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FOR THE A. Malcolm Campbell • Christopher J. Paradise
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Perhaps the most important chemical reactions on the planet
SCIENCES
take place inside a plant’s chloroplasts. In this tiny green organ-
LIBRARY elle, plants have the capacity to capture the energy in light and
Create your own use that energy to convert CO2 gas into building blocks used
Customized Content to produce all four categories of biological molecules—lipids,
Photosynthesis
Bundle—the more carbohydrates, proteins and nucleic acids. Animals could not
books you buy, survive if plants did not exist. Not only do they provide us with
the greater your oxygen to breathe, they also generate the starting materials for
discount! 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
THE CONTENT
to maximize their productivity and minimize their exposure to
• Energy Physics dehydration. All of this regulation is carried out inside every
Engineering plant on earth. In addition to plants, there are microbial primary
• Biotechnology producers that can harvest energy from a range of environmen-
• Biology tal sources so that no place on earth is devoid of life.
• Mathematics
A. Malcolm Campbell teaches biology at Davidson College,
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NC. He received national and international education awards:
Genetics Society of America (2013); American Association for the
THE TERMS Advancement of Science (2012); and American Society for Cell
• Perpetual access Biology (2006). He was the founding co-editor in chief of CBE Life
for a one time fee Sciences Education; founding director of Genome Consortium
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mental studies at Davidson College. He teaches introductory
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Photosynthesis
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Photosynthesis
A. Malcolm Campbell, PhD

Christopher J. Paradise, PhD
Photosynthesis
Copyright © A. Malcolm Campbell and Christopher J. Paradise. 2016.
All rights reserved. No part of this publication may be reproduced, stored

in a retrieval system, or transmitted in any form or by any means—
electronic, mechanical, photocopy, recording, or any other except for
brief quotations, not to exceed 250 words, without the prior permission
of the publisher.
First published in 2016 by

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ISBN-13: 978-1-94474-909-5 (print)

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Momentum Press Biology Collection
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Abstract
Perhaps the most important chemical reactions on the planet take place in-
side a plant’s 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
Introduction��xiii
Chapter 1 Herbicide Paraquat Is Legal in America But Not
in Europe...........................................................................1
Chapter 2 Connecting Brazil’s Rainforest to Greenland’s 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 do—with 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.
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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. David’s 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 habitats—places 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
Is Legal in America
But Not in Europe
In 2003, farmers in the European Union (EU) began using the most com-
mon herbicide on the planet—paraquat (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: 647–657. Reprinted with permission from The Royal Society.
Copyright © 1985.
Plants photosynthesize to capture the sun’s 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 Is Legal in America But Not in Europe 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, Priestley’s 1774 experiment
showing that plants in the sunlight can replenish depleted air. B,
Engelmann’s 1882 experiment showed oxygen-loving bacteria (white
spots) moved to the portion of algae cells (horizontal rectangles)
exposed to particular wavelengths of light. C, Hill’s 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 Priestly’s 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): 232–246. 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: 881–882. 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 Priestley’s 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 Engelmann’s 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 plants—chloroplasts. 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 Hill’s 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
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
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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, Engelmann’s 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.
By not absorbing orange and red, the non-chlorophyll pigments appear
yellow to orange, depending on their concentration. Each autumn, you
can see non-chlorophyll pigments (β-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
but carries less energy than blue light with its shorter wavelengths (Table 1).
Light can be described as both a wave of energy and tiny, massless
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
mitochondria’s 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
of CO2 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 Arnon’s 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
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
3 pH 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 accordingly—P680 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.
photosystem I
“P700*” –
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
PSI also 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 ΔG (−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 (μmoles)
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: 9–16. Reprinted with
permission from AAAS. Panel B original art from common knowledge.
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.
Panel B 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
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 only—the 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
the noncyclic 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
of H+ 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
destroyed—only 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 ΔG 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 1 hour is more than the amount of energy the world
consumes in a year. A quick search of the Internet for the phrase “artificial
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 nature’s 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). Paraquat’s structure allows
it to bind very closely to the electron binding site on PSI and PSII cyto-
chromes. Paraquat’s 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
“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
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
in pH 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.
Bibliography
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445(7128):610–612, 2007.
Allen MB, Arnon DI, Capindale JB, et al. Photosynthesis by isolated chlo-
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77:4149–4155, 1955.
Arnon DI, Whatley FR, Allen MB. Photosynthetic phosphorylation,
the conversion of light into phosphate bond energy. J Biol Chem
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Arnon DI. The chloroplast as a complete photosynthetic unit. Science
122(3157):9–16, 1955.
Arnon DI, Allen MB, Whatley FR. Photosynthesis by isolated chloro-
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Bateman DN. New formulation of paraquat: a step forward but in the
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Campbell, AM. Photosynthetic Antenna Complex and Reaction Center.
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MolStudents/spring2010/Campbell/antenna-jsmol.html. Accessed
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www.Ebook777.com
CHAPTER 2
Connecting Brazil’s
Rainforest to
Greenland’s Glaciers
Almost every week, there is more news about global climate change and
atmospheric CO2 levels. The amount of CO2 released into the atmosphere
as a direct consequence of human activity has increased dramatically over
the last 150 years (Figure 9A). Consumption of petroleum, coal, and natu-
ral gas are the three leading sources of new CO2 in the atmosphere. These
three sources of CO2 are called fossil fuels because like real fossils, these
fuels were once organisms that died millions of years ago. Through pressure
and chemical reactions, their bodies have produced a variety of hydro-
carbons rich in covalent bonds. As human consumption of fossil fuels has
increased, so has atmospheric concentration of CO2 in parts per million
(ppm; see Figures 9B and 9C). The current level of atmospheric CO2 has
crossed 400 ppm, which is nearly 50% higher than it was when America
became a new country. Over the last 400,000 years, the level of CO2 has
fluctuated between 290 and 190 ppm (Figure 9D). CO2 levels had not
reached 400 ppm since 13 million years ago (Figure 9E). Look at the
seasonal fluctuations of atmospheric CO2 in Hawaii (Figure 9F). CO2 levels
peak in May every year and are at their lowest in September and October.
The most recent month’s CO2 levels in Hawaii are freely available online,
as are CO2 levels in the same month of the past 2 years.
The month-to-month variation of atmospheric CO2 in Hawaii is caused
by the seasonal variation in photosynthesis. Plants photosynthesize the
least during the winter, because some plants lose their leaves, the amount
of sunshine is reduced, and the chemical reactions are slowed down by the
cooler temperatures. When plants reduce their CO2 consumption, the gas
22 PHOTOSYNTHESIS
7 human production of 400 Barrow, Alaska air samples
CO2 concentration (ppmv)

CO2 by source WWII
carbon/year × 1 billion
6
380
metric tons of
5
= total
4 = petroleum 360
= coal
3 = natural gas 340
2 = cement
320
1
0 300
1800 1850 1900 1950 2000 1974 1978 1982 1984 1990 1994 1998 2002 2006 2010
A time (date in CE) B time (date in CE)
340 Siple, Antarctica ice-core data 310 Vostok, Antarctica ice-core data

320 270
300 230
280 190
260 150
1800 1880 1900 1950 2000 400 300 200 100 0
C time (date in CE) D time (× 1000 years before present)
2010
500 samples near Solomon Islands 392 monthly CO2 levels
2009 3
450 390 2008 4 5 2
5 3 6
1
400 2007 6
388 4 1
2 7
2006 4 5 3 12
350 386
6 12 7
4 5 3 12 8 11
300 6 2 7
9
384 3 1 12 8 11 10
250 7 9 10
382 2 12 8 11
8
200 1
9
10
380 11
150 9 10
378
20 15 10 5 time (year, month)
E time (× million years before present) F
Figure 9 Energy consumption and CO2 levels. A, The total human

production of CO2 and its sources over the last 200 years. The gray
stripe denotes the 5 years of World War II. Manufacturing cement
produces CO2 as well. B, The amount of CO2 measured directly from
air in Alaska. C, CO2 levels over the past 200 years measured from
ice cores taken in Antarctica. D, CO2 levels over the past 425,000 years
measured from ice cores taken Antarctica. E, CO2 levels over the past
20 million years measured from ocean floor sediment in the South
Pacific Ocean. Error bars are 1/– standard deviation, and the
shaded area indicates the full range of calculated values. F, Monthly
CO2 atmosphere levels taken from Mauna Loa, HI. Numbers indicate
the month for each year with 1 being January.
Source: A: modified from: http://www.unido-ichet.org/ichet.org/fossil_fuels/fossil_fuels/fossil_
fuels.html B: http://www.esrl.noaa.gov/gmd/dv/iadv/graph.php?code=BRW&program=ccgg&
type=ts C. Panels B–D modified from data at this Oak Ridge National Lab web site. http://cdiac
.esd.ornl.gov/trends/co2/contents.htm D. Panel E modified from Tripati et al., 2009, their
figure 2B. Tripati, Aradhna K., Christopher D. Roberts, Robert A. Eagle. 2009. Coupling of CO2
and Ice Sheet Stability Over Major Climate Transitions of the Last 20 Million Years. Science.
Vol. 326: 1394–1397. Panel F is original art from NOAA data. http://www.esrl.noaa.gov/gmd/
ccgg/trends/co2_data_mlo.html
Connecting Brazil’s Rainforest to Greenland’s Glaciers 23
accumulates more in the atmosphere until the new growing season begins
in the spring. In Hawaii, May is the first month the growing season, but in
the southern hemisphere, the peak CO2 levels are shifted by 6 months,
in October or November. In Figure 9C, it took only 300 years for the
CO2 levels to double from 200 to 400 ppm, which is a very short time
compared to the 5 million years that it took in Figure 9E. The recent and
rapid rise in CO2 provides strong evidence that humans are responsible
for the doubling of CO2 in our atmosphere today. Burning fossil fuels for
energy produces CO2 as a gaseous waste product too. In this chapter, you
will focus on how CO2 connects the rainforests in Brazil to the glaciers
of Greenland. When you digest food for energy, you produce CO2 as a
gaseous waste product.
Plants fix CO2 (build multicarbon molecules from CO2) as a distinct
biochemical process from splitting water and producing ATP. In 1955,
M.B. Allen and his colleagues at the University of California (UC) Berkeley
measured the rate of CO2 fixation as a function of time and chloroplast
concentration. Allen and his team isolated spinach chloroplasts and ex-
posed them to 14CO2, containing radioactive 14C, either in the presence
or absence of light. After the indicated amount of time, they determined
how much radioactive carbon was incorporated into organic molecules.
All remaining 14CO2 gas would diffuse away when the experiment was
stopped, leaving radioactive carbon only incorporated into organic mol-
ecules. In the second experiment, the biochemists quantified the amount
of radioactive organic molecules produced by different concentrations of
chloroplasts under constant illumination.
Light is required for photosynthesis, including carbon fixation. Allen’s
data indicated that plants can photosynthesize continuously as long as
they have light, CO2, and water to replace the electrons in PSII (see
Chapter 1). If the electrons were replaced, it would be expected that O2 gas
would be produced from split water. The biochemists were able to mea-
sure a constant production of waste O2 while the plants were fixing CO2.
However, their data generated a surprise. It would be expected that the
amount of carbon fixation would scale proportionally with the amount of
chlorophyll, but when they added 1.5 mg or more, the level of carbon
fixation did not increase. To understand this apparent paradox, think about
a very crowded beach where more and more people congregate. At some
24 PHOTOSYNTHESIS
point, the amount of sun that any one person can receive begins to dimin-
ish simply because the people are casting shadows on each other. Similarly,
too many chloroplasts in a tube caused some of them to get less light, and
the rate of carbon fixation did not increase any more. The data from
Allen’s research was the first time anyone had determined that all compo-
nents needed for all three parts of photosynthesis (water splitting, ATP
production, and carbon fixation) were contained in chloroplasts and not
dependent upon other plant cell parts.
During the 1940s and 1950s, UC Berkeley was home to some of the
best photosynthesis research in the world. A different pair of biochemists,
Melvin Calvin and Andrew Benson, wanted to know how quickly the new
organic molecules were produced by photosynthesis. The two biochem-
ists exposed intact plant cells to radioactive 14CO2 and light for different
amounts of time and then used two-dimensional (2D) thin layer chro-
matography (TLC) to separate and identify the newly produce radioactive
molecules. They stopped their experiments at four different times in four
separate experiments where the plant cells photosynthesized in the pres-
ence of light and 14CO2 for the indicated times.
Calvin and Benson successfully measured the rate of carbohydrate
production after very short exposures to light. With only 5 seconds of light,
the algae cells converted CO2 into the 3-carbon sugar phosphoglycerate
(PGA). A few other sugars were produced after PGA, but the bulk of the
radioactive carbon fixed in the first 5 seconds is PGA. With increasing
amounts of time, more carbohydrates become radioactive as enzymes
shuttled 14C from PGA to more complex molecules. Within 5 minutes,
lipids with many carbons become radioactive as the plant’s biochemical
synthesis converts PGA into much larger molecules.
Calvin and Benson published many papers describing the biochemi-
cal pathway for carbon fixation until biologists clearly understood how
plants produce their organic molecules from CO2—the waste product of
human cellular respiration (Figure 10A). Because of their critical discov-
eries, the cycle of carbon fixation is sometimes referred to as the Calvin
cycle, or Calvin and Benson cycle. Plant cells contain many sugars, includ-
ing a 5-carbon sugar ribulose that has two phosphates covalently linked to
it on the number 1 and number 5 carbons (ribulose 1,5-bisphosphate).
The most abundant enzyme in the entire world is rubisco that covalently
ribulose
1,5-bisphosphate 3
2 1 1
+ 1 =2 2 PGA
rubisco H2O
1 3
14
CO2 2
3 5C + 3 1C
3 ATP + rubisco
3 (2 3C)
1
5 3C
2
3 PGA
6 3C + 6 ATP
1
recycled + 6 NADPH
2
1 3C 3
used
elsewhere G3P
B G3P
Figure 10 Carbon fixation and carbon recycling. A, In carbon
fixation, the enzyme rubisco joins one CO2 and one ribulose
bisphosphate to produce two copies of the 3-carbon sugar PGA.
The outlined carbon represents the radioactive atom. The
outlined oxygen came from consumed water. B, Three rounds of
carbon fixation from A allow chloroplasts to recycle carbons and
regenerate ribulose bisphosphate.
Source: Original art based on common knowledge.
links one CO2 and the doubly phosphorylated ribulose sugar. The newly
formed 6-carbon sugar is unstable, and just as happened in glycolysis, the
sugar splits in half and forms two copies of a 3-carbon sugar.
Like Krebs who realized the citric acid cycle was not linear, plant bio-
chemists deduced that carbon fixation was cyclical as well (Figure 10B).
Recall from Chapter 1 that two water molecules were split when four
electrons were excited by light at the reaction centers. In carbon fixation,
the critical number is three. When three CO2 molecules are consumed by
rubisco to form six PGA molecules (two PGAs for each CO2), the carbon
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26 PHOTOSYNTHESIS
fixation cycle has accumulated enough new PGA to perform its recycling
pathway. When six PGAs are produced, six ATPs and six NADPHs are
consumed to convert PGA into glyceraldehyde 3-phosphate (G3P). At this
step, the chloroplast has produced six G3P molecules containing a total
of 18 carbons. Of these 18 carbons, 15 were already in the three ribulose
bisphosphate molecules, and the three new carbons came from the three
consumed CO2 molecules. If one G3P molecule is removed from the pop-
ulation of six G3Ps produced, five G3Ps would be remaining that contain
15 carbons. An enzyme inside chloroplasts binds to five copies of G3P and
three ATP molecules to produce three copies of ribulose 1,5-bisphosphate,
which brings the carbon fixation cycle back to where it began.
A common misconception among biology students is that plant cells
only photosynthesize and only animal cells perform cellular respiration.
Both plant and animal cells contain mitochondria, so both types of eu-
karyotic cells perform cellular respiration. Although animal cells cannot
photosynthesize, many prokaryotic cells can photosynthesize even though
they do not have chloroplasts. Prokaryote cells also can conduct cellular
respiration, and they use their entire cells as the functional equivalent of
mitochondria, which is consistent with the bacterial origins of mitochondria.
Therefore, plant cells consume O2 and produce waste CO2 from their
mitochondria at all times, whereas their chloroplasts consume CO2 and
produce waste O2 when their chloroplasts are exposed to light.
Rubisco produces a covalent bond between the carbon of CO2 and
the second carbon in ribulose bisphosphate. To facilitate the splitting of the
6-carbon sugar into two copies of PGA, water is consumed and its oxygen
is covalently bound to the short-lived 6-carbon sugar prior to the forma-
tion of two PGA molecules. Two H+ ions accumulate in the stroma where
rubisco is located and carbon fixation takes place. These H+ ions are ca-
pable of being pumped into the thylakoid space during the cyclic and
noncyclic electron pathways that was described in Chapter 1 of this book.
Rubisco’s stromal location means that it functions where ATP and
NADPH are formed, thus increasing efficiency by eliminating the need to
transport these two energy sources used in carbon fixation.
A pair of enzymes converts PGA into G3P at the expense of ATP and
NADPH. Reducing PGA to G3P requires a lot of energy in the form of
ATP and NADPH. PGA is reduced to G3P, which makes sense because
NADPH is oxidized to NADP+ in the production of G3P. The produc-

tion of three ribulose bisphosphate molecules from five G3P molecules
consumes a total of nine ATP and six NADPH. Because chloroplasts re-
quire 50% more ATP than NADPH for carbon fixation, it is adaptive
that the cyclic electron pathway of PSI occurs in bright light about half
the amount of time (midday) as the noncyclic electron pathway of PSII
and PSI in dim light (morning and evening). The noncyclic pathway
produces NADPH and ATP in a 1:1 ratio, whereas the cyclic pathway
produces only ATP (see Figure 4). The intensity of light influences the
homeostatic regulation of carbon fixation by influencing the ratio of
stacked and unstacked thylakoids, which determines the ratio of cyclic
and noncyclic electron pathways. The production of new PGA via the
addition of three new carbons onto three copies of ribulose bisphosphate
is the conversion of light energy into covalent bonds. The first law of
thermodynamics states that energy is not lost or gained during photo
synthesis, only converted from one form to another. The reduction of
entropy, or randomness, by fixing CO2 is consistent with the second law
of thermodynamics, because within this system, energy is consumed to
increase the order of the molecules.
Photosynthesis temporarily stores light energy as ATP and NADPH
and these two molecules are used in carbon fixation. It is time to focus on
homeostasis at the cellular level and understand how the cell coordinates
the production of ATP and NADPH with the production of PGA after
carbon fixation. Rubisco is perhaps the most important enzyme in the
world because this protein is responsible for fixation of carbon from CO2
into usable sugars, amino acids, and lipids. Therefore, plant cells must
have a way to regulate rubisco’s activity (Figure 11). Biochemists quantified
the effect of pH on the rate of carbon fixation by rubisco. The investigators
placed rubisco into buffers with pH ranging from 7 to 10. Rubisco has a
pH optimum in the range of 8 to 9 for maximum activity. Plant physiolo-
gists knew from previous work that when photosynthesis reduces the pH
of the thylakoid space, magnesium ions (Mg2+) move from the thylakoid
into the stroma as a charge counterbalance to the increased positive charge
(H+) inside thylakoids. To understand the function of Mg2+ ion move-
ment during photosynthesis, investigators wanted to measure the effects
of pH and Mg2+ concentrations on the activity of rubisco (Figure 11B).
28 PHOTOSYNTHESIS
20 mM Mg+2
5 mM Mg+2
110 50
enzyme activity (nmoles min–1 mg–1)

100
percent enzyme activity
90
80 25 0.6 mM Mg+2
70
60
50 0
6.0 7.0 8.0 9.0 10.0 11.0 7.0 8.0 9.0 10.0
A pH B pH
Figure 11 Physiological regulation of rubisco. A, Rubisco

activity is sensitive to pH. B, Rubisco activity is sensitive to
Mg21 concentration and pH.
Source: Panel A modified from Chakrabarti et al., 2003, figure 2. Panel B modified from
Lorimer et al., 1976, their figure 5. Reprinted (adapted) with permission from Lorimer,
George H., Murray R. Badger and T. John Andrews. 1976. The Activation of Ribulose-
1,5-bisphosphate Carboxylase by Carbon Dioxide and Magnesium Ions. Equilibria, Kinetics,
a Suggested Mechanism, and Physiological Implications. Biochemistry. Vol. 15(3): 529–536.
Copyright 1976 American Chemical Society.
The investigators prepared three concentrations of Mg2+ ions in buffers

ranging from pH 7 to pH 9.5. The data showed that pH and Mg2+ con-
centrations both affected the activity of rubisco. Plant physiologists deter-
mined the Mg2+ concentration of stroma during photosynthesis is about
5 mM compared to about 1 mM in the dark. It should not be a surprise
to learn that the other enzymes involved in carbon fixation/recycling have
similar pH requirements for maximum activity.
The pH optimum of rubisco is between 8.3 and 9, which is the same
pH as the stroma of intact chloroplasts while photosynthesizing. When
dark, the stroma returns to pH of 7 to 7.5 based on the data for experi-
mentally altered chloroplasts. Therefore, the pH of the stroma, where
rubisco is located, helps regulate the carbon fixing enzyme. Based on the
data in Figure 11B, it is clear that elevated Mg+2 also enhances the activity
of rubisco. The difference in activity between 5 mM and 0.6 mM Mg+2
changes with the pH. At pH 8, the difference in rubisco activity is about
fourfold. During photosynthesis, the stroma’s ionic composition of both
H+ and Mg+2 is ideal for increasing the activity of rubisco. The term photo
synthesis makes sense because light (photo-) leads to the building
(-synthesis) of new carbohydrates. The data in Figure 11 illustrate why it is
a misnomer to call carbon fixation a “dark reaction” simply to contrast it
to the “light reaction” of generating the H+ ion gradient in chloroplasts.
This chapter began by asking how rainforests are connected to Green-
land’s glaciers. Green plants in the rainforest fix carbon during the spring
and summer months, which reduces the global levels of atmospheric CO2.
CO2 is a greenhouse gas, meaning it traps heat and contributes to the
elevation of temperatures on earth, which causes the ice on and around
of Greenland to melt faster than they accumulate during winter. Photo-
synthetic plants fix carbon and atmospheric CO2 levels are intimately
connected to green plants.
Plant cells regulate carbon fixation using changes in pH and Mg2+
concentration. Rubisco activity is regulated as a consequence of light-
induced ionic changes in the stroma. Rubisco uses CO2 and the harvested
light energy contained in the covalent bonds of plant-produced ATP
and NADPH. The timing of carbon fixation is carefully regulated by the
activation of rubisco and its time-sensitive optimal reaction conditions.
Rubisco works best when plants are actively capturing light energy while
the stromal pH and magnesium concentration are elevated. The size and
location of thylakoid membranes and the surrounding stroma minimizes
the energy needed to collect the substrates for carbon fixation. Photosyn-
thesis, like all of life, requires organization and energy. Plants make larger
molecules by reducing CO2 and producing PGA that can be converted
into all the building blocks of life—proteins, lipids, and carbohydrates.
Animals depend on plants for carbon sources, but plants do not need
animals to live. Without plants, animals would die, but would all life
cease to exist? Chapter 3 will present some unusual forms of microbial life
whose diets defy traditional definitions of food and energy harvesting.
Ethical, Legal, Social Implications: National Policies

Affect More Than One Nation
Every country on the planet has laws and policies that were produced to
help someone. Countries regulate how much foreign currency can be
30 PHOTOSYNTHESIS
brought into their economies, they regulate import and export rates and
tariffs, and they regulate who can enter or leave the country. Europe banned
the use of paraquat, but a majority of the world still permits its use. How-
ever, some policies intended for one nation can affect others. For example,
if the United States passed a law that permitted US farmers to remove all
of the water from rivers that flow through their states, Texans in Laredo
might be fine, but their Mexican counterparts on the other side of the Rio
Grande in Nuevo Laredo, Mexico, might suffer from the lack of water.
When it comes to homeostasis, Earth is one interconnected ecosystem
that maintains a balance defined by geography rather than politics. Wind,
water, weather, animals, plants, pathogens… all natural resources are part
of a network that connects every country to one another. In the spring of
2010, two global events illustrated how closely connected everyone is. In
Iceland, a volcano erupted under a glacier that sent steam and ash high
into the atmosphere. The jet stream carried the ash over northern Europe,
which closed airports in at least a dozen countries.
Volcanoes are not regulated by governments, but oil reserves are.
Closer to home, British Petroleum was pumping oil from one mile below
the ocean surface when something went wrong. On the night of April 20,
2010, an explosion followed by a fire left the drilling platform sinking in
the water and three large holes in the pipeline that used to deliver oil
(Figure 12). An estimated 180 million gallons of petroleum oil gushed
into the water for 5 months and currents carried the pollution eastward
toward many independent nations. The United States has a national en-
ergy policy that permits drilling in some locations but not others. Some
politicians chanted “drill baby drill,” whereas others in the same political
party called for a moratorium in waters near their homes. Policies also
govern safety procedures and frequencies of inspections. The oil is ex-
tracted by a British company, in an area claimed by the US, but the oil
spread east and affected fishing and tourism in many countries.
Countries have neighbors, and neighbors sometimes have competing
interests. Should an herbicide be legal or illegal everywhere, or is it okay
for neighboring countries to disagree on its safety? If paraquat fumes from
one farm drift over to another country, should one farmer be punished by
another country’s laws? Because all ecosystems are interconnected, it is
nearly impossible to craft a law in one country that does not produce
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Figure 12 National policies can affect many nations. A, NASA

satellite image of the 2010 Gulf of Mexico oil spill.
Source: From http://www.nasa.gov/multimedia/imagegallery/image_feature_1649.html.
consequences in another country. Everyone agrees that paraquat can be le-

thal to humans, but governments disagree on whether it should be used or
not. What should be done to balance competing interest? A more wide-
spread problem is erosion caused by farming practices and water use. Sand-
storms in China move east and affect North and South Korea. Dust carried
from the Sahara Desert blows over the Pacific Ocean and affects the weather
in North America by altering weather patterns influenced by ocean tem-
peratures that lead to El Niño. Sandstorms are caused in part by poor farm-
ing practices. When people cut down forests and follow bad agricultural
practices, windstorms can lift hundreds of tons of dirt into the air, carrying
away valuable top soil. Prevailing winds carry the dust great distances and
can influence other countries that try to minimize wind erosion of soil.
Bibliography
Allen MB, Arnon DI, et al. Photosynthesis by isolated chloroplasts III:
Evidence for complete photosynthesis. J Biol Chem 77:4149–4155,
1955.
32 PHOTOSYNTHESIS
Arnon DI, Allen MB, Whatley FR. Photosynthesis by isolated chloroplasts.

Nature 174(4426):394–396, 1954.
Bassham JA, Benson AA, Calvin M. The path of carbon in photosynthesis
VIII: the role of malic acid. J Biol Chem 185(2):781–787, 1950.
Calvin M, Benson AA. The path of carbon in photosynthesis. Science
107(2784):476–480, 1948.
Calvin M, Benson AA. The path of carbon in photosynthesis IV: the
identity and sequence of the intermediates in sucrose synthesis.
Science 109(2824):140–142, 1949.
Chakrabarti S, Bhattacharya S, Bhattacharya SK. Immobilization of
D-ribulose-1,5-bisphosphate carboxylase/oxygenase: a step toward car-
bon dioxide fixation bioprocess. Biotechnol Bioeng 81(6):705–711,
2003.
Lorimer GH, Badger MR, Andrews TJ. The activation of ribulose-
1,5-bisphosphate carboxylase by carbon dioxide and magnesium ions.
Equilibria, kinetics, a suggested mechanism, and physiological impli-
cations. Biochemistry 15(3):529–536, 1976.
Portis AR. Evidence of a low stromal Mg2+ concentration in intact chlo-
roplasts in the dark. Plant Physiol 67(5):985–989, 1981.
Tripati AK, Roberts CD, Eagle RA. Coupling of CO2 and ice sheet
stability over major climate transitions of the last 20 million years.
Science 326(5958):1394–1397, 2009.
Ethical, Legal, Social Implications: National Policy Affect More

Than One Nation
Panel a from http://www.nasa.gov/multimedia/imagegallery/image_

feature_1649.html.
CHAPTER 3
No Place on Earth Is
Devoid of Life
With prolonged study of biology comes the realization that some organ-
isms eat food that seems very peculiar. Dead smelly animals are covered in
maggots eating the rotting, putrid flesh. How can a vulture tolerate eating
rotting flesh that smells worse than smelly shoes? How could a mother fly
lay her precious eggs on a corpse that smells so badly vultures can detect
it miles away? Despite human aversion to foods that stink, the diversity of
life ensures that all sources of energy will be consumed by something.
Animals that eat rotting flesh may seem strange, but these large organisms
are mild compared to prokaryotes. Try to think of the harshest conditions
on Earth where nothing could possibly live, and there will be microbes
present. The focus of this chapter is to understand what sorts of metabolic
adjustments microbes have evolved to live in extreme environments.
Bacteria and archaea can live in the harshest environments in the
world, including acid pits where the pH is about the same as a human
stomach at 2.5. Stomachs contain microbes, such as Helicobacter pylori, that
thrive in extreme acidic conditions and can cause ulcers. Other microbes
consume uranium for energy while being exposed to very high levels of
radiation. The uranium-eating bacterium Geobacter sulfurreducens has an
unknown mechanism to prevent radiation-induced mutations unlike
plants, animals, and even most other prokaryotes. Unfortunately, humans
have accumulated so much toxic waste that we don’t know what to do with
it all, but bacteria in the genus Dechloromonas can anaerobically digest the
carcinogen benzene and convert it nontoxic CO2. And perhaps the last place
on Earth one might consider habitable, the bottom of the ocean, microbes
thrive at 2º C and under enormous pressure, and they support entire food
chains, including large animals. Bacteria of the genus Beggiatoa use the
34 PHOTOSYNTHESIS
minerals that seep up from the ocean floor to produce energy for them-
selves and their symbiotic animal hosts. By living under 2.5 miles of water,
these microbes experience 11,400 pounds per square inch of pressure, which
is about the same as piling two Hummers and one Volkswagen Beetle on
top of a postage stamp.
The physical and chemical challenges are diverse, but prokaryotes have
adapted and are able to extract energy by breaking covalent bonds and
transporting the electrons to final acceptors, such as oxygen or sulfur. For
microbes to survive, all that is required is a source of electrons and a final
electron acceptor. Species that do not feed on other organisms are primary
producers, because they convert inorganic carbon into organic molecules
for themselves. Photosynthetic plants are mistakenly considered to be the
only primary producers, but some microbes can also photosynthesize. Some
prokaryotes use chemosynthesis to enzymatically produce organic mole-
cules from inorganic substrates. Chemosynthesis oxidizes H2 gas or sulfur
compounds in the process of metabolizing carbon sources of CO2 and
methane, CH4. The existence of microbes that consume rock and produce
mineral waste prompted the geochemist Heinz Lowenstam to ask, “Is any
mineral at the Earth’s surface produced by purely inorganic processes?”
Once microbiologists realized prokaryotes lived everywhere, they
began to look in more extreme places and quantifying what they found.
One of the most surprising sources of life is places in the ocean floor
where mineral-rich, cold water seeps up from the earth’s rocky surface.
German microbiologists took samples from within the seafloor located
under 2000 meters (1.2 miles) of water in the Black Sea north of Turkey.
Modern bacteria at the bottom of the Black Sea can take 2.8 years to
divide and produce new cells, which indicates that some microbes might
have generation times of a 100 years or more! The investigators took
samples of sediment from known depths and determined the amount of
DNA present at the indicated centimeters below the seafloor. In addition
to living under enormous pressure and away from the sunlight, microbes
can live more than 6 meters under the accumulated sediment of the sea-
floor. However, the Germans were not sampling near a cold seep. An
interdisciplinary team of Japanese marine biologists did sample the sedi-
ment at a cold seep over 5343 meters (3.3 miles) under the Pacific Ocean
near Japan. As a control, they sampled sediment nearby that was separated
No Place on Earth Is Devoid of Life 35
from the nutrient rich water of the cold seep. The Japanese investigators
quantified the number of cells instead of the amount of DNA measured
by the Germans. Despite the different measurements, it is clear that cold
seeps are distinct from other areas of the ocean floor.
The German group found a rapid decline in microbes over the first
102 cm, but from that point on, the number of cells fluctuated and did
not continue to decline. It is worth noting that the deepest sample at
6.6 meters contained as many cells as the sample at 0.74 meters. Unfor-
tunately, it is not possible to convert µg of DNA into number of cells. The
Japanese group discovered a steady decline in cell density over the first
16 cm of sediment away from the cold seep, but cells remained fairly
constant at about 107 (10 million) cells per gram of sediment at the nutri-
ent rich cold seep. The nearly 50-fold difference in cell density between
the two sites was not due to depth of water but availability of nutrients.
Microbes that live in extreme environments are sometimes referred to
as extremophiles, meaning they “love” extreme habitats. Microbes live
on the ocean floor, and at least 6 meters below the seafloor, but can they
live any deeper? Is there only one species of microbe at these extreme
depths under the deepest parts of the ocean? A team of scientists from
Scotland and Wales sampled sediment under 150 meters of water off the
coast of Peru. They knew that the oxygen content of the water at the
ocean floor was nearly zero, and they were looking for anaerobic bacteria
living far below the seafloor. The temperature of the sediment 62 meters
under the seafloor was 15.6º C, which was warmer than the water at the
surface of the sediment. At the indicated depths, the team counted the
total number of live anaerobic microbes and also determined how each
cell obtained its energy. Based on each cell’s metabolism, the investigators
placed the prokaryotes into one of five categories. The details of how the
categories of cells obtain energy are not important at this time. The critical
aspect is whether there were any trends in the distribution of microbes
from 1.5 to 80.2 meters below the seafloor.
At the shallow water site off the coast of Peru, microbes were present
at every depth measured, though the density varies from approximately
330,000 cells per cm2 near the seafloor, to about 10 cells per cm2 at 7.7 meters
below the ocean. Sulfate reducers appeared to be restricted to the top
4 meters of sediment, whereas methane producers, or methanogens,
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36 PHOTOSYNTHESIS
appear to be restricted to the middle 3 to 30 meters. It is interesting to

note that even the most prevalent type of microbe, multi-species hetero-
trophs that consume organic molecules made by primary producers, were
absent from some layers of the sediment. In short, the number of
microbes does not seem to correlate with any trend in depth, although
perhaps the layers containing the methanogens and hexadecane oxidizers
are unable to support large numbers of cells.
Thermal vent lifestyles
Microbes live in extreme environments, they adapt to their surroundings,

and their metabolism is specialized to match the available energy sources.
Consider perhaps the harshest place on earth, deep water thermal vents.
Thermal vents are where the earth’s central molten rock heats water that
spews dissolved minerals into the ocean. The water that comes out of these
holes is 300º C to 400º C, and once the mineral-rich hot water hits the
2º C cold water at the bottom of the ocean, the dissolved minerals quickly
precipitate out of solution. The precipitating minerals look like black
smoke pouring out of smoke stacks as can be seen in images found when
searching the Internet. The presence of hot, mineral-rich water at the
bottom of the ocean was first reported in the 1940s, but it was not until
the 1970s that oceanographers got their first view of the completely
unexpected ecosystem at the bottom of the ocean. Riding in specially
designed submarines, explorers photographed an amazing array of animals
and rock formations that no one had anticipated. Crabs, clams, and giant,
red tube worms 3 meters (9 feet) long surprised everyone. Where no one
expected life to survive, scientists photographed and collected specimens
of exotic and colorful animals. These species have homeostatic mechanisms
to live in an extreme environment.
Over time, biologists realized that the red color on these giant tube
worms was due to microbes living on and in the animals. The red tube
worms have no intestinal tract, and they absorb their nutrients directly
from the microbes that live symbiotically on the worm’s body. Once it was
learned that microbes thrive near thermal vents, the existence of all the
other animals in the areas was understandable, but what is the source of
the prokaryote’s energy? One of the more interesting sources of energy for
prokaryotes was first hypothesized by Ph.D. graduate student, Cindy Van

Dover. Van Dover was curious to understand the albino shrimp, Rimicaris
exoculata, that flourishes around the thermal vents. She wondered why
these shrimp did not have traditional eyes like shallow water shrimp.
Exoculata is Latin and means without eyes. On top of their heads, the
thermal vent shrimp have an elongated structure from which extends a
nerve that leads directly to the brain. Van Dover and her collaborators
isolated a protein from the organ of the thermal vent shrimp and com-
pared its biochemical properties to those of a well-known visual protein
found in all vertebrate eyes called rhodopsin. In 1989, the marine biology
team compared the shrimp protein for its ability to absorb light with that
of rhodopsin isolated from a frog species that had been studied previously.
Van Dover hypothesized the shrimp could see light despite the fact that
they lived under miles of pitch dark ocean. Sunlight cannot reach the ocean
bottom, so the obvious challenge for Van Dover was to find a source of
light at thermal vents. Van Dover would have to wait five years to test her
hypothesis that light came from the thermal vents.
In 1994, Van Dover was a crew member on a mission to the bottom of
the ocean in a specially designed submarine called Alvin. The temperature
of the water leaving the thermal vent was 350º C and the “smoke” was
pitch black. It must have been scary, but they turned off all the lights and
aimed their cameras in the direction of the black smoke and took a picture
of what looked totally dark to the scientists. Much to Van Dover’s delight,
they had the world’s first photograph without artificial light of a thermal
vent. Two years later, Van Dover returned to measure the wavelengths of
light emitted from the thermal vent. She took photographs of the black
“smoke” using filters that allowed only certain wavelengths of light reach
the camera. The number on each photograph was the center wavelength of
light, and the filter allowed light to reach the camera at the wavelength
+/– 50 nm. Using a different piece of equipment, Van Dover quantified the
light intensity at 700, 800, 900, and 1000 nm wavelengths. The intensity
measured from the thermal vent was graphically compared to the calcu-
lated amount of light emitted from an object glowing red hot at 350º C.
Van Dover’s hunch, based on the anatomy of a shrimp, was validated.
Thermal vents are sites where the hot center of the earth interacts
with the cooler surface of our planet. The black “smoke” is a mixture of
38 PHOTOSYNTHESIS
hot water and many dissolved minerals precipitating when they hit the
cold water. The smoke is particulate matter similar to stirring a mud
puddle that produces mud “smoke.” The tube worms are red because
about half of their total body mass is composed of red prokaryotes. The
crabs and other animals are red because microbes live on their surfaces as
well. At this point, it is not clear why the microbes are red and why red
pigment might provide a selective advantage to them. For any ecosystem
to thrive, it needs either organic molecules available for consumption, or
primary producers. If thermal vent microbes are primary producers, then
they could supply the entire ecosystem with organic molecules as food.
Microbes are small, but their vast numbers means their cumulative mass
would be sufficient to support the entire food chain. Remember that half
of the tube worm’s body is composed of these red microbes.
Van Dover’s original observation was that thermal vent shrimp had
modified visual organs that were very different than most shrimp. She
isolated a protein similar to rhodopsin, which is essential for vision of
vertebrates. Van Dover’s data led her to hypothesize that the shrimp must
be seeing light or else the existence of rhodopsin in thermal vent shrimp
did not make sense. The first hard evidence of natural light at the bottom
of the ocean was the photograph. Her photograph was the shot seen
round the world, and it launched a new wave of research into the bio-
physical properties of deep thermal vents. Van Dover demonstrated that
the maximum output of visible light was around 870 nm, but even more
energy at infrared wavelengths of 1000 nm was emitted from the thermal
vents. The camera was not equipped to detect far infrared, so that wave-
length was not detected in her photographs. Infrared energy is the same
wavelengths that can be felt on the skin in warm sunlight. Infrared is not
visible to human eyes, but skin can detect its warmth and perhaps the
shrimp can see the heat with their modified eyes. The calculated light
intensity emitted from a red hot object at 350º C did not predict the
intense light around 700 nm, underestimating the output by about tenfold,
and so the investigators were left wondering about the source of the un-
expected energy. Despite the difference between expected and measured
light, Van Dover and her colleagues were happy to discover visible light
emanating from the thermal vents. Could any organisms besides the shrimp
detect the light?
A team of Canadian and German microbiologists collected samples

of bacteria growing by a thermal vent off the west coast of British
Columbia, Canada. They isolated one particular species called Citromicrobium
bathyomarinum, which appeared yellowish rather than red, like so many
other species living near thermal vents. These cells came in many different
shapes, some of which were perplexing, including cells that looked like
they were dividing into thirds rather than halves. More importantly for this
chapter, how does C. bathyomarinum harvest energy? Does it use chemo-
synthesis or does it use the light energy produced by thermal vents? The
team of microbiologists isolated C. bathyomarinum’s light-harvesting an-
tenna complex and the associated reaction center. The isolated pigments’
absorption spectrum produced a curve similar to chlorophyll. The yellow
color of the carotenoid pigments absorbed light around 500 nm, whereas
bacterial chlorophyll had an absorption peak just above 850 nm. The ab-
sorption spectrum from these bacteria looked surprisingly similar to plant
pigments.
Just east of Clipperton Island in the Pacific Ocean, a multinational
team of microbiologists from Canada, Bermuda, and America isolated a
bacterium that was capable of anaerobic photosynthesis. Anaerobic photo
synthesis is noteworthy because plants produce oxygen but these microbes
did not. The investigators isolated the cells from the black “smoke” billow-
ing out of a chimney. Living near a thermal vent chimney, the bacterial
cells can become matted together with thick, extracellular protein produced
by the cells. H2S and light are required for photosynthesis by this particular
bacterium that uses the ambient light of the thermal vents for photo-
synthesis. Water near thermal vents contains a rich mixture of electron
donors and electron acceptors that provide sufficient resources to support
chemosynthesis (Table 2).
Table 2 List of chemicals enriched in water near thermal vents.

Potential chemosynthesis inorganic compounds
Electron donors at vent Electron acceptors at vent
H2, H2S, CH4, NH3, S, S2O3–2, Fe(II), O2, NO3–, NO2–, Fe(III), Mn2O2, SO4–2,
NO2– CO2
Source: Modified from Jørgensen and Boetius, 2007, their box 2.

40 PHOTOSYNTHESIS
Based on the pigments present in C. bathyomarinum, it appears that

thermal vent ecosystems may produce more light than just the wave-
lengths discovered by Van Dover. If any species produced its own light
using bioluminescence with a fluorescent protein, thermal vent microbes
might be able to use the light to photosynthesize as well. If a cell could use
both photosynthesis and chemosynthesis, it would be able to use more
energy sources and might be better adapted to live near thermal vents.
Thermal vent water is loaded with inorganic CO2 and CH4, which can be
metabolically modified by microbial primary producers into organic
molecules, such as sugars.
Photosynthesis at thermal vents has led some biologists to speculate
that the origin of all photosynthesis is based on light near thermal vents
rather sunlight. Perhaps the earliest microbes used photo detection and
flagella to swim toward the light, warmth, and nutrients of thermal vents.
Over time, these same pigments could have been used in a more compli-
cated biochemical pathway that used light energy to reduce other mole-
cules for use as metabolic fuel. If a microbe that could use light to harness
energy were exposed to sunlight, then this fortunate cell would be in an
optimal location to give rise to the photosynthesis that we see in cyano-
bacteria and plants today. It may seem unlikely, but until there are com-
pelling data refuting the hypothesis, it is possible that photosynthesis in
plants may have evolved from photosynthesis in microbes living at thermal
vents at the bottom of the ocean.
Salt-tolerant lifestyles
It is worth exploring one more habitat that is toxic to every form on life,
with a few notable exceptions. The Dead Sea is famous, but the origin of
its name is unknown to many people. The landlocked Dead Sea is sur-
rounded by Israel, Jordan, and the West Bank at over 1,300 feet below sea
level. No plants or animals live in the Dead Sea because of the extremely
high salt concentration. It may seem odd that the same salt people eat can
be toxic, but too much NaCl is lethal. In a satellite image, it is possible to
see blue water, white salt, and the pink color is an uncountable number
of archaea collectively called halophiles, or salt lovers. Halophiles can live
in water that contains 30% to 35% NaCl. Normal ocean water is
typically 3.5% salt, or one tenth as concentrated as the Dead Sea. Salt
water is toxic to most cells for two reasons. Salt water produces a strong
osmotic pressure that causes water to leave cells where the water concen-
tration is higher in the cytoplasm. One homeostatic mechanism to with-
stand salt that some halophiles have evolved is the ability to import
potassium ions (K+) into their cytoplasm to balance the extracellular os-
motic pressure of Na+. Halophiles that evolved this K+ homeostasis
mechanism are obligate halophiles, meaning they require very high salt
outside in order to survive and they would die in ocean water.
The Dead Sea is also toxic because most proteins and typical bacteria
“salt out,” meaning they precipitate when salt reaches a certain concentra-
tion. The only way to keep proteins and cells in a high salt solution is to
increase their ionic charge to counterbalance the charged salt ions in the
water. By maintaining a charged exterior in a salt solution, proteins and
cells can remain in solution rather than salting out of solution into a solid
at the bottom of the water. Before genomics and bioinformatics became
available, molecular biologists in the 1970s determined the amino acid se-
quences for several highly conserved ribosomal proteins from Halobacterium
cutirubrum and compared these sequences to orthologs from Escherichia
coli. The investigators subtracted the number of basic amino acids (posi-
tively charged) in a protein from the number of acidic amino acids
(negatively charged) in the same protein. Amino acids, aspartic acid and
glutamic acid, carry negative charges, because as acids, they donate a pro-
ton to the solution. Conversely, basic amino acids (arginine, histidine,
and lysine) all accept protons from their local environment and carry a
positive charge. The investigators repeated their overall protein charge anal-
ysis to produce a quantitative comparison for 14 H. cutirubrum ribosomal
proteins and 26 E. coli orthologous proteins. The resulting differences
were plotted along the y-axis with the molecular weight of each protein on
the x-axis. One would predict that halophiles with increased cytoplasmic
K+ ion concentrations would have evolved proteins with more negative
charges.
Halobacteria face several stress factors, including desiccation due to
loss of water and salting out and sinking to the bottom of the lake to die.
Furthermore, their homes are ephemeral by nature, and the shallow water
pools can dry up rapidly. These physical and temporal stresses produce
42 PHOTOSYNTHESIS
selection pressures to evolve homeostatic mechanisms for water balance

and energy production. Because H. cutirubrum imports a lot of K+ ions
to counterbalance the osmotic pressure of extracellular Na+, its genome
encodes more acidic proteins that carry negative charges to balance
the overall charge of its cytoplasm. If positively charged basic proteins
were produced instead, the cells would suffer from a large charge
imbalance across their cell membranes.
In recent years, biologists have sequenced the genomes of several halo-
philes to understand what homeostatic adaptations have evolved to toler-
ate high salt to the point that some species are dependent upon high
salt in order to survive (obligate halophiles). The archaea Halobacterium
salinarum genome revealed that this prokaryote could use arginine in a
novel way. The investigators grew the halophiles in the presence of ele-
vated amino acids (one at a time). In separate experiments, investigators
added each amino acid and measured its concentration over time. All of
these experiments were performed under conditions conducive to photo-
synthesis. Ornithine is a metabolic intermediate in arginine production
and urea cycling, but ornithine is not an amino acid used for protein
production. Therefore, this particular halophile consumes amino acids at
the same time it photosynthesizes.
Because the Dead Sea water evaporates quickly, H. salinarum simulta-
neously generates ATP by photosynthesis and amino acid metabolism.
Arginine is consumed the fastest, followed by ornithine, then proline, and
tyrosine is the slowest. It appears that H. salinarum lives as if there is no
tomorrow, which might be very adaptive given that these shallow bodies
of water dry up quickly. Land plants can photosynthesize and metabolize
amino acids, but they preferentially use sunlight when available. Halophiles
evolved unusual mechanisms to maintain homeostasis by evolving new
metabolic capacity. The last example of this chapter will present how one
species dealt with its genomic “spare parts.”
Tiny photosynthesis specialists
Many halophiles are pink and contribute to the color of flamingos that
eat them. However, cyanobacteria appear very dark, and when they
form biofilms, they produce the dark streaks on shingled roofs of houses.
Cyanobacteria are photosynthetic bacteria that live in many places, in-

cluding the open ocean where there is plenty of sunlight and no chance
for shade-producing trees. In 2010, a private company and a public uni-
versity in America collaborated to sequence the genome of an open ocean
cyanobacterium that does not have a Latin name yet, UCYN-A. The in-
vestigators chose this species because it can fix nitrogen from the air into
organic molecules, and it lacks PSII, which is the portion that splits water
and produces waste O2 gas. The genomics and bioinformatics specialists
deduced the metabolic pathways of this cyanobacterium based on the
genes encoded in the DNA. They placed all of the deduced pathways on
a pictorial map of the cell and made a surprising discovery based on what
they did not find. No species contains all possible biochemical pathways,
but the investigators were surprised to learn that UCYN-A is unable to fix
carbon using the pathway discovered by Calvin (see Figure 10). Further-
more, these cyanobacteria cannot metabolize 2-carbon molecules the way
human cells do, because they lack the genes that encode the citric acid
cycle. This bacterium also lacks the enzymes needed for a urea cycle,
which is essential to H. salinarum. The cells whose DNA was sequenced
were free-floating and not symbionts with any other cells. This species
surprised everyone based on its odd combination of genes.
The 1.4 million base pair genome of UCYN-A is smaller than many
bacterial genomes, which suggests it has lost many genes over time. By
comparison, the E. coli genome is about 4.5 million base pairs, whereas a
typical chloroplast genome is about 140,000 base pairs. Carrying unused
genes in a genome is analogous to fluency with a foreign language that a
person does not get to use very often, or memorizing a long list of meta-
bolic pathways that most people will forget once they have taken the test.
A common biological axiom is, “What you don’t use, you lose.” UCYN-A
can produce some, but not all, amino acids with its own metabolism.
UCYN-A can reduce N2 into NH3, so nitrogen fixation is functional too.
Lipid production, nucleic acid production, and glycolysis all appear to
be functioning adequately. It has an ATP synthase on its thylakoid-like
intracellular membranes even though it is a bacterium. In addition to a
labeled “H+ importer,” light can stimulate the movement of H+ ions
through the cytochromes, which means paraquat would probably kill this
cyanobacterium the way it kills land plants. Rather than producing O2,
44 PHOTOSYNTHESIS
the cyanobacterium appears to reduce O2 into water. PSI probably drives

the cyclic electron transport because the cells lack PSII, and it cannot split
water to fill the electron hole produced by noncyclic electron flow.
This species of cyanobacterium appears to have lost many “vital” meta-
bolic pathways and yet it lives. Based on the number of “sugar” import
proteins on its surface, the investigators hypothesized that it may be a
symbiont for at least some of its life cycle because its reduced collection of
genes indicates it relies on other organisms to supply much of its metabolic
capacity. In this case, homeostasis of the genome responded to a free sup-
ply of nutrients from a host by getting rid of redundant genes. Given a
ready supply of nutrients, the genome lost genes because the cost of main-
taining a large genome was maladaptive and natural selection favored a lean
genome. Evolution does not lead to increasing complexity nor does it lead to
reduced complexity. Evolution is the outcome of natural selection working
on populations of cells over time that must adapt to a changing habitat.
This chapter illustrated that life abhors a vacant niche. If a habitat
contains a source of potential energy, at least one species has adapted to
thrive in what appeared to be an uninhabitable environment. Prokaryotes
can live in cold, hot, salty, and even toxic locations. Life adapts to occupy
niches with carbon and electron donors. Homeostasis is the dynamic pro-
cess where cells balance the concentration of various components. Feed-
back mechanisms, time-dependent processes, and an organism’s size all
play a role in how cells maintain the delicate balance between life and
death. Energy requirements often dominate what portions of a metabolic
pathway are expendable and which parts might require novel solutions.
The physical, chemical and even temporal challenges produce selection
pressures on populations every day and evolution is an ongoing process.
Bibliography
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46 PHOTOSYNTHESIS
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acter abyssi sp. nov., an anaerobic thermophile from deep-sea hydro-
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Conclusion
The second law of thermodynamics states that all cells tend toward ran-
domness unless energy is consumed to maintain order and synthesize
complexity. As early as 1774, biologists had conducted research to under-
stand how plants harness energy from the sun to maintain cellular order
and produce structural complexity. Biochemical gradients require energy
to produce and maintain, which is a central role of cellular homeostasis.
Cells use feedback to regulate enzymatic pathways that convert energy
from one form to another. Proteins function best in narrow windows of
temperature, pH, and ionic concentrations that benefit one species but
might harm another. Information collected by cells produces feedback
mechanisms that drive positive and negative feedback loops. Multistep
biochemical pathways must occur in a particular sequence, placing a tem-
poral constraint that cells address through substrate limiting reactions
and enzyme reaction rate modulation. Chloroplasts and prokaryotes use
all of these components and are the smallest photosynthetic units. The
globe is interconnected through the homeostasis involved in energy pro-
duction and consumption that includes human activity.
Extremophiles defy predictions of where life can exist. Heat, toxins,
salts, pressure, and symbiosis provide archaea and bacteria with new
niches. Cell size, physical properties, and chemical gradients govern how
prokaryotes use resources and reproduce. Perhaps one of the biggest sur-
prises was discovering photosynthesis at the bottom of the ocean where
no sunlight can penetrate. Over time, multicellular land plants evolved
more complexity, but they retained essentially the same photosynthetic
mechanisms found at thermal vents. Digging deeper, microbiologists
have discovered living cells hundreds of meters below the ocean floor.
Life maintains homeostasis by regulating the flow of energy no matter
how harsh the environment.
Glossary
antenna complex. it contains many pigments in a ring of proteins that surrounds
the central core proteins and pigments of chlorophyll a where light energy is
converted to chemical energy.
astrobiologists. biologists who are especially interested in life on planets other
than Earth.
Calvin and Benson cycle. see Calvin cycle.
Calvin cycle. biochemical pathway that converts harvested light energy into fixed
carbons of simple sugars which are used in other pathways to build lipids, amino
acids and nucleic acids.
chemosynthesis. it converts inorganic CO2 or CH4 into organic molecules, such
as sugars, lipids, and proteins.
chlorophyll a. green pigment at the center of the antenna complex that converts
harvested light energy into chemical energy.
chlorophyll b. very similar in structure to chlorophyll a, it too harvests light
energy but passes its energy to chlorophyll a.
cold seep. a place in the ocean floor where nutrient rich, cold water oozes up
from the earth’s crust beneath the sediment.
cyanobacteria. photosynthetic bacteria that capture sunlight energy to produce
multicarbon molecules; cells have internal membranes.
cytochrome. iron containing proteins that contain a heme group which is re-
sponsible for the generation of hydrogen gradient in the electron transport chain
of chloroplasts.
extremophiles. microbes that live in very harsh environments that would kill
most species.
fossil fuels. coal, oil and natural gas are energy sources formed by decomposing
living organisms under ground.
halophiles. bacteria and archaea that live in habitats with very high salt concen-
trations, such as the Dead Sea and the Great Salt Lake in Utah.
lutein. photosynthetic pigment in the antenna complex that gives leaves their
yellow color.
methanogens. prokaryotes that produce methane as a byproduct of their anaero-
bic metabolisms.
obligate halophiles. an organism that can only live in high salt environments.
orthologs. two genes with very similar sequences found in two different genomes.
P680 and P700. the paired chlorophyll a molecules that absorbed slightly differ-
ent wavelengths of light.
52 GLOSSARY
paraquat. herbicide that is also toxic to animals due to its ability to block electron
transport.
photon. a unit of light energy that behaves like a packet of energy rather than as
wave form.
photooxidized. the removal of an electron from chlorophyll a when the pigment
is excited by a photon.
photosynthesis. biochemical process by which light energy is harvested to pro-
duce chemical storage molecules that are used to incorporate carbon dioxide into
sugars.
photosystem I. a self-contained photosynthetic unit that helps plants harvest
light energy.
photosystem II. a portion of the complex system required for photosynthesis,
works in conjunction with photosystem I.
primary producers. it convert inorganic carbon (such as, CO2) into organic mol-
ecules (such as, glucose).
reaction center. proteins and paired chlorophyll a pigments that convert light
energy into biochemical energy.
ribulose 1,5-bisphosphate. substrate for the enzyme rubisco, is a 5 carbon sugar
to which a new carbon will be attached during the first step of the Calvin cycle.
rubisco. the enzyme that covalently attaches CO2 onto ribulose bisphosphate
that leads to the production of PGA.
stroma. fluid filled space inside chloroplast but outside thylakoids.
thermal vents. it is located at the bottom of the oceans and release hot water and
dissolved nutrients that support entire ecosystems.
thin layer chromatography. thin layer chromatography is a method that sepa-
rates chemicals based on their ability to move on a powdery surface.
thylakoid space. the liquid-filled lumen of thylakoids.
thylakoids. the membrane vesicles inside chloroplasts that are green in appearance.
β-carotene. photosynthetic pigment in the antenna complex that gives leaves
their red-orange color.
Index
Adenosine triphosphate (ATP), 7, 8, Cyanobacteria, 42–44
12–13, 19 Cytochromes, 9, 11
Albino shrimp, 37
Allen, M.B., 23 Dead Sea, 40–41
Alvin submarine, 37 Dechloromonas, 33
Ambient light, of thermal vents, 39
Amino acids, 41 Electrons flow, energized by light,
Anaerobic photosynthesis, 39 9–11
Antenna complexes, 5, 6, 7 Energy consumption and CO2
Arginine, 42 levels, 21–22
Arnon, Daniel, 7–8 Engelmann, Theodor Wilhelm, 3–4
Artificial photosynthesis, 16–17 Escherichia coli, 41, 43
Aspartic acid, 41 Europe, banning of paraquat use
Astrobiologists, xiii in, 1, 17–19
European Public Health Alliance, 17
Bacterium termo, 3 Exoculata, 37
Beggiatoa, 33–34 Extremophiles, 35
Benson, Andrew, 24
β-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 Calvin cycle Geobacter sulfurreducens, 33
Calvin cycle, 24 Glutamic acid, 41
Carbon fixation, 23–24 Glyceraldehyde 3-phosphate (G3P), 26
and carbon recycling, 25
Cellular respiration, 26 Halobacterium cutirubrum, 41–42
Chemosynthesis, 34, 39 Halobacterium salinarum, 42, 43
Chlorophyll a, 5, 6, 7, 9 Halophiles, 40–41
Chlorophyll b, 5, 6 Heldt, Hans, 8
Chloroplasts, 4–6, 8–9, 24 Helicobacter pylori, 33
diagram of, 5 Herbicide paraquat, banning in
directing electron and H1 ion Europe, 1, 17–19
flow in, 11 Hill, Robin, 4, 9
Citromicrobium bathyomarinum, 39–40 Homeostasis, of photosynthesis, 13,
CO2 15, 18, 27, 44
connecting rainforests in Brazil to
Greenland’s glaciers, 21–31 Laws of thermodynamics, 16, 49
14
CO2, 23, 24 Light energy, ATP production from, 12
Cold seep, 34–35 Light wavelengths, 6–7
54 INDEX
Lowenstam, Heinz, 34 Primary producers, xiii, 34

Lutein, 5, 6 Prokaryote cells, 26
Prokaryotes, 12, 13, 34, 37, 44
Magnesium ions (Mg2+), Proline, 42
concentrations of, 27–28
Methanogens, 35–36 Rainforests, connecting to Greenland’s
Microbes, 33–36 glaciers, 21–31
Mitochondria, 8, 26 Reaction center, 6
Rhodopsin, 37
Nicotinamide adenine dinucleotide Ribulose 1,5-bisphosphate, 24, 26
phosphate (NADPH), 10 Rimicaris exoculata, 37
Nicotinamide adenine dinucleotide Rubisco, 24, 26, 27
with hydrogen (NADH), 9 physiological regulation of, 28
Non-chlorophyll pigments, 6
Salt lovers, 40–41
Obligate halophiles, 42 Salt-tolerant lifestyles, 40–42
Oil spill, Gulf of Mexico (2010), 31 Sandstorms, 31
Ornithine, 42 Second law of thermodynamics, 49
Orthologs, 41 Stroma, 5, 6
Oxidized chlorophyll, 13–14 Syngenta company, 18
Oxygen, 4, 15
Thermal vent lifestyles, 36–40
P680, 9, 16 Thin layer chromatography
P700, 9 (TLC), 2D, 24
Paraquat, 1 Thylakoid space, 5, 15
connecting to human toxicity, Thylakoids, 5
17–19 Tiny photosynthesis specialists, 42–44
effects of, 17 Two-dimensional thin layer
and mammalian consequences, 2 chromatography (TLC), 24
use, banning in Europe, 1, 17 Tyrosine, 42
pH, 8
Phosphoglycerate (PGA), 24–26 UCYN-A, 43
Photon, 7
Photooxidized, 10 Van Dover, Cindy, 37–38
Photosynthesis, understanding, 1–17
Photosystem I (PSI), 9–10 Water splitting, 15–16, 23
Photosystem II (PSII), 9–10
Priestley, Joseph, 2–3 Zeiss, Carl, 3–4
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Herbicide Paraquat Is Legal in America But Not in Europe 5

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

cyanobacteria. In chloroplasts, photosynthetic pigments cluster together

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

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

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

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

Figure 7 Two homeostatic photosynthetic processes. A, The water

4 photons + 2H2O → 4 H+ + 4e2 + O2

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

reaches the chloroplast, a kinase is activated that phosphorylates the

electrons that reduce the four oxidized chlorophyll a molecules in the

4 photons 1 2H2O → 4 H+ 1 4e2 1 O2

photosynthesis” will reveal how scientists are trying to improve energy

Connecting paraquat to human toxicity

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

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

7 human production of 400 Barrow, Alaska air samples

CO2 concentration (ppmv)

CO2 concentration (ppmv)

Figure 9 Energy consumption and CO2 levels. A, The total human

Connecting Brazil’s Rainforest to Greenland’s Glaciers 25

NADPH is oxidized to NADP+ in the production of G3P. The produc-

enzyme activity (nmoles min–1 mg–1)

Figure 11 Physiological regulation of rubisco. A, Rubisco

The investigators prepared three concentrations of Mg2+ ions in buffers

Ethical, Legal, Social Implications: National Policies

Figure 12 National policies can affect many nations. A, NASA

consequences in another country. Everyone agrees that paraquat can be le-

Arnon DI, Allen MB, Whatley FR. Photosynthesis by isolated chloroplasts.

Ethical, Legal, Social Implications: National Policy Affect More

Panel a from http://www.nasa.gov/multimedia/imagegallery/image_

No Place on Earth Is Devoid of Life 35

appear to be restricted to the middle 3 to 30 meters. It is interesting to

Thermal vent lifestyles

Microbes live in extreme environments, they adapt to their surroundings,

prokaryotes was first hypothesized by Ph.D. graduate student, Cindy Van

A team of Canadian and German microbiologists collected samples

Table 2 List of chemicals enriched in water near thermal vents.

Source: Modified from Jørgensen and Boetius, 2007, their box 2.

Based on the pigments present in C. bathyomarinum, it appears that

selection pressures to evolve homeostatic mechanisms for water balance

Tiny photosynthesis specialists

Cyanobacteria are photosynthetic bacteria that live in many places, in-

the cyanobacterium appears to reduce O2 into water. PSI probably drives

No Place on Earth Is Devoid of Life 45

Beatty JT, Overmann J, Lince MT, et al. An obligately photosynthetic

Miroshnichenko ML, Slobodkin AI, Kostrikina NA, et al. Deferrib-

No Place on Earth Is Devoid of Life 47

Lowenstam, Heinz, 34 Primary producers, xiii, 34