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Light Harvesting in
Photosynthesis
 FOUNDATIONS OF BIOCHEMISTRY
AND BIOPHYSICS SERIES

Light Harvesting in Photosynthesis

Roberta Croce, Rienk van Grondelle, Herbert van Amerongen,
and Ivo van Stokkum

An Introduction to Experimental Biophysics:

Biological Methods for Physical Scientists,
Second Edition
Jay L. Nadeau

An Introduction to Single Molecule Biophysics

Yuri L. Lyubchenko

Biomolecular Thermodynamics: From Theory to Application

Douglas Barrick

Biomolecular Kinetics: A Step-by-Step Guide

Clive R. Bagshaw

An Introduction to Biophysics: Quantitative Understanding

of Biosystems, Second Edition
Thomas M. Nordlund and Peter M. Hoffmann
Light Harvesting in
Photosynthesis

Edited by
Roberta Croce
Department of Physics and Astronomy
Vrije Universiteit
Amsterdam, the Netherlands

Rienk van Grondelle

Department of Physics and Astronomy
Vrije Universiteit
Amsterdam, the Netherlands

Herbert van Amerongen

Laboratory of Biophysics
Wageningen University
Wageningen, the Netherlands

Ivo van Stokkum

Department of Physics and Astronomy
Vrije Universiteit
Amsterdam, the Netherlands
CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742

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Library of Congress Cataloging-in-Publication Data

Names: Croce, Roberta, editor. | Grondelle, Rienk van, editor. | Amerongen,

Herbert van, editor. | Stokkum, Ivo van, editor.
Title: Light harvesting in photosynthesis / [edited by] Roberta Croce, Rienk
van Grondelle, Herbert van Amerongen, Ivo van Stokkum.
Other titles: Foundations of biochemistry and biophysics.
Description: Boca Raton : Taylor & Francis/CRC Press, 2017. | Series:
Foundations of biochemistry and biophysics | Includes bibliographical
references.
Identifiers: LCCN 2017037100 | ISBN 9781482218350 (hardback : alk. paper)
Subjects: | MESH: Photosynthesis--physiology | Biophysical Phenomena |
Light-Harvesting Protein Complexes--metabolism | Plants--metabolism
Classification: LCC QK882 .L47 2017 | NLM QK 882 | DDC 572/.45--dc23
LC record available at https://lccn.loc.gov/2017037100

Visit the Taylor & Francis Web site at

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Contents

Preface vii
Editors ix
Contributors xi

Part 1 BUILDING THE LIGHT-HARVESTING APPARATUS: Pigments 1

1 Pigments: General properties and biosynthesis 3

Min Chen and Robert E. Blankenship
2 Chlorophylls in a protein environment: How to calculate their spectral and redox properties
(from MO to DFT) 21
Carles Curutchet and Benedetta Mennucci
3 Carotenoids: Electronic states and biological functions 37
Harry A. Frank and Bruno Robert

Part 2 BUILDING THE LIGHT-HARVESTING APPARATUS: Proteins 57

4 Light harvesting in higher plants and green algae 59

Lauren Nicol and Roberta Croce
5 Light harvesting in cyanobacteria: The phycobilisomes 77
Leeat Bar-Eyal, Anat Shperberg-Avni, Yossi Paltiel, Nir Keren, and Noam Adir
6 Photosynthetic apparatus in purple bacteria 95
David J. Mothersole, David A. Farmer, Andrew Hitchcock, and C. Neil Hunter
7 Light harvesting in green bacteria 121
Jakub Pšenčík and Tomáš Mančal
8 Light-harvesting complexes in chlorophyll c–containing algae 155
Claudia Büchel
9 Reaction centers: Structure and mechanism 181
Michael R. Jones
10 Organization of photosynthetic membrane proteins into supercomplexes 207
Egbert J. Boekema and Dmitry A. Semchonok
11 Photoprotective excess energy dissipation 219
Alberta Pinnola, Diana Kirilovsky, and Roberto Bassi

v
vi Contents

Part 3 LIGHT-HARVESTING SYSTEMS IN ACTION: Energy Transfer and Electron Transport 247

12 The exciton concept 249

Leonas Valkunas, Jevgenij Chmeliov, and Herbert van Amerongen
13 Modeling of energy transfer in photosynthetic light harvesting 269
Vladimir I. Novoderezhkin and Rienk van Grondelle
14 Quantum aspects of photosynthetic energy transfer 305
Susana F. Huelga and Martin B. Plenio
15 Photoinduced electron transfer in the reaction centers 327
Thomas Renger
16 Modulation of the redox potentials 359
Fabrice Rappaport

Part 4 LIGHT-HARVESTING SYSTEMS IN ACTION: Spectroscopy 379

17 Basic optical spectroscopy for light harvesting 381

Arvi Freiberg and Győző Garab
18 Advanced Ultrafast Spectroscopy Methods 427
Tomáš Polívka and Donatas Zigmantas
19 Experimental evidence of quantum coherence in photosynthetic light harvesting 449
Gregory D. Scholes, Jacob C. Dean, Jessica M. Anna, Gregory S. Engel,
and Rienk van Grondelle
20 Systems biophysics: Global and target analysis of light harvesting and photochemical
quenching in vivo 467
Ivo van Stokkum

Part 5 ARTIFICIAL AND NATURAL PHOTOSYNTHESIS 483

21 Light harvesting, photoregulation, and photoprotection in selected artificial photosynthetic

systems 485
Katherine WongCarter, Manuel J. Llansola-Portoles, Gerdenis Kodis, Devens Gust,
Ana L. Moore, and Thomas A. Moore
22 Light to useful charge in nanostructured organic and hybrid solar cells 511
Tönu Pullerits and Villy Sundström
23 Chlorophyll fluorescence as a tool for describing the operation and regulation
of photosynthesis in vivo 539
Jeremy Harbinson
24 Harvesting sunlight with cyanobacteria and algae for sustainable production in a bio-based
economy 573
Pascal van Alphen and Klaas J. Hellingwerf

Index 587
Preface
This book introduces the basic physical, chemi-
cal, and biological principles underlying the first
steps in photosynthesis: light absorption, excita-
tion energy transfer, and charge separation. In Part
1, we introduce pigments and their spectroscopic/
redox properties. In Part 2, pigment-proteins as
they occur in various natural systems (plants, algae,
photosynthetic bacteria) are described, including
the regulation of light harvesting. Part 3 deals with
the physics underlying light harvesting: energy
transfer and electron transport. Part 4 introduces
basic and advanced spectroscopic methods, includ-
ing data analysis. In Part 5, we discuss artificial
and natural photosynthetic systems, how they are
assembled, and what the energy transfer properties
are.
vii
Editors
Roberta Croce, PhD, (1968) studied chemistry at
the University of Padova and earned her PhD at the
University of Milano. Since 2011, she is a full pro-
fessor in biophysics of photosynthesis/energy and
head of the Biophysics Group at Vrije Universiteit
Amsterdam, the Netherlands. She served as cochair
of the International Congress of Photosynthesis
Research held in Maastricht in 2016. She has pub-
lished more than 130 scientific articles. Since 2013,
she is a member of the Royal Holland Society of
Sciences and Humanities (KHMW).
Rienk van Grondelle, PhD, (1949) studied physics
at Vrije Universiteit Amsterdam (VU) and earned
his PhD in Leiden. He joined the physics faculty of
the VU in 1982, where he was appointed full pro-
fessor in 1987. He built up a large research group
and has made major contributions to elucidating
the fundamental physical mechanisms that under-
lie light harvesting and charge separation. In 2001,
he became a member of the Royal Netherlands
Academy of Arts and Sciences (KNAW). In 2009,
he was awarded an Academy Professorship for his
outstanding contributions to the understanding
of the first stage in photosynthesis. To date, he has
published more than 600 scientific papers, which
have attracted about 27K citations.
Herbert van Amerongen, PhD, (1959) stud-
ied physics at Vrije Universiteit Amsterdam and
earned his PhD in biophysics at the same univer-
sity. Since 2002, he is a full professor of biophysics at
Wageningen University, where he is also director of
the MicroSpectroscopy Research Facility. He pub-
lished more than 170 publications in peer-­refereed
journals and, together with Leonas Valkunas and
Rienk van Grondelle, he is author of the book
Photosynthetic Excitons. In 2016, he served as
cochair of the 17th International Congress of
Photosynthesis Research in Maastricht.
Ivo van Stokkum, PhD, (1962) is associate profes-
sor of computational biophysics in the Department
of Physics and Astronomy, Faculty of Science, at the
Vrije Universiteit, Amsterdam. He earned his mas-
ter’s degree in experimental physics and his PhD
in natural sciences from the Radboud University
Nijmegen. He has coauthored 270 scientific pub-
lications, which have attracted more than 14K
citations.
ix
Contributors

Noam Adir Claudia Büchel

Schulich Faculty of Chemistry Institute of Molecular Biosciences
The Technion Goethe University Frankfurt
Haifa, Israel Frankfurt, Germany

Pascal van Alphen Min Chen

Molecular Microbial Physiology Group
Swammerdam Institute for Life Sciences
University of Amsterdam
Amsterdam, the Netherlands
Herbert van Amerongen
Laboratory of Biophysics
Wageningen University
Wageningen, the Netherlands
Jessica M. Anna
Department of Chemistry
University of Pennsylvania
Philadelphia, Pennsylvania
Leeat Bar-Eyal
Department of Plant and Environmental
Sciences
The Hebrew University of Jerusalem
Jerusalem, Israel
Roberto Bassi
Department of Biotechnology
University of Verona
Verona, Italy
Robert E. Blankenship
Departments of Biology and Chemistry
Washington University in St. Louis
St. Louis, Missouri
Egbert J. Boekema
Groningen Biomolecular Sciences and
Biotechnology Institute
University of Groningen
Groningen, the Netherlands
School of Life and Environmental Sciences (A12)
University of Sydney
Sydney, New South Wales, Australia
Jevgenij Chmeliov
Faculty of Physics
Department of Theoretical Physics
Vilnius University
and
Department of Molecular Compound Physics
Center for Physical Sciences and Technology
Vilnius, Lithuania
Roberta Croce
Department of Physics and Astronomy
Vrije Universiteit
Amsterdam, the Netherlands
Carles Curutchet
Department of Pharmacy and Pharmaceutical
Technology and Physical Chemistry
and
Institute of Biomedicine
University of Barcelona
Barcelona, Spain
Jacob C. Dean
Department of Physical Science
Southern Utah University
Cedar City, Utah
Gregory S. Engel
Department of Chemistry
University of Chicago
Chicago, Illinois

xi
xii Contributors
David A. Farmer
Department of Molecular Biology and
Biotechnology
University of Sheffield
Sheffield, United Kingdom
Harry A. Frank
Department of Chemistry
University of Connecticut
Storrs, Connecticut
Arvi Freiberg
Institute of Physics
and
Institute of Molecular and Cell Biology
University of Tartu
Tartu, Estonia
Győző Garab
Institute of Plant Biology
Biological Research Centre
Hungarian Academy of Sciences
Szeged, Hungary
Rienk van Grondelle
Department of Biophysics
Vrije Universiteit
Amsterdam, the Netherlands
Devens Gust
School of Molecular Sciences
Arizona State University
Tempe, Arizona
Jeremy Harbinson
Department of Plant Sciences
Wageningen University
Wageningen, the Netherlands
Klaas J. Hellingwerf
Molecular Microbial Physiology Group
Swammerdam Institute for Life Sciences
University of Amsterdam
Amsterdam, the Netherlands
Andrew Hitchcock
Department of Molecular Biology and
Biotechnology
University of Sheffield
Sheffield, United Kingdom
Susana F. Huelga
Institute of Theoretical Physics
Ulm University
Ulm, Germany
C. Neil Hunter
Department of Molecular Biology and
Biotechnology
University of Sheffield
Sheffield, United Kingdom
Michael R. Jones
School of Biochemistry
University of Bristol
Bristol, United Kingdom
Nir Keren
Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Jerusalem, Israel
Diana Kirilovsky
Institute for Integrative
Biology of the Cell (I2BC)
Université Paris-Saclay
Saclay, France
Gerdenis Kodis
School of Molecular Sciences
Arizona State University
Tempe, Arizona
Manuel J. Llansola-Portoles
Institute for Integrative Biology of the Cell
Université Paris-Saclay
Gif-sur-Yvette cedex, France
Tomáš Mančal
Faculty of Mathematics and Physics
Charles University
Prague, Czech Republic
Benedetta Mennucci
Department of Chemistry
University of Pisa
Pisa, Italy
Ana L. Moore
School of Molecular Sciences
Arizona State University
Tempe, Arizona
Thomas A. Moore
School of Molecular Sciences
Arizona State University
Tempe, Arizona
David J. Mothersole
Department of Molecular Biology and
Biotechnology
University of Sheffield
Sheffield, United Kingdom
 Contributors xiii

Lauren Nicol Bruno Robert

Department of Physics and Astronomy Institute of Integrative Biology of the Cell
Vrije Universiteit University Paris South
Amsterdam, the Netherlands Atomic Energy Commission
Saclay, France
Vladimir I. Novoderezhkin
A. N. Belozersky Institute of Physico-Chemical Gregory D. Scholes
Biology Department of Chemistry
Moscow State University Princeton University
Moscow, Russia Princeton, New Jersey
Dmitry A. Semchonok
Yossi Paltiel
Groningen Biomolecular Sciences and
Department of Applied Physics
Biotechnology Institute
The Hebrew University of Jerusalem
University of Groningen
Jerusalem, Israel
Groningen, the Netherlands
Alberta Pinnola Anat Shperberg-Avni
Department of Biotechnology Department of Biochemistry
University of Verona Weizmann Institute of Science
Verona, Italy Rehovot, Israel
Martin B. Plenio Ivo van Stokkum
Institute of Theoretical Physics Department of Physics and Astronomy
Ulm University Vrije Universiteit
Ulm, Germany Amsterdam, the Netherlands
Tomáš Polívka Villy Sundström
Faculty of Science Division of Chemical Physics
University of South Bohemia Lund University
České Budějovice, Czech Republic Lund, Sweden
Jakub Pšenčík Leonas Valkunas
Faculty of Mathematics and Physics Faculty of Physics
Charles University Department of Theoretical Physics
Prague, Czech Republic Vilnius University
and
Tönu Pullerits
Department of Molecular Compound Physics
Division of Chemical Physics
Center for Physical Sciences and Technology
Lund University
Vilnius University
Lund, Sweden
Vilnius, Lithuania
Fabrice Rappaport (deceased) Katherine WongCarter
Institut de Biologie Physico-Chimique School of Molecular Sciences
University Pierre and Marie CURIE Arizona State University
Paris, France Tempe, Arizona
Thomas Renger Donatas Zigmantas
Institut für Theoretische Physik Division of Chemical Physics
Johannes Kepler Universität Linz Lund University
Linz, Austria Lund, Sweden
 Part     1
Building the Light-Harvesting
Apparatus: Pigments

1 Pigments: General properties and biosynthesis 3

Min Chen and Robert E. Blankenship
2 Chlorophylls in a protein environment: How to calculate their spectral and redox properties
(from MO to DFT) 21
Carles Curutchet and Benedetta Mennucci
3 Carotenoids: Electronic states and biological functions 37
Harry A. Frank and Bruno Robert

Pigments: General properties
and biosynthesis
MIN CHEN AND ROBERT E. BLANKENSHIP
1.1 Pigments overview
1.2 Chlorophylls and bacteriochlorophylls
1.2.1 Chemical structure and
distribution
1.2.2 Chlorophyll biosynthesis
1.2.2.1 Formation of
protoporphyrin IX
1.2.2.2 Formation of
protochlorophyllide a
1.1 PIGMENTS OVERVIEW
For the energy of sunlight to be converted and
stored into biological systems, it must first be cap-
tured by the pigments present in the organisms.
There are three major classes of pigments involved
in photosynthesis: (bacterio)chlorophylls, carot-
enoids, and phycobilins. Each pigment interacts
with light to absorb only a narrow range of the
spectrum and reflects only certain wavelengths of
light so as to produce their distinctive colors (Figure
1.1). The photosynthetic organisms broaden their
light absorption region and increase their optical
cross section by combining these various pigments,
which have different maximum absorption peaks.
Such a “rainbow” array of pigments permits pho-
tosynthetic organisms to capture maximally most
of the available light; thus there is the opportunity
for competitive advantage in any particular habitat
by developing the most effective combination of
pigments.
1
3 1.2.2.3Chlorophyll a
6 biosynthesis 10
1.2.2.4 Bacteriochlorophyll a
6 biosynthesis 13
9 1.2.2.5 Chlorophyll modification 13
1.3 Anabolic pathway for phycobilins
9 in phototrophs 14
1.4 Carotenoid biosynthesis 15
10 References 17
Chlorophylls are greenish molecules because
they absorb mainly in the blue or near-UV region
and red or near-infrared spectral region and leave
a considerable gap in the green wavelength region.
Carotenoids have their reddish, orange, or yellow
colors due to their major absorption in the blue
spectral region of 420–570 nm. Phycobilins are a
group of molecules that absorb the light in the wave-
length region of 500–650 nm, reflecting the blue and
red photons and producing their blue or pink colors.
Chlorophylls are found in all oxygenic photosyn-
thetic organisms, including plants, algae, and cyano-
bacteria, while bacteriochlorophylls occur in certain
phototrophic bacteria. All chlorophylls have their
common structural elements: a stable ring-shaped
molecule with a magnesium atom in the center
and an attached long carbon–­hydrogen side chain
(phytyl chain) (Figure 1.2). The electrons are free to
migrate around the system of alternating single and
double bonds (conjugated double bonds) in a chlo-
rophyll macrocycle that provides the potential to
3
4 Pigments: General properties and biosynthesis
Chl b
Zea
Absorbance (a.u.)
370 450 550
Wavelength (nm)
Figure 1.1 Absorption spectra of isolated pigments in 100% methanol (except isolated phycocyanin,
which is recorded in 50 mM phosphate buffer, pH = 7.0). Chl, chlorophyll; PC, isolated phycocyanin; Zea,
zeaxanthin.
gain or lose electrons easily. This plays a fundamen-
tal role for chlorophyll capturing the energy of light.
There are five naturally occurring forms of chloro-
phylls: chlorophylls a, b, c, d, and f. Chlorophyll a
(Chl a) is the most widespread pigment in nature
(Björn et al. 2009). It is the only chlorophyll that is
the primary electron donor in reaction centers of
oxygen-evolving phototrophs, with the notable
exception of the newly discovered prokaryotic
oxygenic photosynthetic organism: Acaryochloris
marina, where Chl d acts as the special pair P740
in photosystem I and almost entirely substitutes for
Chl a (Hu et al. 1998).
There are six naturally occurring types of bac-
teriochlorophylls (BChl), all of which are found
in the anoxygenic (non-oxygen-evolving) photo-
trophic bacteria: bacteriochlorophylls a, b, c, d, e,
and g (Figure 1.3). The minor structural modifica-
tions on the periphery of the macrocycles of chloro-
phyll change the electron migration profile around
the macrocycle structure and generate the different
absorption features of chlorophylls (Blankenship
2014; Chen and Blankenship 2011).
Carotenoids are an important group of pig-
ments in photosynthetic organisms. They func-
tion as accessory light-harvesting pigments to
capture the energy of light in the blue-green light
spectral region, where (bacterio)chlorophylls do
not absorb efficiently. The absorbed energy then is
transferred to the (bacterio)chlorophyll. Another
important function of carotenoids is photoprotec-
tion. They protect the organisms from photodam-
age by quenching both singlet or triplet states of
Chl d
BChl a
Chl a
Chl f
PC
650 750 850
(bacterio)chlorophylls under strong illumination
(see Chapter 3). In chloroplasts, carotenoids also
function as photosynthetic membrane stabilizers
(Hayaux 1998). There are many hundreds of chemi-
cally distinct carotenoids, but they can be classified
into two broad groups: xanthophylls and carotenes
(Figure 1.4). Xanthophylls are carotenoids contain-
ing oxygen, such as zeaxanthin in cyanobacteria and
plants, fucoxanthin in algae, and lutein in higher
plants. Carotenes are oxygen-free carotenoids,
which typically only contain carbon and hydrogen
such as α-carotene and β-carotene (Figure 1.4).
The most common backbone of carotenoid chains
contains 40 carbons with 10–13 conjugated double
bonds, which allows electrons to move freely across
this area of the molecule.
There are a large number of various xantho-
phylls based on their oxygen-containing func-
tional groups: carbonyl, epoxy, formyl, hydroxyl,
methoxyl, or oxo groups. In green plants, the com-
position of carotenoids in chloroplasts is remark-
ably similar, and most chloroplast carotenoids are
bound together with chlorophylls located in the
photosynthetic membranes (thylakoid membranes)
(Demming-Adams and Adams 1996; Ruiz-Sola and
Rodriguez-Concepcion 2012). Both chlorophylls
and carotenoids are commonly lipophilic due to the
presence of long unsaturated aliphatic hydrocar-
bon chains, located in membrane-bound protein
complexes. Xanthophylls are involved in the xan-
thophyll cycle in algae and higher plants, but there
may be other uncharacterized roles for carotenoids
(Chapter 3).
 R7
Porphyrin macrocycle
R7 R8
3 5 7
2 4 6 Chl c1
A B 8 R8 CH3 CH2–CH3
1 9
N N Chl c2 CH3 CH=CH2
20 Mg 10 Chl c3 COOCH3 CH=CH2
Y R3 R7 X 11
19
N N
D C 12
18
3 5 7 16 14
17 15 13
R2 2 4 6 8 R8
A B E
1 9
H 132 131
N N
10 O
20 Mg COOCH3
COOH
11 Chlorin macrocycle
N N
19
D C 12
R2 R3 R7 R8
18
H 16 14 Chl a CH3 CH=CH2 CH3 CH2–CH3
15 13
17
E Chl b CH3 CH=CH2 CHO CH2–CH3
H 132 131
Chl d CH3 CHO CH3 CH2–CH3
H3COOC Chl f CHO CH=CH2 CH3 CH2–CH3
O 8-vinyl
H CH3 CH=CH2 CH3 CH=CH2
O Chl a
8-vinyl CHO
O CH3 CH=CH2 CH=CH2
Chl b

Figure 1.2 Structures of chlorophylls. The numbering scheme is based on the current IUPAC standard system. The axis of x and y indicate the direction
of Qx and Qy electronic transitions (see Chapter 2.). R# refers to ring substitutions at the corresponding carbon positions.
1.1 Pigments overview 5
6 Pigments: General properties and biosynthesis

O
BChl g BChl b/BChl g

N N
Mg
N N

BChl g
O
O
Farnesyl O O
O O
Phytyl

Bacteriochlorophyll (BChl) a

OH
R1

R2
N N
R4 Mg R1 R2 R3 R4 R5
BChl c Me Et, Pr, Bu Me, Et Me Stearyl, farnesyl, others
N N
BChl d Me Et, Pr, Bu, neoPent Me, Et H Farnesyl, others
R3 BChl e CHO Et, Pr, Bu, neoPent Et Me Farnesyl, others
BChl f CHO Et, Pr, Bu, neoPent Et H Farnesyl, others
O
O
O
R5
BChls c, d, e, f

Figure 1.3 Structures of BChl a and of BChls b and g represented by the subunit changes replacing the
respective BChl a substituents (as indicated). The structure of BChls c, d, e, and f represented with the R#
refers to ring substitutions at the corresponding carbon positions (as indicated).

Phycobilins are unique chromophores among 1.2 CHLOROPHYLLS AND

the photopigments in that a thioether bond cova-
lently links them to water-soluble proteins, phy-
cobiliproteins. They are open-chain tetrapyrroles
and are found in cyanobacteria as well as in some
eukaryotic algal protists: glaucocystophytes, rho-
dophytes, and cryptophytes, but not in green algae
and higher plants. The phycobiliproteins absorb in
the red, orange, yellow, and green light regions; the
wavelengths 500–650 nm are not well absorbed by
chlorophylls (Figure 1.1). The three main classes
of phycobiliproteins are allophycocyanin, phyco-
cyanin, and phycoerythrin (MacColl 1998). Both
phycobiliproteins and carotenoids function as
accessory light-harvesting components and pass
their absorbed light energy to chlorophyll for pho-
tosynthesis, but are not directly involved with pho-
tochemical reactions in the reaction center (see
Chapter 5).
BACTERIOCHLOROPHYLLS
1.2.1 Chemical structure and
distribution
Several types of chlorophylls, Chls a, b, c, d, and
f, serve in various oxygenic photosynthetic organ-
isms (Table 1.1). All chlorophylls except the
group of Chl c have a chlorin macrocycle and a
phytyl chain as shown in Figure 1.2. Chl c is the
common name for an increasing number of
Mg-pheoporphyrins, which are found mainly in
marine algal protists—in the chromophytes (with
the exception of eustigmatophytes) (Larkum and
Barrett 1983; Stauber and Jeffrey 1988). The mol-
ecule of Chl c has the fully unsaturated porphy-
rin macrocycle and does not carry a phytyl chain
(Zapata et al. 2006).
 1.2 Chlorophylls and bacteriochlorophylls 7

Absorbance (a.u.)
α-carotene (C40H56)

Zea
Fuco
α-Car
β-carotene (C40H56)
370 400 450 500 550
OH Wavelength (nm)

HO
Zeaxanthin (C40H56O2) HO
O

O
C
O
HO O
Fucoxanthin (C40H58O6)

Figure 1.4 Structures of several carotenoids present in photosynthetic systems. Inset shows absorp-
tion spectra of several carotenoids in 100% methanol. The conjugated double bonds are indicated. α-Car,
α-carotene; Fuco, fucoxanthin; Zea, zeaxanthin.

Table 1.1 Chlorophylls and phycobiliprotein functional distributions

Chlorophyll
a ba cb dc fd Phycobiliproteins
Cyanobacteria LHC complexes + + + + +
RC complexes + + ?
Algae LHC complexes + + + +
RC complexes +
Green plants LHC complexes + +
RC complexes +
a Chl b is only found in prochlorophytes, a group of cyanobacteria containing Chl b (or 8-vinyl Chl b).
b Chl c represents a number of chlorophylls having Mg-pheoporphyrins.
c Chl d is only found in Acaryochloris marina spp.
d Chl f was reported in some cyanobacteria, but its function in photosynthesis is undefined yet (see text).

It had generally been accepted that Chl a exists
in all known oxygenic photosynthetic organisms
discovered to date (Scheer 2006). It occurs in both
reaction center and all chlorophyll-bound light-
harvesting complexes (Table 1.1). The importance
of Chl a in the energy phase of oxygenic photo-
synthesis is made known as their special function
in the reaction centers involving charge separa-
tion and passing of electrons on to the transport
chain.
Chl b is the major accessory light-harvesting
pigment in green algae and plants (see Chapter 4),
and additionally, it has been found in the prochlo-
rophytes, cyanobacteria containing Chl a and Chl b.
8 Pigments: General properties and biosynthesis
Up to date, no Chl b has been found in the reaction
centers or the core antenna systems, such as CP43
and CP47 proteins in photosystem II (Chen and
Scheer 2013).
Chl d differs from Chl a only in the C3 position
at ring A, where a formyl group in Chl d replaces
the vinyl group in Chl a (Figure 1.2). Chl d was
first reported from a red algal pigment extract in
1943 (Manning and Strain 1943), and afterward
it was considered as an artificial by-product of
pigment extracts and not present in any organ-
isms (Scheer 1991). However, this belief changed
with the discovery of a cyanobacterium that con-
tains over 95% Chl d as its major pigment in 1996
(Miyashita et al. 1996). Chl d is the only known
chlorophyll to date that can replace the function
of Chl a as a special pair in the reaction center in
oxygenic photosynthetic systems (Hu et al. 1998;
Itoh et al. 2007; Tomo et al. 2007). Interestingly,
Chl d has been reported to occur widely around
the world since then, although all cyanobacte-
ria containing Chl d belong to one monophy-
logenetic clade, Acaryochloris marina, based on
16S rRNA classification (Kashiyama et al. 2008;
Kühl et al. 2005; Loughlin et al. 2013; Miller et al.
2005).
Chl f is the most red-shifted chlorophyll found
in oxygenic photosynthetic organisms to date
(Chen et al. 2010; Kräutler 2011). It differs from
Chl a only in the C2 position at ring A, where a
formyl group in Chl f replaces the methyl group
in Chl a (Figure 1.2) (Willows et al. 2013). It
co-occurs with Chl a and other pigments in the
cyanobacterium Halomicronima hongdechloris,
isolated from stromatolite colonies, and also in the
cyanobacterium CK1 collected from Biwa Lake, a
freshwater lake in Japan (Akutsu et al. 2011; Chen
et al. 2012). Several cyanobacteria containing
Chl f belong to two unrelated genera and have dif-
ferent morphological characteristics (Gan et al.
2015). H. hongdechloris is a marine filamentous
cyanobacterium having allophycocyanin and
allophycocyanin (Chen et al. 2012); in contrast,
cyanobacterium strain CK1 is a unicellular cyano-
bacterium containing phycocyanin, allophycocya-
nin, and phycoerythrin (Akutsu et al. 2011). The
function of Chl f is uncharacterized yet; however,
it is the first chlorophyll reported that is respon-
sive to the changes of light spectrum. Chl f has
been named as a red-light-induced chlorophyll
(Chen et al. 2012; Gan et al. 2014).
Two additional chlorophyll derivatives are
3,8-divinyl Chl a (also named 8-vinyl Chl a)
and 3,8-divinyl Chl b (also named 8-vinyl Chl b)
(Figure 1.2). They are the major chlorophylls found
in Prochlorococcus spp. and replace all functions of
Chl a and Chl b in oxygenic photosynthesis in these
organisms (Chisholm et al. 1992).
Pheophytins are a group of metal-free chloro-
phylls. Acidic conditions promote the displace-
ment of the metal (Mg2+) by two hydrogen ions.
For each single chlorophyll (Chls a, b, d, and f),
there is one corresponding pheophytin, which has
a green color as it has a similar absorption spec-
tral profile as their corresponding chlorophyll.
Pheophytins are often regarded as primarily deg-
radation products of chlorophylls from the loss of
the central metal, Mg. However, the role of pheo-
phytin a in photosystem II is an essential early
electron acceptor in the sequence of electron car-
riers. A. marina, the Chl d–containing cyanobac-
terium, uses pheophytin a instead of pheophytin
d as primary electron acceptor in photosystem II,
although the percentage of Chl a is less than 5% of
total chlorophyll (Tomo et al. 2007). Nevertheless,
the biosynthetic pathway for making pheophytin a
is not yet defined in vivo.
BChl a is widely distributed in many types of
anoxygenic phototrophs. BChl b is found only in a
few species of purple phototrophic bacteria, where
it substitutes for BChl a. BChls c, d, and e are found
in the green sulfur bacteria (GSB), where they are
localized in chlorosome antenna complexes. In
most cases, only one of these “chlorobium chloro-
phylls” is found in a given organism, depending on
the light environment where the cells live. BChl f
is not known from any naturally occurring organ-
ism, but has been produced in mutants of GSB. All
GSB also contain BChl a, which is located in the
chlorosome baseplate, the Fenna–Matthews–Olson
(FMO) protein, and the reaction center. The fila-
mentous anoxygenic phototrophs, formerly called
the green nonsulfur bacteria, contain BChl a, and
some species, such as the widely studied organism
Chloroflexus aurantiacus, also contain BChl c local-
ized in chlorosomes. BChl g is found only in the
Gram-positive heliobacteria, where it is almost the
only chlorophyll pigment found. Small quantities of
a derivative of Chl a are found in the reaction cen-
ters of both the heliobacteria and the green sulfur
bacteria, where it is proposed to function as an early
electron acceptor.
 1.2 Chlorophylls and bacteriochlorophylls 9

1.2.2 Chlorophyll biosynthesis is one of a very small number of reactions known

1.2.2.1 FORMATION OF
PROTOPORPHYRIN IX
Chlorophyll biosynthesis contains multiple enzy-
matic steps, which begin with the formation of
δ-aminolevulinic acid (δ-ALA), the first com-
mon precursor in the biosynthesis of all tetrapyr-
roles including chlorophyll, heme, and phycobilins
(Chen 2014). There are two different biosynthetic
pathways of ALA: one is related to heme biosyn-
thesis in mitochondria and another is related to
the pigment biosynthesis in chloroplasts. In the
chloroplasts of plants, ALA is synthesized from
glutamic acid (Glu) via a two-step reaction: the
reduction of Glu to glutamate 1-semialdehyde and
the aminomutation of glutamate 1-semialdehyde
to form ALA (Figure 1.5). The formation of ALA
in biology in which a tRNA molecule is used in a
molecular synthesis other than peptide synthesis.
On the other hand, a completely different route
for making ALA is defined in mitochondria of all
eukaryotic cells, which is a one-step condensation
from glycine and succinyl-CoA catalyzed by ALA
synthase. Interestingly, the reaction is also found in
some purple photosynthetic bacteria (Zappa and
Bauer 2010) and chloroplasts of Chromera velia for
chlorophyll biosynthesis (Kořený et al. 2011).
Then eight molecules of ALA form an open-
chain tetrapyrrole hydroxymethylbilane via por-
phobilinogen (PBG) synthesis. The next four
steps, including ring closure, oxidative decarbox-
ylations, and the oxidation of protoporphyrinogen
IX, lead to the formation of the symmetric metal-
free porphyrin, protoporphyrin IX (Figure 1.5).

tRNAGlu tRNAGlu
HO HO
O Ligase 1 O
2
H2N Reductase H2N
O O
COOH
H
HO
O
NADPH NADP
CO
3 COOH
Glutamic acid O
(Glu) NH2 N
H2N H
δ-ALA
HO
NH2 O CO2
O
OH
+ Porphobilinogen
O CoA-SH
(PBG)
O SCoA

Glycine Succinyl-CoA
4
(Gly)
COOH

O H
CH2 CH3 CO
Heme

H
COO
CO

H3C
N
OH

NH N CH2 8 7 6 5 H
N

HO
H

HN
H
H

N
N
N
ChlorophyII

H
H3C CH3 O
CO COOH
CO
COO

O
COOH COOH
H
H

Protoporphyrin IX Hydroxymethylbilane

Figure 1.5 Outlined pathway of protoporphyrin IX biosynthesis from Glu. The enzymes that catalyze the
individual reactions are (1) glutamyl-tRNA ligase and glutamyl-tRNA reductase, (2) glutamate 1-semial-
dehyde aminotransferase, (3) PBG synthase, (4) hydroxymethylbilane synthase, (5) uroporphyrinogen III
synthase (ring closure), (6) uroporphyrinogen III decarboxylase, (7) coproporphyrinogen III oxidative decar-
boxylase, and (8) protoporphyrinogen IX oxidase. Two pathways of δ-ALA biosynthesis are highlighted.
10 Pigments: General properties and biosynthesis
Protoporphyrin IX is the first photosensitive col-
ored intermediate and the last common precursor
for chlorophyll and heme biosynthesis (Figure 1.5).
Free protoporphyrin IX molecules can absorb pho-
tons; therefore, the concentration of free proto-
porphyrin and other photosensitive intermediates
after this step is tightly regulated in vivo to avoid
photodamage.
1.2.2.2 FORMATION OF
PROTOCHLOROPHYLLIDE a
Inserting the magnesium into protoporphyrin IX
and the formation of Mg-protoporphyrin IX is cata-
lyzed by Mg-chelatase, a three-component enzyme
(Figure 1.6). The three subunits, ChlD, ChlH, and
ChlI, are conserved from cyanobacteria to higher
plants and are commonly referred to as BchI,
BchD, and BchH in bacteriochlorophyll biosynthe-
sis (Chew and Bryant 2007). ChlH is the porphy-
rin and Mg2+ the binding subunit of Mg-chelatase
(Willows et al. 1996). ChlI and ChlD require ATP
and Mg2+ for the interaction of I-D complex forma-
tion (Jensen et al. 1999). The ChlI:ChlD oligomer
subsequently interacts with the ChlH subunit and
drives the ATP-dependent insertion of Mg2+ into
protoporphyrin IX (Masuda 2008; Mochizuki et al.
2010). The insertion of magnesium needs a sig-
nificant amount of energy, at least the hydrolysis of
~15 ATP (Reid and Hunter 2004). The synthesis of
Mg-protoporphyrin IX is the first unique step in the
biosynthesis of chlorophyll (step 9 in Figure 1.6).
Therefore, Mg-chelatase plays an important role in
channeling protoporphyrin IX into the chlorophyll
branch in response to conditions suitable for pho-
tosynthetic growth, competitively separating the
intermediates from the heme biosynthetic branch.
The Mg insertion can be described as follows:
ATP + protoporphyrin IX + Mg 2 + + H2O ® ADP
+ phosphate + Mg-protoporphyrin IX + 2 H +
in which the four substrates are ATP, protoporphy-
rin IX, Mg2+, and water. This reaction is catalyzed
by Mg-chelatase.
Mg chelation is tightly coupled to the next
step, the methyltransferase reaction for the trans-
fer of a methyl group to the 13-propionate side
chain of Mg-protoporphyrin IX and produces
Mg-protoporphyrin IX monomethyl ester (step 10
in Figure 1.6). The next step of the biosynthesis
is the oxidative cyclization of isocyclic ring E and
generates the intermediate, divinyl protochloro-
phyllide. The formation of the fifth ring (ring E)
structure represents the distinctive macrocycle
feature of chlorophylls from all other tetrapyrroles
(step 11 in Figure 1.6). This cyclization includes a
complex of reactions that proceeds by first esterify-
ing the carboxylic acid moiety and then undertakes
a stereospecific oxidative cyclase reaction. There
are two unrelated cyclization mechanisms based on
the origin of the oxygen atom, the aerobic cyclase
and the anaerobic cyclase (Ouchane et al. 2004;
Raymond and Blankenship 2004). Most oxygenic
photosynthetic organisms use aerobic cyclases car-
rying out the Mg-protoporphyrin IX monomethyl
ester oxidative cyclic reaction in an oxygen-depen-
dent manner. The anaerobic cyclase is a radical
SAM enzyme and is widely distributed in anaerobic
anoxygenic photosynthetic organisms such as green
sulfur bacteria. However, the multistep formation
of the fifth ring suggests that the reactions are cata-
lyzed by a multisubunit enzymatic complex, which
is still uncharacterized (Hollingshead et al. 2012).
The formation of the fifth ring is a decisive
step for chlorophyll biosynthesis. The coexist-
ing oxygen-dependent and oxygen-independent
Mg-protoporphyrin IX methyl ester cyclases
could represent the evolutionary transition from
the anaerobic to the aerobic metabolic reaction
(Raymond and Blankenship 2004), or an adaptation
strategy for the regulation of reactions under con-
tinuously changed microenvironmental conditions.
Accumulation of molecular oxygen in the atmo-
sphere fundamentally changed the redox balance on
Earth, permitted the development of aerobic metab-
olism, and led to development of advanced life
forms (Samuilov 2005). By increasing the oxygen
concentration in the atmosphere, ancient life forms,
living in anaerobic or very limited accessible oxygen
concentrations, had to adapt and evolve new strat-
egies to deal with the increased oxygen concentra-
tion, including reactive oxygen species generated by
excited porphyrin molecules in the cells. Nowadays,
oxygen is directly involved in chlorophyll biosyn-
thesis (Hohmann-Marriott and Blankenship 2011).
It also has a close relationship with photoregulation
of these processes (Kopp et al. 2005).
1.2.2.3 CHLOROPHYLL a BIOSYNTHESIS
From divinyl protochlorophyllide, two similar,
yet separate, reactions on ring B and ring D are
 CH2 CH3

CH2 CH2 CH3 H3C

CH3 N N CH2
O2 Mg
H3C H3C 11 N N
9 N N CH2 10 N N CH2
CH3
Mg Mg H3C
N N N N
O
CH3 CH3 COOCH3
2+ H3C H3C COOH
ATP Mg
ADP 8-vinyl-
COOH COOH COOH COOCH3 13

Protoporphyrin IX
3,8-divinyl- 3,8-divinyl- 12

CH2 CH2 CH3

CH3
13 13
H3C H 3C
N N CH3 N N CH2
CH3 CH3 Mg
Mg
N N H N N
N CH3 CH3
N CH3 H3C CH3 H3C
Mg Mg H
O O
COOCH3 COOCH3
COOH COOH
Monovinyl- Monovinyl- Protochlorophyllide a 8-vinyl chlorophyllide a
Mg protoporphyrin IX Mg protoporphyrin IX
monomethyl ester 14
12

CH2 CH3
CH2 CH3
Chlorophyll d Chlorophyll b H3C R8
H3C N N
O O N N CH3
Mg
Mg N
N 14 H N
O 3 7 H N
2
CH3
Chlorophyll f H 3C CH3 H3C
N N CH2 O2 H H
O
Mg O COOCH3
COOCH3 O O
COOH

Chlorophyllide a
Formyl substitution
Chlorpphyll a (R8 = CH2CH3)
8-vinyl chlorophyll a (R8 = CHCH2)

Figure 1.6 Outlined pathway of chlorophyll biosynthesis from protoporphyrin IX. The enzymes that catalyze the individual reactions are (9) protoporphyrin
IX Mg-chelatase, (10) S-adenosyl-L-methionine:Mg-protoporphyrin IX methyltransferase, (11) Mg-protoporphyrin IX monomethyl ester oxidative cyclase
(oxygen dependent or oxygen independent), (12) light-dependent NADPH:protochlorophyllide oxidoreductase or light-independent protochlorophyllide
oxidoreductase, (13) 8-vinyl reductase, and (14) chlorophyll synthase. The arrows with dashed line relate the possible broad substrate specificity of 8-vinyl
1.2 Chlorophylls and bacteriochlorophylls 11

reductase. The triangle (with O2) indicates the modification of Chls b, d, and f from either chlorophyll a or chlorophyllide a.
12 Pigments: General properties and biosynthesis
catalyzed by two enzymes, 8-vinyl reductase and
protochlorophyllide oxidoreductase, respectively
(steps 12 and 13 in Figure 1.6). Both enzymes are
not sensitive to whether the other changes made
at the opposite side of the macrocycle, that is, the
8-vinyl reductase, have taken place, so that either
the reaction catalyzed by protochlorophyllide oxi-
doreductase or vice versa can take place (Figure 1.6).
The 8-vinyl reductase step is the earliest step in
chlorophyll biosynthesis that is responsible for the
chemical diversity in this class of molecules. Marine
Prochlorococcus spp. are exceptional because they
lack the reductase for the 8-vinyl group (Nagata
et al. 2005) and thus produce divinyl Chl a and
divinyl Chl b (Chisholm et al. 1992). In higher
plants and cyanobacteria, divinyl chlorophylls were
observed in divinyl reductase (dvr) mutants. Those
mutants grow photosynthetically under moderate
and low-light conditions with reduced efficiency
of energy transfer between light-harvesting com-
ponents and reaction centers, but died within a
day after being transferred to high-light conditions
(Islam et al. 2008). One possible explanation is that
the 8-vinyl group causes a higher degradation rate
of chlorophyll-binding protein complexes than
the recycle rate of the complexes, leading to pho-
todamage under high-light conditions. This may
be the reason for the common presence of 8-ethyl
chlorophylls in photosynthetic organisms instead
of 8-vinyl chlorophylls. However, the 8-vinyl chlo-
rophylls in Prochlorococcus provide an advantage
by absorbing wavelengths of light unused by other
marine oxygenic phototrophs. The modified photo-
synthetic protein sequences are reported, and such
distinct site modification plays an important role
in increasing the stability of 8-vinyl chlorophyll-
binding protein complexes (Ito and Tanaka 2011).
Two types of 8-vinyl reductase are identified: one
uses NADPH as reductant and another requires
FAD and iron for activity. The potential application
of unrelated enzymes to catalyze a single reaction
is common in chlorophyll biosynthetic reactions,
such as Mg-protoporphyrin IX methyl ester cycliza-
tion, or 8-vinyl reductase and protochlorophyllide
reductase (Chen et al. 2016). The strategy for using
unrelated enzymes to catalyze the same reaction
provides the photosynthetic organisms with the
capability to grow under particular environments.
In higher plants, one 8-vinyl reductase is responsi-
ble for the multibranched chlorophyll biosynthesis
due to the broad substrate specificity of the enzyme
(step 13 in Figure 1.6), although with significant
differences in the efficiency of enzyme reactions
(Wang et al. 2013).
The reduction of the carbon–carbon double
bond between C17 and C18 in ring D is the step
converting porphyrin-type macrocycle to chlorin-
type macrocycle (step 12 in Figure 1.6). Chlorin-
type macrocycle is the central structure for Chls a,
b, d, and f, and porphyrin-type macrocycle forms
the group of Chl cs. The reduction of the double
band between C17 and C18 is involved directly
with regulating plant development and the assem-
bly of the photosynthetic apparatus. There are two
unrelated enzymes that catalyze this reaction, the
light-dependent protochlorophyllide oxidoreduc-
tase (LPOR) and the light-independent protochlo-
rophyllide oxidoreductase (Tanaka and Tanaka
2007). The LPOR has an unconditional require-
ment for light to catalyze a hydride transfer reac-
tion from NADPH to protochlorophyllide (Heyes
et al. 2003). Upon illumination, light energy is cap-
tured into LPOR–enzyme complexes by protochlo-
rophyllide, and a photochemical reaction occurs
to yield chlorophyllide a (Gabruk and Mysliwa-
Kurdziel 2015). This enzyme can be found in
cyanobacteria, and all eukaryotic oxygenic pho-
tosynthetic organisms and some photosynthetic
organisms contain more than one isoforms of
LPOR. Importantly, LPOR catalytic site residues
are highly conserved and essential for the catalytic
function (Reinbothe et al. 2006).
Light-independent protochlorophyllide oxidore-
ductase is composed of three subunits, ChlL, ChlB,
and ChlN, and uses ferredoxin as reductant instead
of NADPH. It is ubiquitously distributed among
prokaryotic phototrophs, including oxygenic pho-
tosynthetic prokaryotic organisms (cyanobacteria)
and anoxygenic photosynthetic prokaryotic organ-
isms (such as purple bacteria and green sulfur bac-
teria). However, it is not so universally distributed
in eukaryotic photosynthetic organisms. It is only
reported in some lineages of eukaryotic photosyn-
thetic organisms: green algae (Choquet et al. 1992;
Shi and Shi 2006), mosses (Kohchi et al. 1988),
glaucophytes (Stirewalt et al. 1995), and red algae
(Reith and Munholland 1995). Interestingly, cyano-
bacteria and green algae such as Chlamydomonas
reinhardtii have both LPOR and light-independent
protochlorophyllide oxidoreductase, making them

model organisms for the study of the relationship
between light-dependent and light-independent
protochlorophyllide oxidoreductases.
The final step of chlorophyll a biosynthesis is
the attachment of the phytol chain, catalyzed by
“chlorophyll synthase.” The phytol serves to make
the pigment more hydrophobic and facilitates its
binding to proteins, especially integral membrane
proteins such as reaction centers and many antenna
complexes. The reaction can be summarized as
follows:
chlorophyllide a + phytol diphosphate chlorophyll a
+ diphosphate
Chlorophyll synthase is an enzyme belong-
ing to the family of transferases, specifically those
transferring aryl or alkyl groups other than methyl
groups.
1.2.2.4 BACTERIOCHLOROPHYLL a
BIOSYNTHESIS
The biosynthesis of BChl a is generally similar to
that of chlorophyll a in the early steps but diverges
in the later steps (Chew and Bryant 2007). The
major differences are that pyrrole ring B is reduced
by an enzyme complex related to the light-indepen-
dent protochlorophyllide oxidoreductase discussed
above and that the C3 vinyl group is converted to an
acetyl by two enzymes called BchF and BchC.
1.2.2.5 CHLOROPHYLL MODIFICATION
All chlorophylls have very similar structures. The
differences among them come at the end of the bio-
synthetic pathways (Figure 1.6). In general, Chlide a
(or Chl a) represents the precursor of all other types
of chlorophylls, Chl b, Chl d, and Chl f (113–115);
however, the biosynthetic pathway leading to Chl
c is unknown. Interestingly, Chl b, Chl d, and Chl
f contain a formyl functional group at the C7, C3,
or C2 positions, respectively, which determines
their different spectral properties from Chl a. The
formyl group contains a planar carbon that is con-
nected by a double bond to oxygen (C═O) and a
single bond to hydrogen (C–H), which is attributed
to the electron-withdrawing quality of the electron-
withdrawing formyl group and the more polar fea-
ture. The formyl group modification means that a
conjugated carbonyl group (C═O) is introduced
1.2 Chlorophylls and bacteriochlorophylls 13
at the peripheral sites of the macrocycle. The for-
myl group substitution in Chl d and Chl f at the
ring A, along the y-axis, leads to a red-shifted QY
absorbance, while the formyl group modification
in Chl b at the ring B, along the x-axis, leads to a
blue-shifted absorbance (Figure 1.2). All these fine-
tuned absorption shifts are the results of changing
π-electrons of the macrocycle by the orbital overlap
of the C═O groups (see Chapter 2).
Chl b is made from Chl a or chlorophyllide a
by oxidation of the methyl group in C7 to a for-
myl group. This reaction is catalyzed by the chlo-
rophyll a oxygenase (CAO) (Espineda et al. 1999;
Tanaka et al. 1998). The CAO enzyme is a Rieske-
containing, nonheme–iron monooxygenase that
uses molecular O2 and NADPH to perform two suc-
cessive hydroxylations at the C71 position of Chlide
a (Qster et al. 2000). Chl b can be reduced back to
Chl a through a chlorophyll cycle, so the relative
amounts of the two pigments are subject to regula-
tion (Rüdiger 2006; Tanaka and Tanaka 2011). The
ratio of Chl a and Chl b regulated by the chlorophyll
cycle interacts directly with the assembly of light-
harvesting complexes in response to changing light
environments. The mutual conversion between Chl a
and Chl b may provide higher plants with the ability
to optimize their adaptation to varying light condi-
tions (see Chapter 4) and may also be important for
chlorophyll degradation as needed.
Chl f biosynthesis has recently been proposed
to be carried out by a divergent version of the D1
protein of photosystem II (Ho et al. 2016). Chl d
biosynthesis must have a different mechanism
from that of Chl b and Chl f, because it requires the
transformation of a vinyl group to a formyl group.
Small amounts of Chl d were detected from some
cyanobacteria as the results of far-red light photo-
acclimation (Gan et al. 2014, 2015). Chl d synthase
is proposed as a P-450-type enzyme due to the fact
that Chl d biosynthesis is inhibited by bubbling
CO-enriched air, and this reaction can be reversed
by O2-enriched air (Chen et al., unpublished data).
Our current knowledge of the formyl substitutions
in Chls b, d, and f is very limited, but one fact is
common for the formyl formations in chlorophyll
modification: molecular oxygen is required (Porra
and Scheer 2000; Schliep et al. 2010). However, the
oxygen level seems not to be a limiting element for
the biosynthesis of Chls b, d, and f, because photo-
synthesis continuously provides it.
14 Pigments: General properties and biosynthesis

1.3 ANABOLIC PATHWAY organisms starts with the cleavage of heme by heme

FOR PHYCOBILINS IN
PHOTOTROPHS
Bilins are a common name for open-chain tetra-
pyrrole pigments. They are widely distributed in all
kingdoms and have several distinct functions. In
heterotrophic organisms, bilins can be considered as
catabolic products mainly related to iron acquisition
from heme. However, in phototrophs, the biosyn-
thesis of bilins (phycobilins) is considered as an ana-
bolic process because of their function as cofactors
of light-harvesting protein complexes or light-sens-
ing phytochromes (Dammeyer and Frankenberg-
Dinkel 2008). Here we will only focus on the
biosynthetic pathway of phycobilins, photosensitive
linear tetrapyrroles, which act as chromophores in
light-harvesting complexes (Chapter 5). The phy-
cobilin pigment biosynthesis in photosynthetic
oxygenase that produces biliverdin IXα (common
name: biliverdin) (Kikuchi et al. 2005). Biliverdin is
the first committed intermediate and is subsequently
reduced by ferredoxin-dependent bilin reductases
for the synthesis of the linear tetrapyrrole precursors
of their phycobiliprotein light-harvesting antenna
complexes (Figure 1.7). The differences in position
of the carbon–carbon double bond in phycocya-
nobilin (PC) and phycoerythrobilin (PE) result in
a shifted spectral absorbance: purple-red-colored
PE with its main absorbance peak at ~550 nm and
blue-colored PC with its main peak at ~640 nm
(Figure 1.7). As two major phycobiliprotein chro-
mophore precursors, the biosynthesis of PC and PE
requires different ferredoxin-dependent bilin reduc-
tases and several double-bond isomerases in order to
produce the specific double carbon-bond positions.
The phycocyanobilin:ferredoxin oxidoreductase

2 18

3 A D 17
3O2/7e– CO/Fe2+
–
OOC COO–
N N
5 FeII 15
N N
7
B C 13 2 3 7 8 12 13 17 18
A 5 B 10 C 15 D
8 10 12 Heme oxygenase (HO) O N N N N
O
H H H
COOH HOOC
Biliverdin IXα (BV)
Heme

b A
Pe
2e–
PcyA
4e–
– –
OOC COO
PebS
H
4e–
O N N N 16 N O
15 H
H H
15,16-dihydrobiliverdin
2e–
Pe
b B

–
OOC COO– 2
18
H 3C 1
18
H 18
–
O OOC COO–
O N N N N
H H H H3C
Phycocyanobilin H H
O N N N O
N
H H H

Phycoerythrobilin

Figure 1.7 Outlined biosynthetic pathway of phycobilins from heme in photosynthetic organisms. PcyA,
phycocyanin:ferredoxin oxidoreductase; PebA, 15,16-dihydrobiliverdin:ferredoxin oxidoreductase; PebB,
phycoerythrobilin:ferredoxin oxidoreductase; PebS, phycoerythrobilin synthase.
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 In the heart of Montreal’s Wall Street is the huge Church of Notre
Dame. It seats twelve thousand people, and in its tower is the largest
bell in America, weighing about twenty-nine thousand pounds. That
dome farther over marks the location of the Cathedral of St. James.
It is a replica, on a reduced scale, of St. Peter’s at Rome. It seats
several thousand worshippers; nevertheless, when I went there last
Sunday morning hundreds were standing, and within fifteen minutes
after one service was concluded it was again filled to capacity for the
next.
Downtown Montreal is built largely of limestone. It has a massive
look, but skyscrapers are barred by a city ordinance. Erection of
modern steel and concrete office buildings is now under way, and
they stand out conspicuously against the background of more old-
fashioned structures. Big as it is and important commercially,
Montreal seems a city without any Main Street. St. Catherine Street
has the largest retail stores and the “bright lights” of theatres and
cafés, but I have seen more impressive thoroughfares in much
smaller places at home. This is essentially a French city, though less
so than Quebec. The French do not naturally incline toward “big
business.” They seem content with small shops, which since the
days of their grandfathers have grown in numbers rather than in size.
They are by nature conservative, and though they make shrewd
business managers, they care little for innovations in either public or
private affairs.
I have visited the biggest market, the Bonsecours. It is quite as
French as those I have seen in southern France. This market takes
up a wide street running from the heart of Montreal down to the
wharves. The street is the overflow of the market proper, which fills a
church-like building covering an acre of ground. When I arrived the
open space was crowded with French farmers, who in the early
morning had driven their cars and light motor trucks loaded down
with fruits and vegetables into the city. Fully half of the wagons were
in charge of women, who looked much like those in the Halles
Central in Paris. As I pressed my way through the throng many of
them called out to me in French and some thrust their wares into my
face and urged me to buy.
 The mayor of Montreal is always a French Canadian, and he is
usually reëlected for several terms. I talked with His Honour and
found him a most pleasant gentleman. Discussing his city, he said:
 In the French market one feels he is indeed in a
foreign land, and among a people of alien tongue.
When he buys, however, he discovers that the
farmers understand perfectly when money does the
talking.
 Kipling did not endear himself to Montreal when
he called Canada “Our Lady of the Snows,” yet the
people are really proud of their facilities for winter
sports, which include a toboggan slide down Mt.
Royal.
 “Montreal is thriving as never before. Our population is rapidly
increasing and we expect soon to have more than a million. We have
taken in some of the suburbs, as your great cities have done, and
our increasing opportunities are constantly attracting new people.
“I believe we are one of the most cosmopolitan communities on
the continent,” continued the Mayor. “About seventy per cent. of us
are French, and a large part of the balance are English Canadians.
We have also Americans, Germans, Belgians, Italians, and Chinese,
besides large numbers of Irish and Scotch, and some of the peoples
of southeastern Europe. We are the Atlantic gate to Canada, so that
a large portion of our immigrants pass through here on their way
west. Many of them go no farther, as they find employment in our
varied industries.
“It costs us more than twenty million dollars a year to run
Montreal, but we feel that we can afford it. The value of our taxable
buildings amounts to nearly seven hundred and fifty millions, and is
increasing at the rate of fifteen millions a year. We have more than
one million acres of public parks, or in excess of an acre for every
man, woman, and child in the city.”
Montreal is one of the great sport centres of Canada. In the
warm months, the people play golf, baseball, football, and lacrosse.
The latter is a most exciting game, borrowed from the Indians, with
more thrills and rough play than our college football. It is a cross
between hockey and basketball. A light ball is tossed from player to
player by means of a little net on the end of a long curved stick, the
object of each side being to get the ball into the opponents’ goal. In
the game I saw, the players were often hit on the head and
shoulders, and before the afternoon was over there had been a good
deal of bloodshed from minor injuries. I was told, however, that this
match was exceptionally rough.
In the winter, hockey is the great game of Canada. Every large
city has its hockey rink, and, where there are many Scotch, curling
rinks as well. In curling, great round soapstones are slid across a
designated space on the ice toward the opponents, who stand guard
with brooms. By sweeping the ice in front of the approaching stone,
they try to veer it out of the course intended by the player who
started it toward their goal.
As far as the masses of the people are concerned, skiing,
snowshoeing, and coasting are the chief winter sports, and in them
nearly everybody takes part. In Montreal, toboggan slides are built
on the sides of Mount Royal, and its slopes are covered with young
men and women on snowshoes and skis.
Montreal used to build an ice palace every winter. Then the
business men feared the city was acquiring an antarctic reputation
that would discourage visitors. Consequently, organized exploitation
of winter sports fell off for a time, but this fall a fund of thirty thousand
dollars is being subscribed to finance them on a large scale.
 CHAPTER X
CANADA’S BIG BANKS

There are more than eight thousand national banks in the United
States, but Canada has only sixteen. While new ones are organized
in our country every month, the number in Canada tends constantly
to grow less, and to-day is not half what it was twenty years ago. The
banking system of the Dominion is patterned somewhat after the
Scotch, and was worked out largely by men of that shrewd, hard-
headed race. The people think it suits their conditions better than
any other. Certainly it is true that while Canada has had its ups and
downs, the people have suffered far less than we from bank failures
and panics.
One might think that with all the banking business of Canada
monopolized by only sixteen institutions, they might make fabulous
profits. However, such is not the case. I have before me the current
monthly statement which the government publishes regarding the
condition and operation of each bank. This shows that all are making
money, but their dividends range from six to sixteen per cent., and
the Bank of Nova Scotia is the only one that paid the highest rate.
Nine of the banks paid twelve per cent. on their capital stock last
year, while the shareholders of five got less than ten per cent.
In the United States a handful of business men can start a bank
on a few thousand dollars. Here it is not so easy a matter. Canadian
law requires a minimum capital of five hundred thousand dollars, half
of which must be paid in, before a bank can be chartered, and there
are other conditions to be met that make the establishment of a new
bank a big undertaking. The smallest bank in Canada, at Weyburn,
Saskatchewan, is the only one with a capital of less than one million
dollars, while the largest, the Bank of Montreal, has paid-up stock
amounting to twenty-seven and one quarter millions. The total
combined capital of all the banks is one hundred and twenty-three
millions.
The great banks extend their service throughout the Dominion by
means of branches. These now number nearly five thousand, and
new ones are being constantly added. The branch plan is the most
striking difference between Canada’s banking system and ours,
which prohibits the establishment of branches except within a bank’s
home city, and, under certain regulations, in foreign countries. The
larger Canadian banks are represented by their own branches in
every city, from coast to coast, while the Bank of Montreal alone has
more than six hundred agencies. Nearly all the banks have their
head offices in Eastern Canada. Six of them are located in the
province of Quebec, seven in Ontario, and one each in Nova Scotia,
Manitoba, and Saskatchewan. Three of the banks in Quebec are
controlled by the French Canadians. Their combined capital is just
under nine million dollars, or not quite half that of the Royal Bank of
Canada, the second largest in the Dominion.
An official of the Canadian Bankers’ Association has explained to
me some of the advantages of this system. He said:
 When the discoverers sailed up the St. Lawrence
to what is now Montreal they thought these rapids just
above the city blocked their passage to China, and so
named them “La Chine.”
 Montreal’s rise as a great port began a century
ago when the Lachine Canal was built around the
rapids, and gave the city a water passage to the
upper St. Lawrence and the Great Lakes.
 Many homes have the Rideau Canal and its fringe
of park at their front door. Built originally for military
reasons, the canal now makes possible a boat trip
through the Rideau Lakes to the St. Lawrence.
“Our plan of branch banks is based partly on the principle that
there is more strength in a bundle of fagots joined together than
there is in the same number of sticks taken separately. Poor
management or bad times, under your system, may bring disaster to
a single bank, whereas with us losses in any branch would be easily
absorbed in a great volume of business covering the whole country,
and the shock hardly felt at all. Under our system it is a simple
matter for a bank to concentrate its funds in the districts where they
are most needed, and money flows easily into the channels where
there is the greatest demand. This is of the utmost importance to
Canada, for we have limited capital, and therefore must keep it liquid
at all times.
“Canada is still a young country, not yet done with pioneering,
and its banks must lend a hand in promoting its development. When
a branch bank is opened in a tent or shack in a new mining camp,
the people know that the manager is there to give them service, and
that he represents a strong institution with millions in assets. A
remote fishing village or new paper-mill town is thus provided with
banking facilities quite as effective as those of Montreal or Toronto.
The difference in rates of interest charged is never more than two
per cent., no matter how remote from the money centre a branch
bank may be. The only reason it is ever higher is that where the
operations of a branch bank are small, the overhead expenses are
proportionately greater, and must be compensated for by the bank’s
customers. In recent years our wheat farmers of southern
Saskatchewan have been getting money cheaper than have the
farmers of your North Dakota, just over the border. The banks
represented in our three prairie provinces frequently have more
money on loan in that territory than the sum total of the deposits in
all their branches in the same area.”
The banks of Canada all obtain their charters from the Dominion
government, and their operations are strictly defined by law. This
law, known as the Canadian Banking Act, dates from 1870, and it
automatically comes up in Parliament for revision every ten years.
Under the act, the banks are permitted to issue paper money, which
ordinarily must not exceed the amount of their capital. Shareholders
are made liable for the redemption of bank notes up to the amount of
twice the value of the capital stock. In addition, each bank is required
to keep on deposit with the government a sum equal to five per cent.
of its note circulation. This goes into what is called the redemption
fund, which was created to make it absolutely certain that in case of
the failure of a bank, all its notes will be redeemed at face value.
During the period from September to February, when the crops are
moving to market, the banks may issue notes to fifteen per cent. in
excess of their capital, but must pay a tax of five per cent. on all such
extra circulation.
Canada’s banks are not audited by government examiners, as
with us, but each bank must submit a monthly statement of its
condition to the Minister of Finance. These reports are more detailed
than our bank statements and are regularly published by the
government. They show, among other things, the amount each bank
has loaned to members of its board of directors, or to firms in which
they are partners. The banks are not allowed to lend money on real
estate; this service is confined to loan and mortgage companies.
Nearly all the chartered banks of Canada conduct savings banks and
many of them also operate trust companies. The activities of the
latter are almost exclusively confined to acting as trustees and as
administrators of estates.
In the relations between the banks and the government, the
Canadian Bankers’ Association plays an important part. It has a
semi-official status, in that it was incorporated by special act of
Parliament, and is recognized as the joint representative of all the
chartered banks. It establishes clearing houses, supervises the
issues of bank notes, and manages the central gold reserves. The
chief executive officers of the Association are frequently consulted
by the government on financial questions.
During my stay in Montreal I had an interview with Sir Frederick
Williams-Taylor, president of the Association and general manager of
the Bank of Montreal, the oldest and largest financial institution in
Canada. In the Dominion, the chief executive of a bank is called the
manager. While the president occupies an important position as
chairman of the board of directors, he has not the same relation to
the daily transaction of business as is usually the case with us.
Canada’s banks are likewise distinguished for the long service of the
men in charge of their affairs. At the Bank of Montreal, for example,
the president and manager have put in, between them, nearly one
hundred years with the one institution. In all the banks, as a rule, the
men in authority have risen from the ranks to their present positions.
The Bank of Montreal is one of the great banks of the world. It
was founded more than one hundred years ago, about the time that
James Monroe was beginning his first term as President of the
United States. In those days, there was still fresh in the minds of the
Canadians knowledge of disastrous financial methods that had been
common in both the American colonies and Canada. In the time of
the French, for example, one of the governors, not receiving funds
expected from home, cut playing cards into small pieces, and wrote
thereon the government’s promises to pay. These he distributed
among his unpaid soldiers, and “card money,” as it was called,
continued to circulate for a great many years. Our own colony of
Massachusetts, learning of this easy method of “making” money,
produced a similar currency which later led to the phrase “not worth
a continental.” Even after banks were established in Canada, their
notes had different values in various parts of the country.
The home of the Bank of Montreal in St. James Street faces the
old Place d’Armes, a large square where formerly stood the
stockade built for protection against the Indians. Now it is the centre
of the financial district of Montreal, and, indeed, of all Canada. Of the
total capital of Canada’s banks, considerably more than half is held
by institutions having their main offices in this city.
When I went to call upon Sir Frederick, I passed through a
doorway supported by huge Corinthian pillars. Once inside, I found a
banking room larger than any I have ever seen in the United States.
Its great size, and the rows of counters and wicket windows
reminded me somewhat of the New York railroad stations and their
batteries of ticket offices. The roof, more than one hundred feet
above the floor, is supported by columns of black granite from
Vermont, each as big around as a flour barrel and as bright as
polished jet. The building has not the shine and new look of some of
our great banks, but everything about it is stately, and the servants
are as imposing as those of the Bank of England. A sleek, black-
haired attendant, who looked like Jerry Cruncher, wearing a blue suit
trimmed with red and a bright red vest with brass buttons, ushered
me into Sir Frederick’s office.
In speaking about Canadian banking, Sir Frederick said:
“By means of our branches in all parts of Canada we have our
hand on the pulse of the whole country. Every one of the great banks
receives constantly from its own representatives accurate
information of the state of business in his locality. We do not have to
depend upon friendly correspondents or outside agencies, but know
promptly and at first hand just what is going on. In this way we can
always anticipate the needs of a particular section, and act
accordingly. We can see the signs of any trouble ahead, and adopt
measures to prevent disaster. The managers of our branches are
responsible directly to us, and are therefore not likely to be
influenced so much by purely local considerations as might be the
case under a different system. On the other hand, it is our practice to
include in our board of directors men who reside in western and
central Canada, and are therefore in close touch with conditions in
those sections.”
“With such sources of information,” I said, “you should be in a
position to judge of the condition of Canada as a whole. I wish you
would tell me, Sir Frederick, just how you see her situation?”
“Canada is suffering from three great disadvantages,” he replied.
“I don’t wish to emphasize our troubles, but there is no country
without them, and we have our share, just as does the United States.
Our handicaps are the high cost of living, high taxation, and loss of
population.”
“But is Canada losing population?” I asked.
“I have mentioned these difficulties in the inverse order of their
importance,” said Sir Frederick. “Our loss of population is not only
the most serious problem, but it grows out of the other two. Here we
are, a nation of some eight million people. To the south of us is your
country, with a population twelve times as great. You are the richest
country in the world to-day. Canada occupies the north end of the
continent, and while she is larger than the United States in area, and
can match you in some of her natural resources, there are some
things that we lack. For example, we cannot grow cotton. We have
no hard coal. Most of our soft coal lies on our coasts, while a great
part of our industry and population is located in the eastern and
central sections of the country. This year, I believe, our bill for coal
from the United States will be something like one hundred and
twenty-five million dollars, or nearly thirteen dollars per capita of our
total population.
“We used to be a country of low costs and low taxes,” continued
Sir Frederick. “Now we are nearly up to you with regard to both the
cost of living and high taxes. On the other hand, you have created a
partial vacuum in the United States by your restrictions on
immigration. These do not, however, apply to Canadians. Just as
great bodies exercise a certain power of attraction upon smaller
ones, so your one hundred and ten millions draw upon our eight
millions. You are admitting fewer immigrants than your country could
easily absorb, with the result that you afford opportunities to our
people to better their condition. Strange as it may seem to you, there
are many of us who prefer, no matter what happens, to live our lives
under the British flag, but there are also others to whom this does
not seem so important. It is they who drift over to you.”
While Sir Frederick thus outlined the problems confronting his
country, his further remarks made it quite clear that he firmly believes
in her future and is proud that he has a part in her development.
In talking with business men, I find that they consider that
Canada has been especially fortunate in the extension of her banks
abroad. The Royal Bank of Canada and others have branches in the
United States and Great Britain, as well as in France and Spain. The
branch banks of Canada furnish the entire banking system of
Newfoundland, and I have myself done business with their branches
in the course of my travels in South and Central America, the British
and other European West Indies, Cuba, and Mexico. Canada’s
branch banks have gone to those countries with which the Dominion
has the largest foreign trade, and are an important factor in
promoting Canadian business abroad. They furnish Canadian
exporters with first hand data on markets, tariffs, and credits in
foreign countries. They help to finance exports and also aid the
importers to secure materials they need from other lands. An
American banking expert has made the statement that with the
exception of Great Britain, Canada has the best banking facilities for
foreign trade of any country in the world.
I find that the Dominion is gaining in financial strength. In the last
ten years the assets of her banks have increased seventy per cent.,
and the bank deposits have practically doubled. At the same time the
value of her production, both in agriculture and industry, has
mounted far above what it was before the World War. There is much
evidence to show that the people themselves are better off than they
used to be. For one thing, they have nearly two thousand million
dollars on deposit in the chartered banks, an average of one
hundred and eighty-eight dollars per person. They are buying more
life insurance than ever before, the total value of the policies now in
force in Canada amounting to over three thousand five hundred
millions of dollars. If they continue to increase at the present rate, by
1947 the lives of Canadians will be insured to the amount of more
than twelve thousand millions. This insurance represents a sum that
will be sufficient to buy three million homes, to keep in comfort
sixteen hundred and eighty thousand people, or to educate about
four million Canadian children.
 “From my window overlooking the wooded ravine
through which the Rideau Canal descends in locks to
the Ottawa River. I can see the towers of the
university-like quadrangle of government buildings.”
 The library of Parliament stands on the high bank
of the Ottawa River, a bit of old England in the
Canadian capital. It survived the fire that destroyed
the House and Senate chambers.
 CHAPTER XI
OTTAWA—THE CAPITAL OF THE DOMINION

I have come to Ottawa to get a “close-up” of the government of

Canada, and to see for myself if the city deserves its name, the
“Washington of the North.” Ottawa gives one an impression of vigour,
youth, and energy. It seems up to the minute, and not hanging on the
coat-tails of the past like Quebec. It has some of the English flavour
of Halifax, but is more modern. Like Washington, it is built on plans
that, as they are developed, will emphasize its natural beauties.
Ottawa is becoming a centre of intellectual life as well as of
political activity. The city is attracting people of wealth and leisure
who find it a pleasant place of residence for all or a part of the year.
The government service includes men and women of unusual
attainments, who are less likely to lose their places on account of
politics than those holding similar offices in the United States.
Ottawa is also becoming the headquarters for scientific and other
organizations, and is developing rapidly as an educational centre.
Washington has the Potomac, but this capital is on the banks of
two rivers, the Ottawa and the Rideau. Its site was chosen only after
a bitter struggle between rival cities. Quebec, Montreal, Kingston,
and Toronto each wanted the honour, but in 1859 all gracefully
accepted the arbitration of Queen Victoria, who chose Ottawa. It was
then a town of less than ten thousand people. It now has more than
one hundred thousand. It lies in the province of Ontario, but is
separated from Quebec only by the Ottawa River.
In contrast with our national capital, Ottawa is an important city
in its own right aside from the presence of the Dominion government.
It is one of the chief lumber centres of all Canada, and besides saw