre-

tion creates a chemiosmotic potential across the membrane, which produces ATP as it

passes back into the cell through an enzyme complex. To form carbohydrates, the bacteria

need ATP and NADPH

. Bacteria require an external chemical reducing agent to form

NADPH

, such as H

S, or organic matter. The ATP and NADPH

then feed the

dark reactions to produce carbohydrates as described below. No oxygen is produced as

it is by plants. Indeed, oxygen is toxic to these bacteria. An exception is the prokaryotic

nitrogen-ﬁxing cyanobacter, which does produce oxygen.

Light Reactions Plants and algae retain the cyclic photophosphorylation pathway but

have developed noncyclic photophosphorylation , which has the advantage of not requir-

ing an external reducing agent to replace the electron given up by the chlorophyll

(Figure 5.12). Instead, in photosystem II, water is hydrolyzed to hydrogen and oxygen;

the hydrogens provide the needed electrons, and the remaining protons enter the thylakoid

lumen to augment the chemiosmotic gradient (ultimately for ATP production). The oxy-

gen formed by hydrolysis of the water is released. After passing through the electron

transport chain of photosystem II, using their energy to pump more protons, the low-

energy electrons can then replace electrons promoted by another photon absorbed by

photosystem I. The reenergized elect rons, now in photosystem I, pass through another

electron transport chain and ultimately are used to reduce NADP to NADPH

. (Note

400 500 600 700

Wavelen

th (nm)

Action

spectrum

Absorption

spectrum

Chlorophyll a

Relative light absorption

Relative photochemical efficiency

Figure 5.11 Absorption spectrum of chlorophyll and of a green leaf, and the action spectrum for

the rate of photosynthesis vs. wavelength. (From Fried, 1990. # The McGraw-Hill Companies, Inc.

Used with permission.)

BIOCHEMICAL PATHWAYS 109

the use of NADP instead of NAD as in respiration. NADP is used preferentially when the

reducing power is to be used for synthesizing compounds, not just for transporting elec-

trons.) The sequence of events takes about 5 ms. The overall reaction for noncyclic photo-

phosphorylation is

12 H

O þ 48 hn þ 12 NADP þ 12 ADP þ 12 P

) 6O

þ 12 NADPH

þ 12 ATP

ð5:55Þ

Equation (5.55), as written, involves two electrons, each of which requires two

photons. The protons produced by photolysis of water, plus additional protons pumped

by the electron transport system (not shown), wind up in the thylakoid lumen. The che-

miosmotic gradient across the thylakoid membrane can be as much as 3 pH units, with an

electric potential of up to 100 mV. About one ATP is produced per NADPH

. Overall,

then, noncyclic photophosphorylation requires four photons to produce one ATP and

one NADPH

Noncyclic photophosphorylation produces NADPH

and ATP in about equal amounts;

but glucose production requires additional ATP, and the cell has othe r uses for ATP as

well. To get more ATP, plants are able to exploit cyclic photophosphoryla tion, similar

to bacteria, which does not produce oxygen or NADPH

. It does this by a sort of

‘‘short circuit’’ that shunt s electrons excited by photosystem I back to the electron trans-

port chain of photosystem II (see the dotted line in Figure 5.12). The process is controlled

by NADPH

levels; high levels hinder the ﬂow of electrons out of photosystem I, forcing

them into the other pathway. Thus, the cell can control somewhat independently the rela-

tive amounts of NADPH

and ATP that it produces.

The energy of a mole of photons, E, is related to the frequency, n (or wavelength, l)by

E ¼ hn ¼

ð5:56Þ

where h is Planck’s const ant and c is the speed of light. The two peak wavelengths shown

in Figure 5.11 are 430 and 650 nm. The corresponding energy levels are 67 and 43.5 kcal/

mol, respectively. Four moles of photons of light energy must be absorbed by each of the

−800

−600

−400

−200

200

400

600

800

1000

1200

1400

1600

Standard electrode potential (mV)

Photosystem

P700

P680

ATP

Cyclic photophosphorylation

P430

Cyt b563

Two

photons

Two

photons

2H+

1/2O

2e-

NADP

NADPH

ADP

Figure 5.12 Noncyclic photophosphorylation.

110

ENERGY AND METABOLISM

two photosystems (eight photons in all) to produce one molecule of O

, two of NADPH

and two of ATP. To produce a six-carbon sugar by the dark reac tions, the cell will need

12 NADPH

and 18 ATP. This can be satisﬁed most efﬁciently by 48 photons in noncyclic

photophosphorylation (making 12NADPH

and 12ATP) and 12 photons in cyclic photo-

phosphorylation (six more ATP), for a total of 60 photons. Assuming that a conservative

40 kcal/mol of photons gives a total of 2400 kcal/mol glucose formed since the standard

Gibbs free energy of formation of glucose is 686 kcal/mol, the potential efﬁciency is 29%

(based on photons absorbed). The actual efﬁciency is less, due largely to a wasteful side

reaction called photorespiration, described below.

Dark Reactions The conversion of CO

to glucose is calle d CO

ﬁxation. It is accom-

plished by two pathways. The ﬁrst is a series of 12 reactions called the Calvin cycle

(Figure 5.13). The cycle starts in the stroma of the chloroplast when CO

combines

with a pentose (ﬁve-carbon sugar) to form two three-carbon acids:

ribulose-1;5 biphosphate þ CO

) 2;3-phosphoglycerate ð5:57Þ

Note that this step may be considered to be the actual point of carb on ﬁxation. Yet

it does not require energy from light or even ATP. But ATP and the reducing agent

NADPH

are needed to ensure a supply of the ribulose to keep this reaction going. Several

6 Molecules of

Ribulose 1,5-diphosphate

(C-5)

12 Molecules of

3-Phosphoglycerate

(C-3)

6 Molecules

of CO

12 Molecules of

1,3-diphosphoglycerate

(C-3)

12ATP

12ADP

12 NADPH

12 NADP

The Calvin Cycle

12 Molecules of

Glyceraldehyde

3-phosphate

(PGAL) (C-3)

12ATP

12ADP

10 molecules

PGAL

2 molecules

PGAL

Carbohydrate Synthesis

(glucose, sucrose, starch)

(Photorespiration)

Figure 5.13 Carbon dioxide ﬁxation.

BIOCHEMICAL PATHWAYS 111

subsequent reac tions use two NADPH

and two ATP to produce phosphoglyceraldehyde

(PGAL, or glyceraldehyde-3-phosphate). Most of the PGAL goes on to be converted back

into the ribulose, to keep the cycle go ing. This requires another ATP.

Two of every 12 PGALs formed are converted to another triose, which leaves the chlor-

oplast for the cytoplasm. There they can be converted to glucose or other carbohydrates in

the second pathway. The enzymes for forming glucose are the same as the ones in glyco-

lysis, acting in reverse. In fact, PGAL is one of the key intermediates in glycolysis. PGAL

can also be converted into glycerol and fatty acids for fats, or into amino acids for pro-

teins. Overall, since each turn of the cycle incorporates a single CO

, it takes six cycles to

produce one molecule of glucose. The overall stoichiometry for the Calvin cycle is

6CO

þ 12 NADPH

þ 18 ATP ) C

þ 12 NADP þ 18 ADP þ18 P

þ 6H

ð5:58Þ

Strangely, most plants have a wasteful side reaction, called photorespiration, which

uses the same enzyme as reaction (5.57). The reaction occurs during hot, dry conditions

when leaf pores close to conserve water. CO

is depleted inside the leaf and O

builds up.

The oxygen competes with the CO

for the enzyme, producing a side reaction with the

ribulose-1,5 biphosphate. Waste products are formed instead of carbohydrates, and ATP is

consumed. There seems to be no beneﬁt to the plant. This is a major drain on biological

productivity for the world’s plants and can reduce the net efﬁciency of photosynthesis

below 1%.

A minority of plants (about 100 species are known) have developed a mechanism to tilt

the balance back toward normal CO

ﬁxation. This has occurred in plants that grow in hot,

arid regions. Closing the stomates to limit water loss also limits CO

entry to the leaf. In

these plants, instea d of forming the three-carbon phosphoglycerate in reaction (5.57), cells

near the outside of the leaf use a different reaction that forms the four-carbon oxaloace-

tate, which is then reduced by NADPH

to the four-carbon malate. The malate diffuses to

other cells in the leaf interior, where it reacts to form pyruvate, CO

, and NADPH

.This

has the net effect of transporting CO

and NADPH

to the inner cells at a higher concen-

tration, where they enter the Calvin cycle. Twelve additional ATPs are used per glucose,

but the net efﬁciency increases because photorespiration is relatively low. Plants that do

this include the important food crops sorghum, corn, and sugarcane. Because they form a

four-carbon product with CO

, they are called C

plants. The more common plants with-

out this ability are called C

plants.

Actual maximum photosynthetic efﬁciencies of the C

crops sugarcane (Saccharum

ofﬁcinale), sorghum (Sorghum vulgare), and corn (Zea mays) have been measured to

range from 2.5 to 3.2%; for the C

crops alfalfa, sugar beet, and the alga Chlorella, the

range is 1.4 to 1.9%. C

plants can ﬁx 15 to 40 mg of CO

per dm

of leaf surface per

hour, while C

plants can ﬁx 40 to 80 mg/dm

per hour. C

plants lose much less water by

transpiration than do C

plants. The optimum daytime temperature for growth of C

plants

is higher: 30



to 35



C vs. 20



to 25



C for C

plants. Examples of C

crop grasses are

wheat (Triticum aestivum), rye (Secale cereale), oats (Avena sativa), and rice (Oryza

sativa).

A third strategy for photosynthesis is carried out by succulents such as the jade

plant and some cacti. These are called CAM (for ‘‘crassulacean acid metabolism’’)

plants. CAM plants ﬁx carbon at night with the stomata (pores in the leaves) open. During

the heat of the day the stomata close, and the Calvin cycle obtains its carbon from the

112 ENERGY AND METABOLISM

nighttime storage. Note that C

and CAM plants have all the photosynthetic machinery of

plants: namely, the photosystems and the Calvin cycle. However, they have additional

mechanisms that enable them to utilize CO

more efﬁciently.

The difference between C

and C

plants has caused concern about the effect of the

global CO

increase that is under way. Fossil fuel consumption has caused CO

in the

atmosphere to increase from 280 ppmv in preindustrial times to 356 ppmv in 1993. C

plants are more sensitive to low CO

levels. Experimental results have veriﬁed that

they can beneﬁt more from an increase than C

plants. This has the potential to cause

ecological changes as the competitive balance between plant species changes. It is also

feared that some of the C

food plants could face increased competition from C

weeds. On the other hand, the lawn grasses Kentucky Bluegrass (Poa pratensis) and

creeping bent (Agrostis tenuis) are C

plants, whereas crabgrass (Digitaria sanguinalis)

is a C

plant, ordinarily giving it an advantage during hot, dry summers.

5.4.6 Biosynthesis

Many of the smaller molecules of the cell, whether those used directly or those used as

building blocks of macromolecules, are synthesized from precursors found among the

intermediates of respiration. Th ese anabolic pathways connect respiratory intermediates

with other sugars, amino acids, fatty acids and fats, and nucleic acids. Virtually all the

pathways in a cell are interconnected in a network of reactions.

Nitrogen is assimilated by cells by forming glutamat e and glutamine from ammonia

and ketoglutaric acid. In nitrogen-poor environments, energy must be expended. Rooted

plants and algae can use ammonia, but primarily take nitrogen in as nitrate. Some micro-

organisms can take in nitrate or ﬁx atmospheric nitrogen, but ﬁrst convert these to ammo-

nia. Other amino acids are then formed using the glutamate, possibly with other

precursors, many of which are intermediates in respiration, such as pyruvate or oxaloace-

tate. Formation of proteins from amino acids is discussed in Chapter 6.

Nucleotide synthesis begins with ribose for purines and glutamin e for pyrimidines. The

nitrogens are obtained from the amino acids glycine, glutamine, and aspartate. Fatty acids

are formed using acetyl-CoA, similar to a reverse of the fatty acid oxidation described

above. The process occurs in the cytoplasm and requires NADPH

,CO

, and Mn

2þ

Mammals can synthesize the saturated and monounsaturated fatty acids.

The biopolymers (starch, glycogen, protein, and nucleic acids) are produced by succes-

sive addition to the ends of the molecules. Often, ATP is converted to another nucleoside

triphosphate for the reaction, such as uridine triphosphate, cytosine triphosphate, guani-

dine triphosphate, or thymine triphosphate. The reaction usually splits the second phos-

phate bond, producing a monophosphate instead of a diphosphate. For example, if a

monomer M is joined to a polymer of n units,

ATP þ M þ½M

) AMP þ½M

nþ1

þ PP

Then the resulting pyrophosphate (PP

) is hydrolyzed to orthophosphate. By eliminating

the pyrophosphate reaction product, the ﬁrst reaction is pushed toward completion by the

mass action law.

Sulfur in the form of sulﬁde (S

2

) is needed for the amino acid cysteine, which forms

the disulﬁde bonds that are so important to protein folding. However, our aerobic envir-

onment provides sulfur mostly in the form of sulfate, SO

2

. The sulﬁde can be formed

BIOCHEMICAL PATHWAYS 113

anaerobically by microorganisms that use the sulfate as a terminal electron acceptor in the

electron transport chain. Sulfate can also be reduced by a series of steps starting with ATP,

followed by use of one NADPH

to form sulﬁte ðSO

2

Þ and then three more NADPH

reduce the sulﬁte to sulﬁde.

PROBLEMS

5.1. Compute G



and K

for the complete oxidation of ethanol.

5.2. Compute G



and K

for methanogenesis C

, 3CO

þ 3CH

5.3. Compute the oxidation states of glucose, pyruvate, and lactic acid. Is the conversion

of glucose into two pyruvates an oxidation? How about the conversion of glucose

into lactate?

5.4. For pyruvic acid, glucose, ethanol, and glycine: Using the molecular formula,

compute the oxidation state, the theoretical oxygen demand, and the total organic

carbon content (TOC). Use equation (5.9) to compute the mean oxidation state of

carbon. Compare with the value computed directly from the formula. Discus s the

results.

5.5. Use the Arrhenius equation to compare the temperature increase that doubles the

reaction rate coefﬁcient starting from 25



C for the hydrolysis of gluc ose example

given in the text, for cases with and without enzyme catalysis.

5.6. In Example 5.4, at what concentration will the reaction rate be double the ﬁrst value

measured?

5.7. (a) Write a computer program or develop a spreadsheet to solve Michaelis–Menten

equations (5.30) to (5.32) numerically using Euler’s rule with t ¼ 0:001 min. Start

by writing a differential equation based on elementary kinetics for d½P=dt based on

equation (5.29). Use values for all rate coefﬁcients equal to 1.0 (units are min

1

minL/mg), initial values are [S]

¼100, and [E]

¼50.0, and [ES] ¼ [P]

¼ 10.

Plot the values of [S], [ES], and [P] from 0.0 to 0.5 min. How accurate is the

quasisteady-state assumpt ion?

(b) Repeat part (a) using [E]

¼100. How is the rate of conversion of S to P

affected?

5.8. Using the data of Figure 5.4, equation (5.47) gives reaction rates of 145.2, 185.8,

and 234.2 mm

/min for temperatures 10, 20, and 30



C, respectively. Use the data

for 20 and 30



C in equation (5.48) and solve for y. Then use (5.48) with your value

of y to estimate the reaction rate at 10



C. How does this compare to the value from

equation (5.47)?

5.9. What is the difference between Le Cha

telier’s principle and the law of mass action?

5.10. If a ﬁrst-order reaction has a half-life of 1 h, what is the rate coefﬁcient for that

reaction? How long will it take for the reactant to fall to 1% of its initial

concentration?

5.11. If K

in the Michaelis–Menten equation is equal to 0.02 M, at what concentration

will the reaction proceed at 90% of the maximum rate? 99%?

114 ENERGY AND METABOLISM

5.12. A sample of water containing photosynthetic algae (and negligible amounts of

heterotrophs) is placed in a sealed bottle in sunlight. After a time it is observed that

the dissolved oxygen level in the water has increased and dissolved carbon dioxide

decreases. How will the rate of change of these two substances change immediately

after the bottle is placed in the dark? (Don’t forget about the dark reactions of

photosynthesis.) What about several hours after being in the dark?

REFERENCES

Bailey, J. E., and D. F. Ollis, 1986. Biochemical Engineering Fundamentals, McGraw-Hill, New York.

Fried, G. H., 1990. Schaum’s Outline: Theory and Problems of Biology, McGraw-Hill, New York.

Grady, C. P., Jr., G. T. Daigger, and H. C. Lim, 1999. Biological Wastewater Treatment, Marcel

Dekker, New York.

Henze, et al., 1986. Activated Sludge Model No. 1, International l Association on Water, London.

Lange’s Handbook of Chemistry, 1987. McGraw-Hill, New York.

Lehninger Principles of Biochemistry, 3rd ed., W.H. Freeman, New York.

Smith, E. L., R. L. Hill, I. R. Lehman, R. J. Lefkowitz, P. Handler, and A. White, 1983. Principles of

Biochemistry: General Aspects, McGraw-Hill, New York.

Stryer, L., 1995. Biochemistry, 4th ed., W.H. Freeman, New York.

Vogel, F., J. Harf, A. Hug, and P. R. von Rohr, 2000. The mean oxidation number of carbon (MOC): a

useful concept for describing oxidation processes, Water Research, Vol. 34, No. 10, pp. 2689–

2702.

Watson, J. D., 1968. The Double Helix, Atheneum, New York.

Weast, R. C. (Ed.), 1979. CRC Handbook of Chemistry and Physics, 60th ed., CRC Press, Boca Raton,

FL.

REFERENCES 115

GENETICS

Genetics is one of the most fascinating areas of biology. It has effects at all scales from the

molecule to populations. Its study involves a wide variety of tools, from biochemical tests

to microscopy to breeding experiments. It relies on sophisticated mathematical analysis,

especially from probability and statistics. It is one of nature’s best examples of ampliﬁca-

tion, in which a small change in a single molecule can spell the difference between

disaster and delight at the birth of a child.

Genetics is the science of heredity. Heredity is the transmission of traits from one

generation to another. By traits, we mean a distinguishing observable characteristic of

an organism, such as color or shape of one of its parts, or its ability to metabolize a

particular substance. Each trait is controlled by one or more genes.

6.1 HEREDITY

Gregor Mendel was one of the ﬁrst biologists to use mathematical analysis to prove

hypotheses. He used elementary probability theory in his work. He was also inspired

by the atomic theory of matter (an appropriate example of cross-fertilization in science).

He wondered whether hereditary traits were also passed as particles to future generations.

Previously, it was thought that traits from parents blended to form a new mix in offspring.

Mendel proved his hypothesis and published his results starting in 1865. However, his

contribution was not recognized until the principles were rediscovered inde pendently

by others some 35 years later.

Mendel deduced several of the basic principles of heredity. Here we summarize all of

the principles as known today. Then several of Mendel’s and others’ results will be

described as examples. The principles of heredity can be summarized as eleven rules:

Environmental Biology for Engineers and Scientists, by David A. Vaccari, Peter F. Strom, and James E. Alleman

116

1. A gene is a sequence of nucleotides that codes for a speciﬁc polypeptide. [Recall

that a protein can consist of several polypeptides, and possibly other factors such as

metal atoms (e.g., hemoglobin, which has four polyp eptides and iron atoms).] Not

all genes in a particular cell actually produce their polypeptide. Cells that do

produce the polypeptide associated with a gene are said to express the gene.

2. The genes are contained in the chromosomes.

3. A gene may come in a variety of mutated forms, called alleles. For example, the

gene for eye color may have an allele for blue eyes and another allele for brown

eyes. Although all the organisms of a single species will have the same genes, each

individual can have a unique combination of alleles.

4. The particular combination of alleles that an individual has is called its genotype.

The particular set of genetically controlled traits possessed by an individual is

called its phenotype. That is, the phenotype is the result of expression of the

genotype.

5. Most higher organisms, in particular most plants and animals, are diploid, having

chromosomes in pairs. Thus, they have two copies of each gene.

6. The two copies can have the same or different alleles. If both chromosomes have

the same allele, the organism is said to be homozygous for that gene. If the alleles

are different, the organism is heterozygous. For example, a human can have a blue-

eyed allele on one chromosome and a brown-eyed allele on the other. That

individual would be heterozygous for eye color. Alternatively, both alleles could

be for blue eyes, and the person would be homozygous for eye color.

7. When the two alleles for a gene are different, several situations can occur:

a. Complete dominance: one allele is expressed; the other is not. An allele that is

expressed at the expense of another is said to be dominant. The allele that is not

expressed in a heterozygous genotype is said to be recessive. For example,

brown eye color is dominant and blue eye color is recessive. Blue eye color is

expressed only if both alleles are for blue eyes. When a gene is homozygous for

a recessive allele, it is said to be double recessive, and the recessive allele can be

expressed.

b. Incomplete, or partial, dominance : In this case, a mixed phenotype results in a

heterozygous individual. For example, if snapdragons with red ﬂowers (homo-

zygous for red) are crossed with those with white ﬂowers (homozygous for

white), all the offspring will be heterozygous and will have pink ﬂowers.

However, if these are then crossbred with each other, about one-fourth of the

next generation will be red, one-fourth whi te, and one-half pink.

c. Codominance is when both traits are fully expressed in the heterozygous

organism. This is usually seen only in biochemical traits. An example is

human blood type. If a heterozygous individual has allele A and allele B,

their blood cells will have both type A and type B antigens.

8. Meiosis separates the two alleles of a diploid organism. Thus, gametes have only

one allele. This is called segregati on .

9. Random assortment in meiosis distributes the chromosomes to the gametes

independently. That is, the chromosomes of an individual’s gametes can have

any combination of its maternal and paternal chromosomes. In genetics, this is

HEREDITY 117