Photosynthesis

Photosynthesis

A. Malcolm Campbell, PhD

Christopher J. Paradise, PhD
Photosynthesis
Copyright A. Malcolm Campbell and Christopher J. Paradise. 2016.

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 Abstract
Perhaps the most important chemical reactions on the planet take place in-
side aplants chloroplasts. In this tiny green organelle, plants have the capacity
to capture the energy in light and use that energy to convert CO2 gas into
building blocks used to produce all four categories of biological molecules
lipids, carbohydrates, proteins and nucleic acids. Animals could not sur-
vive if plants did not exist. Not only do they provide us with oxygen to
breathe, they also generate the starting materials for everything we eat.
Rather than focusing on names and trivial details, this book shows how
plants harvest energy in a way that self-regulates. Plants shift how they
process light energy to maximize their productivity and minimize their
exposure to dehydration. All of this regulation is carried out inside every
plant on earth. In addition to plants, there are microbial primary produc-
ers that can harvest energy from a range of environmental sources so that
no place on earth is devoid of life.

Keywords
primary producers, paraquat, photosynthesis, chlorophyll a, chlorophyll b,
thylakoids, stroma, thylakoid space, antenna complex, reaction center,
photon, photosystem I, photosystem II, cytochrome, photooxidized, fos-
sil fuels, Calvin cycle, ribulose, rubisco, chemosynthesis, cold seep, ex-
tremophiles, methanogens, thermal vents, halophiles, orthologs
 Contents
Preface...................................................................................................ix
Acknowledgments....................................................................................xi
Introductionxiii
Chapter 1 Herbicide Paraquat Is Legal in America But Not
in Europe...........................................................................1
Chapter 2 Connecting Brazils Rainforest to Greenlands Glaciers.....21
Ethical, Legal, Social Implications: National Policies
Affect More Than One Nation......................................29
Chapter 3 No Place on Earth Is Devoid of Life.................................33
Conclusion............................................................................................49
Glossary................................................................................................51
Index....................................................................................................53
 Preface
This book on photosynthesis is part of a thirty book series that collectively
surveys all of the major themes in biology. Rather than just present infor-
mation as a collection of facts, the reader is treated more like a scientist,
which means the data behind the major themes are presented. Reading
any of the thirty books by Campbell and Paradise provides readers with
biological context and comprehensive perspective so that readers can learn
important information from a single book with the potential to see how
the major themes span all size scales: molecular, cellular, organismal, pop-
ulation and ecologic systems. The major themes of biology encapsulate
the entire discipline: information, evolution, cells, homeostasis and emer-
gent properties.
In the twentieth century, biology was taught with a heavy emphasis
on long lists of terms and many specific details. All of these details were
presented in a way that obscured a more comprehensive understanding.
In this book, readers will learn how plants harvest energy from abiotic
environmental sources and some of the supporting evidence behind our
understanding. Furthermore, this book addresses the vast diversity of
microbes that can harvest different energy sources from the environment
in surprising ways. Historic and more recent experiments and data will be
explored. Instead of believing or simply accepting information, readers of
this book will learn about the science behind harvesting energy from the
abiotic world the way professional scientists dowith experimentation
and data analysis. In short, data are put back into the teaching of biologi-
cal sciences.
Readers of this book who wish to see the textbook version of this content
can go to www.bio.davidson.edu/icb where they will find pedagogically-
designed and interactive Integrating Concepts in Biology for introductory
biology college courses or a high school AP Biology course.
 Acknowledgments
Publishing this book would not have been possible without the generous
gift of Dr. David Botstein who shared some of his Breakthrough Prize
with AMC. Davids gift allowed us to hire talented artists (Tom Webster
and his staff at Lineworks, Inc.) and copyeditor Laura Loveall. Thanks go
to Kristen Mandava for project management and guidance on the pub-
lishing process. In particular, we are indebted to Katie Noble and Melissa
Hayban for their many hours of help and attention to detail.
Kristen Eshleman, Paul Brantley, Bill Hatfield and Olivia Booker
helped us with technology at Davidson College. We are grateful to ad-
ministrators Tom Ross, Clark Ross, Carol Quillen, Wendy Raymond,
Verna Case, and Barbara Lom who had confidence in us and encouraged
us to persist despite setbacks along the way.
These books were the product of the shared labor of my two visionary
coauthors Laurie Heyer and Chris Paradise. We shared the dream and
the hardships and developed this book from scratch. My family has been
very supportive and I thank Susan, Celeste and Paulina for their support
and patience. I also want to thank Jan Serie, my pedagogical mentor,
who taught me so much about the art and science of helping students
learn. I benefited from the support of the Howard Hughes Medical In-
stitute grant 52006292, the James G. Martin Genomics Program, and
Davidson College. This book would not have survived its first draft with-
out my students who endured the typos and the early versions of this
book. These undergraduates participated in a bold experiment to see if
beginners could construct their own knowledge, retain what they learned,
and transform the way they see themselves and the discipline of biology.
While many people said that beginning students were not up to the task,
my students proved them wrong.
 Introduction
Animals can only survive if they eat other organisms. Many microbes and
some plants also feed on other species. However, plants and some microbes
have the impressive capacity to generate energy from non-living sources;
they are called primary producers. Chapter 1 explains how plants sustain
all animals on Earth by harvesting light and storing this energy into new
covalent bonds. Chapter 2 provides insight into how plants make com-
plex molecules such as proteins, carbohydrates and lipids using their
stored solar energy and CO2 that was produced as a waste product during
cellular respiration. Chapter 3 considers some of the less well known spe-
cies of microbes that live in extreme habitatsplaces where most people
think no life exists. By learning about microbes in extreme habitats,
astrobiologists prepare themselves to discover life on other planets. Over-
arching all three chapters will be an attention to homeostasis at the cel-
lular level. Energy production by definition relates to homeostasis as
demonstrated by the high degree to which these processes are regulated
through feedback loops. This book focuses on the big concepts and fol-
lows the energy rather than becoming distracted by details that cause
people to miss the exciting processes that make life on Earth possible.
 CHAPTER 1

Herbicide Paraquat
IsLegalin America
ButNotinEurope

In 2003, farmers in the European Union (EU) began using the most com-
mon herbicide on the planetparaquat (Figure 1A). Paraquat is used in
over 100 countries to kill unwanted plants, especially weeds that reduce crop
yields. In 2007, an EU court blocked the use of paraquat in Europe. Farmers
in the EU are not allowed to use paraquat, because it [f ]ails to satisfy the
requirement of protection of human health. Most cases of paraquat poison-
ing are due to oral ingestion, but some people have died due to absorption
through the skin. How does paraquat work on plants? Can an herbicide kill
plants and humans? Pathologists quantified the level of paraquat in lab rats
that had consumed potentially lethal doses of the herbicide (Figure 1B).
Physicians can try to lower the harm of ingested paraquat, but lowering the
blood level of paraquat is easier than stopping the accumulation in lungs.
When rats consume paraquat, the poison steadily accumulates in their
lungs, and even blood transfusions fail to lower the concentration of para-
quat from their lungs. It would be unethical to perform similar experi-
ments on humans, but it is reasonable to deduce that all mammals would
accumulate paraquat in their lungs. Paraquat is water soluble as expected
given its +2 net charge. Paraquat is sold as a chloride salt, which makes
the powder form extremely dangerous to breathe. The electrical charge of
paraquat is central to its role in plants and humans.

Understanding photosynthesis

To understand how paraquat works in plants and how this might

affect humans, it is important to understand photosynthesis first.
2 PHOTOSYNTHESIS

paraquat

H3C N+ N+ CH3

100

80
nmoles paraquat

60 lungs

40

blood
20

0
1 8 15 30
B time (hours)
Figure 1 Paraquat and its mammalian consequences. A, Molecular
structure of the herbicide paraquat. B, Paraquat levels in the blood
(per mL) and lungs (per gram) of rats fed paraquat. Error bars are
standard error; n 5 5 rats per time point.
Source: Panel A from public domain, common knowledge. Panel B modified from LL Smith,
1985; his figure 1. Smith, L. L. 1985. Paraquat Toxicity. Philosophical Transaction of the Royal
Society of London. Vol. B 311: 647657. Reprinted with permission from The Royal Society.
Copyright 1985.

Plants photosynthesize to capture the suns energy to produce their own

food, but what does this really mean? Research into photosynthesis
began before the existence of the United States. In 1774, the British
theologian and scientist, Joseph Priestley, was experimenting with the
composition of air. What was in the air we breathe that supports the
flame of a burning candle? Priestley placed an airtight glass dome over a
burning candle and a sprig of mint picked from his garden (Figure 2A).
After a few minutes, the flame went out because it had consumed some-
thing in the air. The apparatus was placed in the sunlight for many days
before Priestley used a magnifying glass to relight the candle. If the
equipment was kept in the dark or lacked a mint leave, the candle could
not be lit again. The light and the mint leaves combined to replenish
what the flame had consumed.
 Herbicide Paraquat IsLegalin America ButNotinEurope 3

day 1 minutes 1 week minutes

later later later

in sunlight

A
light
500 500 600 700 800
100

saturation (%)

light intensity
relative
oxygen
light

deplete
oxygen
50

d
0
0 5 20 25
B C time (min)
Figure 2 Plants produce oxygen. A, Priestleys 1774 experiment
showing that plants in the sunlight can replenish depleted air. B,
Engelmanns 1882 experiment showed oxygen-loving bacteria (white
spots) moved to the portion of algae cells (horizontal rectangles)
exposed to particular wavelengths of light. C, Hills experiment
measured oxygen production (y-axis, left side) from purified
chloroplasts exposed to different intensities of light (boxes, y-axis
right side).
Source: Panel A original art based on Joseph Priestlys 1774 written description. Panel B
modified from Engelmann, 1882, his figure 1. Kamen, Martin D. 1986. On creativity of eye and
ear: a commentary on the career of T. W. Engelmann (page 242). Proceedings of the American
Philosophical Society. Vol. 130(2): 232246. Reprinted with permission from the American
Philosophical Society. Panel C modified from Hill, 1937; part of his figure 1. Hill, R. 1937.
Oxygen evolved by isolated chloroplasts. Nature. Vol. 139: 881882. Reprinted by permission
from Macmillan Publishers Ltd.

More than 100 years after Priestley, German physiologist Theodor

Wilhelm Engelmann conducted experiments to understand what happened
to plants when they were exposed to sunlight (Figure 2B). Engelmann
worked with a rod-shaped algae and a species of bacteria he called Bacterium
termo that exhibited a surprising behavior. Engelmann had discovered
that B. termo was able to detect very small quantities of oxygen and swim
toward areas of higher oxygen when presented with two solutions of dif-
ferent dissolved oxygen levels. Engelmann used a specially designed micro
scope that was built by his friend, Carl Zeiss, who founded the famous
4 PHOTOSYNTHESIS

microscope company. The microscope could separate the different colors

of light as seen in a rainbow. Engelmann knew of Priestleys research and
wanted to determine what the plants produced when they were exposed
to sunlight. Engelmann exposed algae to a rainbow of light and watched
through the microscope to see what B. termo would do. Engelmann did not
have a camera to capture the image, so he drew his observations to docu-
ment plants producing a substance that attracted oxygen-loving bacteria.
Priestley realized that a gas in the air we breathe is consumed by fire.
Of course, the gas is oxygen (O2), but Priestley called it something else at
the time. More importantly, Priestly discovered that plants can replenish the
air with oxygen if and only if the plants were exposed to light. Engelmann
added to the understanding of photosynthesis by discovering that some
wavelengths of light are more effective than others at stimulating plants to
produce oxygen. From his frequency distribution-like drawing, it can be
seen that blue light and red light stimulated the most oxygen production,
and green light stimulated the least amount of oxygen production.
Approximately 50 years after Engelmanns experiments with B. termo,
biochemist Robin Hill at Cambridge University in the UK made signifi-
cant discoveries about the process of photosynthesis (Figure 2C). Hill
determined the green colored chloroplasts were subcellular organelles that
used sunlight to produce oxygen. Hill disrupted spinach leaf cells and used
centrifugation to isolate the intact chloroplasts. Hill exposed the chloro-
plasts to light and measured the concentration of dissolved oxygen in the
buffer containing the chloroplasts. Hill demonstrated that the rate of
oxygen production was influenced by the intensity of light. Between the
two light exposures, Hill used a chemical that rapidly consumed all the
oxygen.
Hill focused his attention on the only organelle that looked green
inside plantschloroplasts. Hill realized that if plants cannot use green
light to produce oxygen, and chloroplasts are green, this organelle is the
likely source of oxygen production in response to light. The results of
Figure 2C confirmed Hills hypothesis and demonstrated that the rate of
oxygen is proportional to the intensity of light.
By the 1940s, botanists and biochemists focused their attention on
the pigments in chloroplasts that absorbed light and gave plants their
green appearance (Figure 3). Different types of plants can vary in their
 Herbicide Paraquat IsLegalin America ButNotinEurope 5

1 chloroplast 1 thylakoid
(thylakoid
space inside)

stroma
2 membranes

CH2
CHO in chlorophyll b
CH CH3

CH3 I II CH2CH3
N N
Mg
CH3 N N
O IV III CH3
CH3 CH3 CH3 CH3 CH3 H
C CH2 H
O CH2 H C O
CH3O O
chlorophyll a

Figure 3 Chloroplast pigments absorb light and direct it to the reaction

center. A, Diagram of chloroplast and its parts. B, Structure of
chlorophyll a and b. C, Diagram of antenna complex of photosynthetic
pigments and the colors of light absorbed. The reaction center is
outlined in black in the middle of the structure.
Source: Original art from common knowledge.

shade of green, but most plants share a common set of four pigments
chlorophyll a, chlorophyll b, b-carotene, and lutein. When cell biologists
visualized chloroplasts in detail, they could distinguish internal mem-
branes called thylakoids that floated in the liquid stroma. Thylakoids are
hollow and flattened membrane vesicles that enclose the thylakoid space.
Chloroplasts contain their own chromosomal DNA and two layers of
external membranes, which are evidence of their evolutionary origin as
6 PHOTOSYNTHESIS

cyanobacteria. In chloroplasts, photosynthetic pigments cluster together

in structures referred to as antenna complexes. The antenna complex sur-
rounds chlorophyll a molecules, and pigment molecules are embedded
within the thylakoid membrane. The antenna complex contains many
pigments in a ring of proteins that surrounds the central core proteins and
pigments. The central core is where light energy is converted to chemical
energy.
Most plants appear green, and Engelmann demonstrated that plants
do not use the green spectrum of light. Objects appear a particular color
because they do not absorb that color. By separating light into its color
spectrum, Engelmanns results raised a new set of questions about the
nature of light absorption by plants. Photosynthetic pigments absorb
violet through blue light and orange through red light. In particular, the
combination of four photosynthetic pigments do not absorb green light,
which is reflected back to your eyes, so the leaves appear green to you.
Bynot absorbing orange and red, the non-chlorophyll pigments appear
yellow to orange, depending on their concentration. Each autumn, you
can see non-chlorophyll pigments (-carotene and lutein) in the colorful
display of tree leaves. All photosynthetic pigments have structures similar
to chlorophyll with a hydrophobic tail and a hydrophilic head. The differ-
ence between chlorophyll a and b is a simple substitution of a COH
group in chlorophyll b instead of CH3 found in chlorophyll a (Figure 3B).
The hydrophobic tails force pigments go to places such as membranes and
hydrophobic portions of proteins, while the portion containing the charged
Mg+2 ion must be positioned in an aqueous environment. Inside chloro-
plasts, the photosynthetic pigments are embedded in the thylakoid mem-
brane. The stroma does not contain any pigments, nor does the thylakoid
space.
The inner core of the antenna complex is composed of proteins that
position two chlorophyll a molecules that form the heart of this reaction
center. The reaction center is a combination of proteins and chlorophyll
a molecules, and it is the location where light photons are converted into
biochemical energy carried by other proteins. The energy of photons can
be felt in the form of warm sunlight. Red light has long wavelengths
butcarries less energy than blue light with its shorter wavelengths (Table 1).
Light can be described as both a wave of energy and tiny, massless
 Herbicide Paraquat IsLegalin America ButNotinEurope 7

Table 1 List of light wavelengths, their colors and energy levels.

wavelength color kJ/mole
700 nm far red 171
600 nm orange 199
500 nm green 239
400 nm violet 299

particles or units of energy. The term photon is used to describe this

packet of light, and it was derived from the familiar atomic terms of elec-
tron, proton, and neutron. When the reaction center chlorophyll a mol-
ecules absorb light, one electron in the outer most shell of the central
magnesium ion is boosted to a higher energy level, or an excited state.
Photosynthesis requires this excited state electron to be harnessed into
new forms of chemical energy.
The antenna complex contains many proteins and photosynthetic
pigments arranged in neat circles. The antenna complex and the reaction
center are all embedded in the phospholipid bilayer of thylakoid mem-
branes. As the name implies, the antenna complex traps light of different
wavelengths and shuttles the energy toward chlorophyll a at the reaction
center. Satellite dishes perform a similar function when energy beams
collected by the dish are bounced to the receiver in the middle. Violet
light carries more energy (299 kJ/mole of photons) than orange or far red
light (171 kJ/mol), and the different pigments allow different levels of light
energy within white light to be captured. The function of the a ntenna
complex is to shuttle light of different energy levels to the reaction center.
Biochemists working on the mechanism of trapping energy hypothesized
that a gap in the outer ring of antenna complex proteins permits another
molecule to gain access to the excited state electron of chlorophyll a.
Removal of an electron by a protein is similar to what happens in the
mitochondrias electron transfer chain taking place in a hydrophobic
environment of the mitochondrial membrane. It is time to learn more about
how photosynthesis works.
After World War II, biologists made many discoveries about how plants
function. Daniel Arnon, working at UC Berkeley, was a pioneer in photo
synthesis research. By the mid-1950s, it was clear that plants could split
(or consume) water, produce adenosine triphosphate (ATP), and convert
8 PHOTOSYNTHESIS

CO2 into multicarbon sugars (carbon fixation). Arnon measured the rate
of all three processes when they were exposed to different concentrations
of an enzymatic inhibitor. He placed chloroplasts in four different solu-
tions containing 1.5 1024 M inhibitor and compared the rate of water
splitting to chloroplasts without any inhibitor. For the remaining two
experiments, Arnon measured the rate of ATP production and the rate
ofCO2 fixation over a range of inhibitor concentrations. By testing the
ability of chloroplasts to perform all three functions in the presence of
four concentrations of an inhibitor, Arnon made an important discovery
about the overall process of photosynthesis.
Arnon made several major contributions to our understanding of
photosynthesis that stimulated a wave of new experiments. Arnon discov-
ered that the three processes were inhibited differently from each other.
The conclusion from Arnons work is that splitting water, producing ATP,
and fixing carbon are performed by three distinct enzymatic pathways.
The significance of his findings was apparent to his colleagues, because
now they could design experiments to test one pathway at a time in order
to understand how each pathway worked on its own. Once the three
separate pathways were isolated and characterized, investigators could
examine how water splitting, ATP synthesis, and carbon fixation were
interrelated in the overall process of photosynthesis.
Working in Munich, Germany, Hans Heldt and his colleagues wanted
to focus on ATP production. The mitochondria use a proton gradient to
drive ATP synthase, so it is logical to expect similar proteins in chloroplasts
would produce ATP. The German biochemists simultaneously measured
the pH inside thylakoids and pH in the stroma of chloroplasts. After
1 minute of measuring in the dark, the investigators turned on a light and
monitored the pH in both compartments. Three minutes later, they turned
off the light and continued to record the pH in both compartments inside
of the chloroplasts. A good scientist asks new questions after every experi-
ment. Are my data reproducible? Does the pH change more than once for a
given thylakoid? How quickly can the change in pH be reestablished after
turning on or off the lights? Although the chloroplasts used in these experi-
ments were not in the same conditions as normal chloroplasts due to the pH
sensors, in the dark the pH difference was about 1 pH unit. A pH differen-
tial of 1 is a tenfold difference in H+ ions with the higher concentration of
 Herbicide Paraquat IsLegalin America ButNotinEurope 9

protons located in the thylakoid space. When exposed to lights, the thyla-
koid space accumulates more H+ ions for a difference of 2.26 pH units,
which is a 182-fold (102.26) H+ ion concentration gradient. pH measure-
ments of undamaged chloroplasts indicate that the difference is about
3pH units, which is a 1000-fold (103) H+ ion concentration gradient.
By the early 1970s, biochemists had discovered that like mitochondria,
chloroplasts produce a pH gradient across a phospholipid bilayer. How-
ever, light was the source of the energy in chloroplasts, not reducing agents
nicotinamide adenine dinucleotide with hydrogen (NADH) or flavin
adenine dinucleotide with two hydrogens (FADH2) as found in mito-
chondria. Once again, Robin Hill and his collaborators provided critical
data and insights into how light is converted into a pH gradient. Although
we know many more details now than Hill did, he correctly deduced the
flow of electrons from chlorophyll a in reaction centers. Working with
spinach chloroplasts, biochemists had discovered that the chlorophyll a in
the reaction centers came in two slightly different forms. Investigators
could bleach the two versions with intense lights at two different wave-
lengths of 680 nm and 700 nm due to slight differences in their sur-
rounding proteins. Once biochemists could distinguish the two forms of
chlorophyll a based on their bleaching wavelengths, the two reaction
centers were named accordinglyP680 and P700 (P stands for pigment).
However, the two reaction centers function the same way, which is more
important than the subtle differences in their names or chemical properties.
Antenna complexes and their chlorophyll reaction centers can trap
many different wavelengths of light, but the P680 pigments can capture
light with slightly higher energy levels than the P700 version (Figure 4).
For historical reasons, the proteins associated with P700 were collectively
called photosystem I (PSI) and those associated with P680 were called
photosystem II (PSII). When the chlorophyll a in PSII absorbs the en-
ergy of a photon, one of its electrons becomes excited and is boosted to a
higher energy level. The gap in the antenna complex probably enables an-
other protein to be located nearby so that the excited state electron from
P680 can be pulled away from the chlorophyll a molecule (see Figure 4).
The energized electrons are passed from one molecule to another, includ-
ing a cytochrome similar to those found in mitochondria. At the same
time, PSI has also been stimulated by light, and one of its electrons has
10 PHOTOSYNTHESIS

photosystem I
P700*
e photosystem I
1.5 A e P700*
B e e
photosystem II A e
C e
1.0 P680* B e
e D e
1 C e
e E
2 D e
0.5 e e 2e + NADP+ e
3
E (volts)

e NADPH
cytochromes
cytochromes
0.0 e e
5 e 1 photon e 5
e
1 photon
0.5 P700 P700

1 photon

1.0
P680

Figure 4 Flow of electrons energized by light. Left side,

Photosystems I (right) and II (left) absorb two photons and use
electron carrier molecules to pass excited electrons that eventually
form a new covalent bond in nicotinamide adenine dinucleotide
phosphate (NADPH) formed in the stroma. Right side, when
working alone, photosystem I (PSI) has the ability to pass its
electrons back to its own reaction center via the shared components
of PSI and PSII (cytochromes).
Source: Redrawn from Figure adopted from Nelson and Cox, 2000; their figure 19-46. Nelson,
David and Michael Cox. 2000. Lehninger Principles of Biochemistry, 3rd Edition. Worth
Publishing. New York.

been excited and pulled away to an electron acceptor. In both PSI and
PSII, their chlorophyll a molecules are photooxidized, meaning light has
caused them to give up an electron. As in mitochondria, the electrons
flow to successive proteins, but the two photosystems have different out-
comes. The excited electron from PSII eventually travels to PSI and re-
places the missing electron from oxidized PSI chlorophyll a. The electron
that began at PSII and moved to PSI combines with H+ and forms a new
covalent bond onto NADP+ to produce NADPH. Sometimes PSI is not
near PSII, and the excited state electron travels to a subset of the same
proteins but jumps over to a cytochrome and then right back to PSI again;
this happens in a cyclic pathway over and over (Figure 4, Right). PSI can
either produce NADPH or not, depending on whether PSII is nearby or not.
 Herbicide Paraquat IsLegalin America ButNotinEurope 11

photosystem I
P700*
e
photosystem II A e
P680* B e
e e

1 e C e
2 e D e
3 e 2H+ 2H+
e
stroma cytochromes stroma
cytochromes thylakoid
e space e
thylakoid 5 e e 5
space
P700
P700
A photosystem I B
Figure 5 Directing electron and H1 ion flow in chloroplasts. A,
The movement of electrons from PSII to PSI converts high energy
electrons into an H1 ion gradient. B, Cyclic electron flow within
PSIalso converts high energy electrons into an H1 ion gradient.
Source: Original art adapted from Figure 4.

The homeostatic balance between cyclic PSI by itself and PSII interacting
with PSI will be explained later in this chapter.
Biochemists and botanists performed thousands of experiments in
order to elucidate the pathways summarized in Figure 4. However, the
reader has not seen how the flow of electrons is converted into a pH gradi-
ent across the thylakoid membranes (Figure 5). When electrons move
from PSII to PSI, they pass through the cytochromes where H+ ions are
transported across the thylakoid membrane. Similarly, when PSI is mov-
ing its electrons in the cyclic pathway, the electrons are shuttled through
the thylakoid membrane with the assistance of cytochromes, which pump
H+ ions across the membrane again. Cytochromes are also in the mito-
chondria generating an H+ as part of the electron transport pathway.
Natural selection results in the use of particular molecules in multiple ways.
Cyclic and noncyclic electron flows use many of the same compo-
nents; they both transport electrons down a chain of carrier molecules.
The movement of electrons down the photosynthetic chain of carriers
within the thylakoid membrane has a negative G (180 kJ/mole) as should
have been predicted, because there is less potential energy to perform
work in NADP+ than NADPH, or other oxidized molecules prior to
their being reduced. In both pathways, the electron is energized by light
12 PHOTOSYNTHESIS

absorption of the antenna complex, which channels the energy to the

reaction center chlorophyll a molecules. Both electron pathways produce
an H+ ion gradient when the electrons are passed through the cyto-
chromes. The cyclic electron pathway replaces its own missing electron
that was produced when chlorophyll a was photooxidized originally. Non-
cyclic electron flow produces NADPH in the chloroplast stroma as the
final electron acceptor just as NADH was produced by the citric acid
cycle and beta oxidation of fatty acids in the mitochondria matrix. The
cyclic flow of electrons only produces a proton gradient (that drives ATP
synthesis) and no NADPH, but the noncyclic electron flow results in
both ATP and NADPH. There are several other differences and similari-
ties, but these are the key points.
The last step to understand is the connection of light-induced pH
gradient to ATP production is in Figure 6. ATP production is very tightly
coupled with exposure to light. The chloroplast ATP-synthase is embedded
in the thylakoid membrane, such that the entrance to the H+ ion channel

14 light H+ ions

12
ATP produced (moles)

low pH
chloroplasts
10

6
mitochondria
4
high pH
ADP
2 ATP
+ Pi H+ ions
dark
0
0 20 40 60 prokaryotes
time (min)
A B
Figure 6 ATP production from light energy. A, Purified chloroplasts
produce ATP when exposed to light but not when they are kept in
the dark. B, Evolutionary comparison between three distinct but
evolutionarily related ATP synthesis systems. Lighter gray areas
have lower pH than the darker areas.
Source: Panel A modified from Arnon, 1955; his figure 1. Arnon, Daniel I. 1955. The
chloroplast as a complete photosynthetic unit. Science. Vol. 122: 916. Reprinted with
permission from AAAS. Panel B original art from common knowledge.
 Herbicide Paraquat IsLegalin America ButNotinEurope 13

faces the lower pH compartment, whereas the proteins that generate the
new covalent bond between adenosine diphosphate (ADP) and Pi are lo-
cated in the high pH compartment. The proteins involved in the chloro-
plast and mitochondrial ATP-synthases are very similar to each other,
which reflects their common prokaryotic origins. Bacteria and archaea
living today also use a pH gradient and ATP-synthase because the two
organelles and prokaryotes all have the same evolutionary heritage.
The production of a light-induced pH gradient is the consequence of
an excited state electron in the PSII and PSI reaction centers. Each elec-
tron that moves through the cytochromes causes the passage of 2 H+ ions
to move from the stroma to the thylakoid space. Light lowers the pH in-
side the thylakoids, which is a functionally equivalent compartment to
the intermembrane space of mitochondria or prokaryotes (Figure 6B).
H+ ions move down their gradient and in the process cause ATP synthases
to spin and produce ATP from ADP and inorganic phosphate (Pi or PO4-3).
If the H+ ion gradient were dissipated, ATP production would stop in
chloroplasts. Similarly, NADP+ reduction to NADPH in the chloroplast
stroma is tied to noncyclic H+ ion accumulation inside thylakoids.
During darkness, there are ten times more H+ ions in the thylakoid space
than the stroma, but when exposed to light, the ratio jumps to somewhere
between 180:1 to 1000:1. After H+ ions accumulate in the thylakoid
space, H+ ions can rush through the ATP synthase and back into the
stroma to drive the production of ATP. Photosynthesis produces ATP by
harnessing the energy in photons (Figure 6B). Prokaryotes and mitochon-
dria use the reducing power in FADH2 and NADH and their electron
transport chains to produce H+ ion gradients that powers the ATP syn-
thase to produce ATP.
The information presented above explains how light is converted into
ATP but now it is time to understand two aspects of homeostasis. The
first aspect is photooxidized PSII. After the PSII reaction center loses its
energized electrons, the entire photosystem stops because light is not
strong enough to remove more electrons from an oxidized chlorophyll a
molecule. Oxidized chlorophyll is very electronegative, which means it
has a strong affinity for electrons. Reaction centers contain multiple chlo-
rophyll a molecules, and when four of them become photooxidized, two
water molecules will be split with the assistance of an enzyme so that the
14 PHOTOSYNTHESIS

photosystem II
P680*
e thylakoid space PSI
1
PSII
bright
light
water splitting (blues)
4e PO4
enzyme
stroma
2H2O dim
light
4 photons (reds)
4H+ 4e
thylakoid fill P680
space O2 holes thylakoid space
waste
A product B

Figure 7 Two homeostatic photosynthetic processes. A, The water

splitting enzyme generates replacement electrons as well as useful
waste products. B, Stacking and unstacking of thylakoid membranes
is part of the homeostatic regulation of energy flow through plants.
Source: Panel A based on common knowledge and original art adapted from Figure 11.7.
PanelB modified from Nelson and Cox, 2000; their figure 19-48.

four electrons are used to reduce all four chlorophyll a molecules back to
their original charge (Figure 7A):

4 photons + 2H2O 4 H+ + 4e2 + O2

Each oxidized chlorophyll a is reduced by a single electron, and PSII is

reset and ready to absorb light again and further contribute to the H+ ion
gradient.
How does PSI know when to perform cyclic versus noncyclic elec-
tron flow? Remember that noncyclic electron flow results in split water,
NADPH, and ATP production, whereas cyclic flow produces only ATP.
Therefore, the regulation of cyclic versus noncyclic electron flow has pro-
found consequences for the plant. To understand the regulation of non-
cyclic and cyclic electron flow, return to Figure 3A. Some thylakoids are
stacked and others are not. The regulation of stacked versus non-stacked
is a key mechanism that governs cyclic versus noncyclic (Figure 7B). PSI is
primarily located in the non-stacked thylakoids along with ATP synthase,
but PSII is more abundant in the stacked membrane regions. The antenna
complex associated PSII has the ability to move horizontally in the thyla-
koid membrane between stacked and non-stacked thylakoid regions. The
location of antenna complex is determined by the type of light reaching
the chloroplasts. When bright light containing high levels of blue light
 Herbicide Paraquat IsLegalin America ButNotinEurope 15

reaches the chloroplast, a kinase is activated that phosphorylates the

antenna complex and causes the thylakoids to separate and become un-
stacked membranes. Phosphorylated antenna complexes migrate within
the thylakoid membrane and associate with PSI (more cyclic electron
flow) as a result of bright light. Conversely, dim light (which contains
more red light) activates a phosphatase to remove the phosphate from the
antenna complex. In response to losing the phosphate, the antenna com-
plex facilitates more stacking of thylakoids and re-associates with PSII
(only noncyclic electron flow). Light intensity determines whether cyclic
or noncyclic electron flow will predominate.
One dynamic example of homeostasis in photosynthesis is the regula-
tion of cyclic to noncyclic electron flow. When leaves absorb bright light
with high energy blue wavelengths (~450 nm), the antenna complexes
associated with PSII become phosphorylated. The addition of a phosphate
to the antenna complex causes the stacked thylakoids to become unstacked,
and the covalently modulated antenna complex moves closer to PSI elec-
tron transport chains, which favors cyclic electron flow. When lower energy
(~650 nm) red light predominates, the phosphates are removed from
antenna complexes, the thylakoids become more stacked, and the cap-
tured light energy is more frequently delivered PSII and the noncyclic
electron flow. Therefore, dim light favors the production of NADPH.
Around noon with the sun directly overhead, blue light would be most
abundant and electrons tend to move in the cyclic pathway, which reduces
the need for water. When the sun is rising or setting, red wavelengths pre-
dominate (think pretty sunrises or sunsets) and noncyclic electron flow
dominates and water is split. However, biological systems are very rarely
100% of anything, so cyclic electron transport can happen when light is
dim, and noncyclic electron flow is possible when the sun is brightest. It is
important to remember that absolutes are very rare in the biological world.
Water is in every subcellular compartment of plant cells, but water is
split in one place onlythe thylakoid space. Splitting water inside the
thylakoid is more efficient that splitting in the stroma because the newly
produced H+ ions are stockpiled inside the thylakoid, which adds to the
proton gradient used to produce ATP. Oxygen is nonpolar, so it can dif-
fuse across all of the membranes of the chloroplast and be released to the
air via the stomata. The third and final products of water splitting are four
16 PHOTOSYNTHESIS

electrons that reduce the four oxidized chlorophyll a molecules in the

reaction center of PSII. Water splitting occurs when electrons flow via
thenoncyclic pathway and PSII is photooxidized. ATP production is the
consequence of accumulating an H+ ion gradient, which was formed
when the electrons from PSII and PSI were shuttled by cytochromes.
Therefore, ATP production and water splitting are related but not depen-
dent upon each other. If an inhibitor were able to block the pumping
ofH+ ions into the thylakoid space but not inhibit the photooxidation of
PSII, then the water splitting enzyme would still function normally while
ATP would not be produced efficiently with an inhibitor.
Learning about photosynthesis is partly a bookkeeping exercise. The
first law of thermodynamics states that energy cannot be created or
destroyedonly changed. Similarly, atoms are not lost in biochemical
processes. Consider the summary equation for water splitting at PSII:

4 photons 1 2H2O 4 H+ 1 4e2 1 O2

With every two waters split, four protons are added to lower the pH
of the thylakoid space. With the production of four electrons, eight H+
ions are pumped through the cytochromes into the thylakoid space.
Therefore 12 H+ ions accumulated when two waters are split by P680.
The equation states that four photons are required to split two waters,
but this count ignores the photons required for the second half of the
noncyclic electron flow. Four more photons must be absorbed by PSI to
reenergize four electrons to reduce NADP+ and H+ to form two mole-
cules of NADPH and new covalent bonds. Therefore, eight photons are
required to split two water molecules and form two NADPH molecules
with 12 H+ ions added to the thylakoid space.
Plants are very efficient at converting the low pH inside thylakoids
into ATP. The G of 3 moles of ATPs is 296 kJ, which means plants
capture about 48% of the free energy available in the proton gradient
produced by photosynthesis. Animal cells are less efficient (35%) at con-
verting their pH gradients into ATP, which means plants are models of
efficient energy conversion. The amount of energy from the sun that
reaches Earth in 1hour is more than the amount of energy the world
consumes in a year. A quick search of the Internet for the phrase artificial
 Herbicide Paraquat IsLegalin America ButNotinEurope 17

photosynthesis will reveal how scientists are trying to improve energy

efficiency of our machines. The key step is mimicking the conversion of
light into a proton gradient and coming close to natures efficient chemi-
cal storage of the trapped energy.

Connecting paraquat to human toxicity

This chapter began with the information that the EU banned paraquat,
although it is still used in over 100 countries including the United States.
How does paraquat affect photosynthesis, and why is it toxic to humans?
The structure of paraquat reveals that it contains two positive charges,
which makes it very electronegative (Figure 8). Paraquats structure allows
it to bind very closely to the electron binding site on PSI and PSII cyto-
chromes. Paraquats strong electronegativity draws the electrons away from
the cytochromes. Paraquat poisoning in humans most often happens
through oral ingestion, but some people have died through skin exposure.
Swallowing only 10 mL of a 20% paraquat solution is sufficient to kill an
adult. Unlike in plants, the mode of toxicity is the production of oxygen
radicals (O2-), which are highly reactive molecules. The European Public
Health Alliance evaluates all pesticides and herbicides for their toxicity to
humans with animal tests to be used only as a last resort. The company

paraquat

+
H3C N N+ CH3
photosystem I
P700* + 1e
e
photosystem II A e
P680* B e H3C N+ N CH3
e e
1 C e
e
2 paraquat D
e e
O2 O2 cell damage
e 3
cytochromes
cytochromes

5 5 H3C N+ N+ CH3

P700*
P700*
A photosystem I B

Figure 8 Effects of paraquat. A, Paraquat binds near the

cytochromes and pulls electrons toward itself and away from
the biological flow of energy. B, Oxygen radical production from
paraquat in human tissues.
Source: Both panels original art adapted from previous figures.
18 PHOTOSYNTHESIS

that produces and sells paraquat, Syngenta, has begun to redesign para-
quat to reduce its toxicity in humans, but the data on its success were not
available when this book was written. Syngenta argues the public benefits
from increased crop production when farmers use paraquat justifies the
low probability of a lethal human exposure.
Paraquat kills plants by absorbing the electrons intended for the cyto-
chromes in cyclic and noncyclic electron transport pathways. When elec-
trons are diverted from the cytochromes, H+ ions do not accumulate in
thylakoid spaces, and ATP cannot be produced. Furthermore, NADPH
would not be produced because PSII would not be able to supply PSI
with electrons for noncyclic electron transport. Green plants cannot sur-
vive in the absence of ATP and NADPH. Treating plants with paraquat is
functionally equivalent to growing plants in total darkness. In mammals,
paraquat accumulates in our lung cells. Paraquat can absorb the electrons
from the electron transport chain of cellular respiration and produce
highly reactive oxygen ions (O2-) that destroy the structure and function
of proteins, lipids, and nucleic acids. Human death is the result of tissue
damage in the lungs and subsequent loss of oxygen. If someone survived a
sublethal dose of paraquat, DNA damage by O2- might lead to long-term
health problems, such as cancer.
Everyone agrees paraquat is a very effective herbicide that kills all
plants. Likewise, all interested parties agree that paraquat can kill humans
if consumed. People are exposed to many substances that are considered
beneficial and yet toxic to humans. What is the best way to evaluate risks
and benefits of chemicals designed to improve the quality of human life?
Herbicides are not intended to be consumed by people, so should they be
evaluated for their safety when accidentally ingested? How little exposure
to paraquat is safe, and how much exposure should we tolerate? Is animal
testing appropriate to ensure human safety, or should animals be spared
from the potential harm caused by deliberate exposure of potentially toxic
compounds? Formulating public policy is a very difficult task, but policy
should be grounded in scientific understanding of biochemical processes.
Homeostasis of photosynthesis affects the ratio of cyclic and noncyclic
electron transport in chloroplasts. Bright light produces mostly ATP through
cyclic electron flow. Dim light produces NADPH plus ATP through non-
cyclic electron flow that also consumes water. The consumption of water
 Herbicide Paraquat IsLegalin America ButNotinEurope 19

to reduce photooxidized PSII is regulated by light through changes in the

stacking of thylakoid membranes. Before ATP can be produced, electrons
must be energized by the absorption of energy in photons. The movement
of energized electrons generates a pH differential in chloroplasts that is
the potential energy used to produce ATP. ATP production is a time-
dependent process affected by the small space inside thylakoids. The
extremely small space of the thylakoid lumen accelerates the rapid drop
inpH that increases the potential energy of H+ ions to diffuse unidirec-
tionally toward the stroma. The compact nature of thylakoid membranes
enables the antenna complex from PSII to quickly bump into PSI and
minimize the down time of the light capturing pigments when the light
is less intense. Every activity of cells requires energy, and thus the homeo-
stasis of photosynthesis is essential to life. Chapter 2 explains how plants
convert ATP and NADPH into sugars that sustain plant and animal life.

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 Index
Adenosine triphosphate (ATP), 7, 8, Cyanobacteria, 4244
1213, 19 Cytochromes, 9, 11
Albino shrimp, 37
Allen, M.B., 23 Dead Sea, 4041
Alvin submarine, 37 Dechloromonas, 33
Ambient light, of thermal vents, 39
Amino acids, 41 Electrons flow, energized by light,
Anaerobic photosynthesis, 39 911
Antenna complexes, 5, 6, 7 Energy consumption and CO2
Arginine, 42 levels,2122
Arnon, Daniel, 78 Engelmann, Theodor Wilhelm, 34
Artificial photosynthesis, 1617 Escherichia coli, 41, 43
Aspartic acid, 41 Europe, banning of paraquat use
Astrobiologists, xiii in,1, 1719
European Public Health Alliance, 17
Bacterium termo, 3 Exoculata, 37
Beggiatoa, 3334 Extremophiles, 35
Benson, Andrew, 24
-carotene, 5, 6 First law of thermodynamics, 16
British Petroleum, 30 Flavin adenine dinucleotide with two
hydrogens (FADH2), 9
Calvin, Melvin, 24 Fossil fuels, 21
Calvin and Benson cycle.
See Calvincycle Geobacter sulfurreducens, 33
Calvin cycle, 24 Glutamic acid, 41
Carbon fixation, 2324 Glyceraldehyde 3-phosphate (G3P), 26
and carbon recycling, 25
Cellular respiration, 26 Halobacterium cutirubrum, 4142
Chemosynthesis, 34, 39 Halobacterium salinarum, 42, 43
Chlorophyll a, 5, 6, 7, 9 Halophiles, 4041
Chlorophyll b, 5, 6 Heldt, Hans, 8
Chloroplasts, 46, 89, 24 Helicobacter pylori, 33
diagram of, 5 Herbicide paraquat, banning in
directing electron and H1 ion Europe, 1, 1719
flowin, 11 Hill, Robin, 4, 9
Citromicrobium bathyomarinum, 3940 Homeostasis, of photosynthesis, 13,
CO2 15, 18, 27, 44
connecting rainforests in Brazil to
Greenlands glaciers, 2131 Laws of thermodynamics, 16, 49
14
CO2, 23, 24 Light energy, ATP production from, 12
Cold seep, 3435 Light wavelengths, 67
54 INDEX
Lowenstam, Heinz, 34
Lutein, 5, 6
Magnesium ions (Mg2+),
concentrations of, 2728
Methanogens, 3536
Microbes, 3336
Mitochondria, 8, 26
Nicotinamide adenine dinucleotide
phosphate (NADPH), 10
Nicotinamide adenine dinucleotide
with hydrogen (NADH), 9
Non-chlorophyll pigments, 6
Obligate halophiles, 42
Oil spill, Gulf of Mexico (2010), 31
Ornithine, 42
Orthologs, 41
Oxidized chlorophyll, 1314
Oxygen, 4, 15
P680, 9, 16
P700, 9
Paraquat, 1
connecting to human toxicity,
1719
effects of, 17
and mammalian consequences, 2
use, banning in Europe, 1, 17
pH, 8
Phosphoglycerate (PGA), 2426
Photon, 7
Photooxidized, 10
Photosynthesis, understanding, 117
Photosystem I (PSI), 910
Photosystem II (PSII), 910
Priestley, Joseph, 23
Primary producers, xiii, 34
Prokaryote cells, 26
Prokaryotes, 12, 13, 34, 37, 44
Proline, 42
Rainforests, connecting to Greenlands
glaciers, 2131
Reaction center, 6
Rhodopsin, 37
Ribulose 1,5-bisphosphate, 24, 26
Rimicaris exoculata, 37
Rubisco, 24, 26, 27
physiological regulation of, 28
Salt lovers, 4041
Salt-tolerant lifestyles, 4042
Sandstorms, 31
Second law of thermodynamics, 49
Stroma, 5, 6
Syngenta company, 18
Thermal vent lifestyles, 3640
Thin layer chromatography
(TLC),2D, 24
Thylakoid space, 5, 15
Thylakoids, 5
Tiny photosynthesis specialists, 4244
Two-dimensional thin layer
chromatography (TLC), 24
Tyrosine, 42
UCYN-A, 43
Van Dover, Cindy, 3738
Water splitting, 1516, 23
Zeiss, Carl, 34
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