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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
The proteins that gather light for plant photosynthesis are embedded within cell membranes in a site called the thylakoid membrane (or the "photosynthetic membrane"). These proteins form the light harvesting antenna that feeds with energy a number of vital photosynthetic processes such as water oxidation and oxygen evolution, the pumping of protons across the thylakoid membranes coupled with the electron transport chain of the photosystems and cytochrome b6f complex, and ATP synthesis by ATP synthase utilizing the generated proton gradient.
The Photosynthetic Membrane: Molecular Mechanisms and Biophysics of Light Harvesting is an introduction to the fundamental design and function of the light harvesting photosynthetic membrane, one of the most common and most important structures of life. It describes the underlying structure of the membrane, the variety and roles of the membrane proteins, the atomic structures of light harvesting complexes and their macromolecular assemblies, the molecular mechanisms and dynamics of light harvesting and primary energy transformations, and the broad range of adaptations to different light environments. The book shows, using the example of the photosynthetic membrane, how complex biological structures utilize principles of chemistry and physics in order to carry out biological functions.
The Photosynthetic Membrane: Molecular Mechanisms of Light Harvesting will appeal to a wide audience of undergraduate and postgraduate students as well as researchers working in the fields of biochemistry, molecular biology, biophysics, plant science and bioengineering.Sie lesen das E-Book in den Legimi-Apps auf:
Seitenzahl: 504
Veröffentlichungsjahr: 2012
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Contents
copyright Page
Preface
Acknowledgements
1 Life, Energy and Light
1.1 The Definition of Life
1.2 The Energy of Matter
1.3 Energy for the Future
1.4 Photosynthesis by Life
2 The Space of the Cell
2.1 The Cell Concept: Fundamental Nature of Life
2.2 Compartmentalization: The Cult of the Membrane
2.3 Membrane Components: Fundamentals of Proteins
2.4 Functional Classification of Membrane Proteins
3 The Photosynthetic Membrane: Outlook
3.1 Knowledge of the Pre-Atomic Structure Era: Organization of the Photosynthetic Membrane System
3.2 Composition of the Photosynthetic Membrane
3.3 Oligomerization, Interactions and Mobility of the Photosynthetic Proteins: Enabling Functions and Adaptations
4 Popular Methods and Approaches to Study Composition, Structure and Functions of the Photosynthetic Membrane
4.1 Biochemistry and Molecular Biology Approaches
4.2 Visualization Techniques
4.3 Function Probing Methods
5 Primary Processes of the Light Phase of Photosynthesis: Principles of Light Harvesting in Antennae
5.1 The Nature of Light
5.2 Absorption of Light by Molecules
5.3 Fate of Absorbed Light Energy
5.4 The Need for the Photosynthetic Antenna and the Fifth Fate of Excitation Energy
5.5 Photosynthetic Antenna Pigments
5.6 Variety and Classification of Photosynthetic Antennae
5.7 Principles of Light Harvesting: Summary
5.8 Connecting Light Harvesting Antenna to the Photosystems: Red Energy Traps
6 Towards the Atomic Resolution Structure of Light Harvesting Antennae: On the Path of Discoveries
6.1 Discovery and Primary Characterization of the Higher Plant Antenna Complex
6.2 Development of Isolation Methods: Intactness, Purity and Quantity
6.3 LHCII Crystallography: The Beginnings
6.4 Revealing the Atomic Resolution Structure of LHCII Antenna Complexes
6.5 Structure of a Minor LHCII Complex CP29
6.6 Comparison of LHCII Structure with the Structure of a Simpler Light Harvesting Complex from Purple Bacteria, LH2
7 Structural Integration of Antennae within Photosystems
7.1 Light Harvesting Complexes Gene Family
7.2 Toward the Structure of a Complete Photosystem II Unit: Supercomplexes
7.3 Supramolecular Structure of Photosystem I: LHCI
7.4 Photosynthetic Membrane Protein Landscapes
7.5 Robustness of the Light Harvesting Antenna Design: Resurrecting the Structure to Preserve the Function
8 Dynamics of Light Harvesting Antenna: Spectroscopic Insights
8.1 Steady-State Optical Spectroscopy of LHCII: Composition and Order
8.2 Time-Resolved Spectroscopy of LHCII: Energy Migration
8.3 Spectral and Structural Identity of LHCII Xanthophylls
8.4 Plasticity of Light Harvesting Antenna Design: Tailoring the Structure to Optimize the Function
8.5 LHCII Oligomerization: Dynamics of the ‘Programmed Solvent’
8.6 Kinetics of the Collective LHCII Transition into the Dissipative State: Exploring ‘The Switch’ Control
9 Adaptations of the Photosynthetic Membrane to Light
9.1 The Need for Light Adaptations and their Various Strategies
9.2 Long-Term Regulation of the Photosystem Ratio and their Antenna Size: Acclimation
9.3 Short-Term Adaptations to Light Quality: State Transitions
9.4 Short-Term Adaptations to Light Quantity
10 What is in it for Plant, Biosphere and Mankind?
10.1 Science and Society
10.2 Energy Balance of Photosynthesis: A Wasteful Process?
10.3 Crops and Light Harvesting
10.4 Light Harvesting Principles for Future Applications: Liberation from Saturation Constraints
10.5 Effects of Changing Climate – The Onset of Disorder
11 Conclusions
Index
Plates
This edition first published 2013© 2013 John Wiley & Sons, Ltd.
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Library of Congress Cataloguing-in-Publication Data
Ruban, Alexander (Alexander V.)The photosynthetic membrane : molecular mechanisms and biophysics of light harvesting / Alexander Ruban.p. cm.Includes index.
ISBN 978-1-119-96054-6 (cloth) – ISBN 978-1-119-96053-9 (pbk.) 1. Photosynthesis. 2. Photosynthetic pigments. 3. Light absorption. I. Title.QK882.R83 2013572′.46–dc23
2012025765
A catalogue record for this book is available from the British Library.
Dedicated to my family
Preface
The science of biophysics of light harvesting has accumulated vast amount of knowledge in the last 20 years about the workings of the photosynthetic membrane of higher plants. The subject is a manifestation of a grand molecular design of the complex photosynthetic machinery performing a sequence of primary energy transformation events. Hence, it represents an excellent example for learning the principles of structure and mechanisms of functioning of membrane proteins, their interactions with each other and their cofactors, dynamics in the membrane and in the isolated state and various mechanisms of adaptation to the environment. The author’s own 30 years’ experience in the field of biophysics of photosynthesis and work done by his numerous colleagues has been presented in the context of gradual explanation of complexity, historical development and multidisciplinary character of the subject, The Photosynthetic Membrane. The need for such a text is long overdue, since it does not cover the whole photosynthesis but focuses on its light phase processes, concentrating on the light harvesting: a well-structured and regulated process that ensures phenomenal flexibility of adaptations of plants to light that are essential for their survival. The book starts from a general introduction to the essential features of life; one of the most important is the energy requirement that is fulfilled almost solely by sunlight. Further, the advantages and peculiar physicochemical features of the nanoscale level of the photosynthetic membrane organization are described and the general makeup is presented setting the scene and preparing the reader for the detailed up-to-date description of numerous methods of investigation of the photosynthetic membrane structure and functions, light harvesting principles, atomic structure of light harvesting antenna complexes, the macrostructural organization and integration of antennae within photosystem complexes, dynamic nature of light harvesting proteins studied by various spectroscopies and adaptations of the light harvesting machinery in the intact membrane to light. This book also contains a chapter considering the potential of the educational and practical applications of the knowledge obtained in studies of the photosynthetic membrane organization and light harvesting processes. The author contemplates the role of the fundamental knowledge in general and explains possible ways it can be used in crop science, solar energy utilization by mankind and in solving the problems associated with the global climate change.
The author addresses this book, first of all, to the final year undergraduate students of various biology specializations. Therefore, he makes all effort to adapt it to different levels of training in chemistry and physics. The level of complexity gradually increases towards the end of the book making it relevant to postgraduate students and for a broader audience of those involved in photosynthesis research as well as bioenergetic membranes in general. With this book, the author hopes to awake an interest of a broad audience of students, scientists and those who are attracted to the phenomenon of energy transformation processes in living nature and welcomes any feedback.
Welch Schauspiel! Aber ach! Ein Schauspiel nur!Wo fass ich dich, unendliche Natur?Euch Brüste, wo? Ihr Quellen alles Lebens,An denen Himmel und Erde hängt,Dahin die welke Brust sich drängt-Ihr quellt, ihr tränkt, und schmacht ich so vergebens?
(Ah! what a view! Alas and but a view!Where shall I, endless Nature, seize on you?Ye breasts, and where? Ye sources of all lifeOn which the heaven, the earth depends,Towards which the withered bosom tends —Ye nourish, flow; yet vain my thirsty strife?) Faust: Der Tragödie erster Teil by Johann Wolfgang von Goethe
For undergraduate and postgraduate students and also those with an interest in the molecular engines of life.
Acknowledgements
The author likes to thank several of his colleagues, particularly Drs Matthew Johnson and Christopher Duffy for their engagement in many discussions on various topics of this book that helped him to shape and improve his ideas and the original outline. He thanks Dr Matthew Johnson for reading almost all chapters and Dr Christopher Duffy for reading Chapters 4, 5, 10 and 11, giving him a number of useful comments. Dr Matthew Johnson is also acknowledged for preparing Figure 2.4. The author thanks Dr Christopher Duffy for preparing Figures 5.11 and 5.12. The author also thanks Professor Leonas Valkunas for reading Chapters 5, 8 and 9 and giving him various useful comments. The author is grateful to Professor Conrad Mullineaux and Dr Tomasz Goral for providing confocal microscopy material for Figures 3.1(b), 3.2(b), a freeze-fracture electron microscopy image of Figure 7.1 and the fluorescence recovery after photobleaching results presented on Figure 9.17. The author thanks Dr Erica Belgio for preparing Figure 4.3 and Dr Erik Murchie for providing him with the solar radiation spectrum for Figures 5.3, 10.2 and 10.4. The author would like to thank Dr Rudi Berera, Dr John Kennis and Professor Rienk van Grondelle for providing with a transient absorption spectrum of isolated LHCII trimer for Figure 8.6. Dr Gene Carl Feldman is acknowledged for allowing him to use the NASA satellite image of the global chlorophyll redistribution in the Biosphere. The author finally thanks Mrs Kateryna Law for providing him with the image used for Figure 10.3.
The author appreciates the encouragement, help and advice received from the Wiley publishing team; Paul Deards, Sarah Tilley and Rebecca Ralf.
Instructors can access PowerPoint files of the illustrations presented within this text, for teaching, at: http://booksupport.wiley.com
1
Life, Energy and Light
1.1 The Definition of Life
Since the Big Bang, the Universe went on a path of losing energy density, gaining entropy and expanding, which causes continuing separation of its elements in space. Life seems to be engaged in fighting these fundamental developments in the world’s fate by:
In order to be successful in its apparently feeble refusal of matter’s fate, life is trying to expand constantly in space and change in time. In spite of extreme environments, it designs various ways to sustain this expansion process and invents new adaptations in order to exist and continue to ‘harmonize’ the matter. In ordered and smaller space myriads of choices can be realized, creating zillions of combinations of molecules, nonrepeatable events which are often perceived as increasingly deterministic as if there is a clever plot behind it all. Instead, life is a chain of reflections copying matter, building more complex matter and reproducing it. In order to do these unorthodox performances life needs energy: a fundamental means to enable reflection, memorizing, building in its work and multiplying.
Another feature of life is the ability to recycle biomolecules within the organism, ecological niche and the entire Biosphere. Mankind generally does it, however, only in extremely confined environments such as travel vessels: ships, submarines or spacecraft. Life always uses the recycling principle.
Life is difficult to define in one or two simple sentences. Therefore, taking into consideration all arguments provided previously we can present them in the ordered fashion in form of a number of statements.
Life is existence of protein and nucleic acid-containing autonomic open systems exchanging energy and substance with environment in order to maintain their higher levels of negative entropy (order) and proliferate in time and space.
Life is largely based on molecular affinity, dialectics of attraction and repulsion forces of the Universe, replicating itself using simple molecular coding principles, resulting in constant evolution of dynamic molecular forms.
In a way, life is a complex and far from equilibrium path towards condensing of matter. It exists at rather low temperatures on the temperature scale achievable in the Universe. Therefore whilst the high temperature irreversibly kills life the low temperature has a tendency to preserve and even stimulate it in some cases (winter crops, Snowball Earth theory, etc.).
Currently, life seems to be impossible to create from the non-living substance, apparently due to a long-term requirement for the evolution and selection of systems working against the second law of thermodynamics. It is, however, likely that the selection process which led to the creation of life forms is based upon a nonlinear chain of events and of a fractal nature, that is can be characterized by sudden emergence of an infinite regularity from some apparently chaotic and unpredictable trends. It cannot, therefore, be ignored that tomorrow science would succeed in creating at least a primitive artificial life form.
An essential prerequisite of life was the incidence of unlimited amount of easily transferred in space energy (radiation), gradual cooling and condensing matter processes
Life is a form of ‘revolt’ against the second law of thermodynamics achieved by very unstable, ‘vulnerable’ (soft matter) systems, a fragile lip of matter towards order and high organization on the way to the thermodynamic equilibrium and energy drain in the expanding Universe.
Life is an inherent property of our Universe and therefore is potentially as old as it is.
It is important to think of life origins from the thermodynamic point of view. In the end, energy supply is a decisive factor for life in general and mankind, in particular.
1.2 The Energy of Matter
Energy equals matter and matter carries a lot of energy:
(1.1)
And this little formula means a lot for the Universe and life. Of universal energy, life requires very little. If the energy hidden in a tiny nucleus is about 1 GJ per mole, the energy stored in the most common biological energy carrier, ATP, is 30.5 kJ per mole, which is nearly 200 000 times smaller than the energy carried by tiny nucleus. Hence, the question of energy supply to life should not be such a big deal. In a world of forces building the very blocks of the Universe; nuclei, atoms and molecules, the forces enabling life are the weakest:
Fortunately for life, elemental and atomic energy transformations generate one of the by-products – electromagnetic radiation – a broad range, speed-of-light travelling patches of energy, capable to interact with matter. This is the best wireless and custom-addressed (not all matter stuff can get it) form of energy ever known to man. Quanta of electromagnetic radiation are spanning our Universe. Stars are the major sources of them. We sometimes look at them at night, just registering small coloured sparkles of light – all energy is left for us on the path of billions of years of its travel, just barely enough to cause a simple photobiological act of the retinal isomerization initiating the chain of the events of vision in our eyes – all that remains for us from the mighty energy of a star.
1.2.1 The Source of Life’s Energy
What if the star can be brought to us a little bit closer, say a few light years or so? The one we see every morning – the weather permitting – our Sun. People always wondered if they have to thank it for something a bit more than just daylight, a suntan and warm weather. Indeed, the Sun is giving to Earth 100 000 TJ of energy every second, a little more than that required to tan our skins. It is actually enough to boil 100 thousands of billions (1014) of kettles, roughly 10 thousands per capita of the planet’s population. For someone preferring a Bugatti-Veyron to tea, this is enough to run 20 Bugattis per person; mind you, it has got to be a car driving on a ‘green’ fuel! But here comes the limited amount of space on our planet to host not only all those cars but us, mankind with our tendency to scavenge the nature which brought us into this world.
1.3 Energy for the Future
The point is that the Sun was, is and will be for some time, a very charitable body in the sky: it gives us all this energy for free, unlike the energy supplying companies. The question is how can we use just a tiny fraction of it in order to be alive and happy, driving our modest vehicles, being curious about the word around us? Let us leave the question of our lifestyle for a moment and think of how we can use the Sun’s generous energy? Naturally, from solar cells: the devices capable of converting the light energy into electricity, a variety of photovoltaic gadgets, which use the principles of photon energy conversion into the energy of moving electron or electric current. The industry is growing, in some countries faster than in the others, and is certainly the way towards the era of recycling, renewal of goods and energy for the future generations to come. Returning to life we may guess as well how it has solved the question of energy supply in order to exist in the luxury of the Biosphere: a carefully settled thin film of organic matter around the globe. Indeed, the key to fixing all global crises is not just to find a quantity of matter or energy but to find the ultimate way to live in balance in limited space and conditions. Indeed, the laws of Biosphere do require the kind of lifestyle that is based not only upon the renewable energy utilization but also uses a great biological principle of recycling substances. Without acknowledging these laws one cannot succeed in sustaining life, including our species, Homo sapiens. We have to find the solutions Nature found some 3 billion years ago. This solution was building the living matter using the energy of Sun and later its most successful variety; oxygenic photosynthesis.
1.4 Photosynthesis by Life
Photosynthesis is a process of conversion of energy of light into chemical energy of organic compounds, carbohydrates. Oxygenic photosynthesis uses water as an electron donor for redox reactions involved in the primary light energy stabilization.
(1.2)
Photosynthesis is a process by which organisms capture and store energy of light by a series of events that converts it into biochemical form of energy. Photosynthesis is a process that is directed to increase levels of negative entropy (order) of living forms.
(1.3)
where (–S) is negative entropy, kB is the Boltzmann constant and W is a number of possible states the system can exist. W is also proportional to amount of information required to describe the whole system and its dynamics. The more disorganized is the system, the less predictable it becomes, and hence, it will require a lot of information in order to describe all possible states the system can adopt and/or move into in time. Biological matter needs input of negative entropy in form of energy and substance: hence, it must exist in an open form. The energy type needs to be an ‘organized’ one, not just thermal or mechanic (lowest types) but electromagnetic and/or chemical – ‘organized’ forms. The ‘organized’ character of these forms comes from their specificity: they can be addressed to a specific atom, molecule or group of molecules and cannot be ‘felt’ by the rest of the cell or organism. Input of substances brings chemical form of energy as well as the material required for the organism growth and reproduction.
Photosynthesis has emerged on the very early stages of evolution. It remains one of the most complex biological processes, which is not surprizing, since it holds the key to the very heart of life: it is the means of fighting the universal entropy. How is the energy of a tiny particle/wave, photon, used for this? The dualistic nature of something as casual as light often appeared puzzling to scientists. A photon exhibits properties of both particle and wave. Sometimes it is capable of propagating through two distant slits on the dark chamber at the same time. Moreover, it has no rest mass. As Confucius said: ‘The hardest thing of all is to find a black cat in a dark room, especially if there is no cat.’ Photosynthesis by living organisms seems to be well-equipped to deal effectively with such an elusive form of matter as light.
Photosynthesis is, first of all, a sequence of reactions of light energy transformation that is evolved to solve two major tasks:
This looks something like catching a wild cat, making sure it gets calmer, slowing down and is put safely into a space (cage, etc.) it cannot easily escape from. Catching a photon is no lesser task for photosynthetic organisms. The principal difficulty here is to catch something, which has no mass when immobile, meaning that at rest it vanishes and ceases to exist. How does life manage to slow the photon without killing it? Nature has found a neat solution by using means of rapid transformation of photon energy.
1.4.1 Photon Energy Transformations
To catch the photon the pigment molecule’s optically-active electrons must react very quickly, within 1 femtosecond (10–15 s). Excited by light pigments can easily exchange their energy of excited electron. This occurs via the electromagnetic resonance events, which cause excitation energy wondering from one pigment to another, exciting without direct molecular interaction. The energy is kept among the ‘collective’ of pigments and is waiting for its fate, which can be various. The photon can reappear again, having less energy than the absorbed one. Alternatively, the energy of a pigment can simply be wasted into heat, contributing to the rise in the Universe’s entropy. Also, the electron spin can change to the opposite creating so-called tripled excited state. Finally, the energy can be trapped by the photochemically active pigment of the reaction centre to initiate the chain of electron and coupled proton transport events leading to the chemical storage of light energy in the two final products of the light phase of photosynthesis, ATP and NADPH (Figure 1.1). Those can later be used elsewhere and when light is no longer present. These two substances are the universal biological currency, always in demand for the ‘dark’ photosynthesis to fix carbon from carbon dioxide of the air or just a synthesis of biological matter. Light harvesting is therefore a staged process of photon-exciton-electron-proton transformations, handling the most elementary and fundamental forms of energy and matter. Light harvesting is the essence of photosynthesis in our planet. Remarkably, this energy transformations and stabilization occur in one tiny kind of site, more specifically, surface, called the photosynthetic membrane.
Figure 1.1Light energy accumulation processes: a sequence of particle transformation events (a simple scheme).
This book will talk about the composition, structure, variety of functions, adaptations, assembly, biological importance and ways to study and to understand the photosynthetic membrane as the oldest and, so far, greatest light-harvesting nanostructure ever existed on our planet that supported and continues to support all its life.
Reference
Confucius (1979) Analects. Penguin Books.
Bibliography
Barber, J. (2007) Biological Solar Energy. Phil. Trans. R. Soc. A, 365, 1007–1023.
Blankenship, R. (2002) Molecular Mechanisms of Photosynthesis. London: Blackwell Science.
Clayton, R.K. (1980) Photosynthesis: Physical Mechanisms and Chemical Patterns. Cambridge: Cambridge University Press.
Gleick, J. (1998) Chaos: Making a New Science. Vintage.
Hall, D.O. and Rao, K.K. (1995) Photosynthesis. Cambridge: Cambridge University Press.
Schrödinger, E. (1992) What is Life? With Mind and Matter and Autobiographical Sketches. Cambridge: Cambridge University Press.
Vernadsky, V.I. (1997) The Biosphere: Complete Annotated Edition.Heidelberg: Springer.
Walker, D. (1992) Energy, Plant, Man. Brighton: Oxygraphics.
2
The Space of the Cell
Adde parvum parvo magnus acervus erit(Add a little to a little and there will be a great heap)
Ovid
2.1 The Cell Concept: Fundamental Nature of Life
All life forms apart from those very primitive ones, which are dependent upon other life forms to provide them with homes where they live and proliferate (viruses, etc.), have a very common building block, the cell. We are not a solid mass of matter (remember the T-1000 terminator in ‘Terminator 2’ built of liquid metal? Or the planet-brain Solaris: both apparently a homogenous mass that is alive?). Hence, life forms are represented by one, several or many cells. The fact reminds us that we have evolved from a unicellular organism. Cells are usually small, one tenth of a millimetre. Why do they have to be so tiny? The answers are many. The first is actually, why not? These cells still contain millions of various molecules organized in dozens of different compartments or organelles. Hence, in spite of their small size the cell is much larger than the individual biomolecules within it and therefore can be a complex, heterogeneous and multifunctional structure.
Indeed, there is a lot of space in the microworld. Richard Feynman (1960) named his lecture given at an annual meeting of American Physical Society in 1959: There’s plenty of room at the bottom. What did he mean? Well, this physicist’s jargon refers to the geometrical scales of matter: ‘bottom’ is the lower limit of special dimension and top, the higher limits of special dimension. The lower limit is obviously infinitely small, asymptotically approaching zero. But near it resides the world which is named with the very frequently used term nowadays, nanoworld. The dimensions there are within nanometres range (10-9 m). The borders are arbitrary and gradually drifting up to the micrometer scale (10-6 m) approaching the millimetre border. A border that arbitrarily divides these worlds of nano and micro from macro: the scale of existence in human dimensions. Basically it is an invisible versus visible worlds division. Hence, from the lower limit of our macroworld down the bottom of the nanoworld there are approximately six orders of magnitude of dimensional space. That is one million! The space scale it covers can be compared to the space scale between the size of a man and a country like the United Kingdom. There was, and is a lot going on in the country. Imagine an endless list of institutions such as history, geography, politics, arts, industry, agriculture, nature, science, religion, family, and so on. An entire universe of human existence! In the same respect, the cell is an entire universe of fundamental life on this planet. It is the basis for all Nature’s and our activities on it. Feynman was seriously fascinated by the biological design:
A biological system can be exceedingly small. Many of the cells are very tiny, but they are very active; they manufacture various substances; they walk around; they wiggle; and they do all kinds of marvellous things – all on a very small scale.
But why have all life’s engines been evolved on the nanoscale rather than macroscale? Is there any advantage or even absolute requirement for life processes to be organized on a tiny invisible scale, as if we are not meant to see and learn what is going on? Hidden from the eye cellular processes enabling life to take place where some laws of physics are very different from those of a visible the macroworld. At the nanoscale the forces of surface tension in the cell prevail over the forces of gravity. Hence, the capillary effects enable trees to deliver kilograms and tons of water and nutrients upwards against gravity. For humans it would require the use of powerful pumps: a macroworld solution to the problem.
Another peculiarity of the cell environment is the very high viscosity and high surface area to volume ratio. These features enable cell robustness and at the same time extremely high rates of substance exchange with the environment providing cells with power required for fast growth and division. Another advantage of the nanoscale cell design is the very high rates of thermal conductance. Indeed, excess thermal energy released as a result of a multitude of biochemical processes can quickly be removed into the environment without altering or causing any harm to delicate balance of cellular processes, the vast majority of which are temperature sensitive.
An additional property of the nanoworld is that electrical charge concentration and dynamics can be extremely high. Since electricity is utilized by the cell in a number of very important functions, charge concentration and dynamics are important factors ensuring the effectiveness and power of such processes as signal transduction, biological movements and energy generation. And finally, arguably the most important property of the nanoworld is that in some cases it provides the right space for otherwise entropic processes to become pseudo-entropic or even organized. The fundamental grounds for this point can be seen experimentally in the phenomenon of Brownian motion. There, the entropic motion of the tiny pollen particles is driven by the collisions with a relatively small number of tiny molecules of water, in the nanoworld the particle motion becomes visible simply because of much smaller populations of water molecules are interacting with it. At a first glance, Brownian motion is a problem for life. However, the entropic energy of spontaneous molecular movements is utilized by life throughout, simply because it introduces certain structural restrictions that can be imposed upon apparently stochastic processes. The energy of molecular vibrations together with the energy of various gradients (that will be described in the next chapter) is used to drive highly autonomic and directed processes in the cell. Therefore these processes are subject to nonequilibrium thermodynamics, an instrument to describe and understand the mechanics of molecular processes of life. Later this point will become more apparent with the introduction of macromolecules and their works in the nanoworld of the cell. The first chapter, describing the features of life, stated that one of the major properties was the lowering levels of entropy in life forms. The nanoscale seems to be a perfect field for this very fundamental feature of life in the elementary space of the cell.
2.2 Compartmentalization: The Cult of the Membrane
When the space boundaries are defined like those of the ticket hole of the railway station, where a crowd of people moves in unpredictable manner, the system looks highly entropic, disorganized. How to make it more organized? The answer could be to create various specialized sub-spaces. Then the system would look more organized so that one should be able to trace the reasons for people’s movements and behaviour in those different compartments of space. The cell is a much compartmentalized structure. The walls of compartments are made of similar structures to the wall of the cell – the lipid bilayer membrane – a remarkable example of biological self assembly system. The order starts with establishment of defined molecular interactions forming condensed states, like a plane made of a double layer of molecules. Why a double layer? From inorganic chemistry we know that some reactions lead to formation of water insoluble salts which form sediments of various shapes or even organized crystals on the bottom of a test tube, a simple self-organizing system. The property that made salts form those pellets is the stronger interaction between salt molecules then between salt and water molecules. A simple but remarkable birth of order! Like honey that attracts flies by making them all fly in one direction, abandoning their chaotic movements in warm, summer afternoon light. One single property determines the shape of substance in the water phase.
Molecules that form membranes, lipids, have a higher affinity to each other than to the water molecules, therefore they form structures. But the 2D shape of the membrane and its bilayer structure is determined by one additional property of the lipid molecule: amphiphilicity or possession of both, hydrophobic and hydrophilic properties. Indeed, a lipid molecule has one or more long hydrocarbon linear tails as well a hydrophilic head built of oxygen-containing glycerol, alcohols, sugars or simply hydroxyl groups. In addition, the head is attached to the tail via ester linkages containing ester and carbonyl oxygen. Some lipids can contain dozens of oxygen atoms. Therefore, during lipid interactions in the water phase, a bilayer structure is formed as a lowest energy thermodynamic state where hydrophobic fatty acid chains interact with each other via van der Waals forces and are hidden from water and hydrophilic heads are exposed to water and interact with it via hydrogen bonds. Hence, specific molecular properties and weak interaction forces enable the process of biological self assembly based entirely on reaching the thermodynamic energy minimum in the water system.
Figure 2.1The forces driving biological membrane self-assembly: calculation of energy drop during interaction of two molecules of laurate.
Membrane self-assembly process is driven by weakest molecular forces that define hydrophilicity and hydrophobicity of lipid molecular structures. This is easy to see in the simple computer stimulation experiment (Figure 2.1) that uses a molecular docking algorithm. Here the van der Waals interactions are driven by the energy drop of a few kcal mol-1 in the simple associate of two short fatty acid molecules (laurate) enabling hydrophobic parts of the molecules to align for the maximum interactive configuration. In the water phase the polar (hydrophilic) oxygen-containing groups (depicted in darker shading) would in turn interact with water via much stronger then van der Waals hydrogen bonds. These interactions would further stabilize lipid associations (Figure 2.2) so that they self-organize into bilayer structures reaching the stable energy minimum of the whole system carefully dividing the structure and forces defining hydrophobic and hydrophilic domains.
Because the biological membrane is built of the weakest molecular interaction forces it is a very dynamic structure. Lipid molecules are free to move laterally relative to each other, since at ambient temperature the entropy will provide enough energy to break (and re-establish again and again) van der Waals interactions, making them change all the time without compromising the overall stability of the membrane structure and keeping the system at a relatively stable minimum energy. Increasing the ambient temperature will inevitably lead to the increase in molecular movement within the membrane making it more dynamic and will eventually exceed the membrane stabilization forces causing damage and disassembly. Hence, the types and structure of molecules that build the biological membrane could define its robustness and resilience to the environmental temperature. One of the adaptive ‘measures’ could be to increase the area of van der Waals surfaces. This can be achieved by increase in saturation of fatty acids making the ‘tail’ structures more flexible and ready to adopt the very minimum of collective lipid energy. In addition, this surface could be enhanced by introduction of methyl groups into fatty acids. It is achieved in membranes of Archaea. As a result these organisms can leave at extremely high environmental temperatures, up to 80 °C and even higher.
Figure 2.2Protein stabilization in the biological membrane. Atoms in molecules are bound by covalent forces of about 100 kcal mol-1. Hydrophilic domains of a membrane protein interact with the lipid head groups with electrostatic (10–40 kcal mol-1) and hydrogen (1–10 kcal mol-1) bonds. The hydrophobic fatty acid tails and protein domains interact via Dynamic van der Waals forces (0.1–1 kcal mol-1).
The biological membrane is a typical and primary example of molecular antagonism that leads to the automatic formation of biological structure. Perhaps the emergence of life in the water environment was preceded by the formation of organic molecules that possessed amphiphilic properties: amphibious characters, accommodating an inherent antagonism between hydrophilia and hydrophobia. It will be further revealed, using the examples of protein structures, that living nature is well designed for exploring thermodynamics in its use to minimize levels of entropy and hence organize itself. The variety of lipid types offers the biological membrane some flexibility in properties, such as fluidity, interactions with environment, permeability, electric potential and accommodation of nonlipid membrane components, such as sugars and proteins.
The biological membrane is a two-dimensional structure, but its space is very small. It is a nanoscale structure that inevitably (thermodynamically predetermined) encapsulates a closed space forming a vesicular structure, a prototype of the cell. The cell is an entire fortress. Take, for example, The Tower of London. The cell and the Tower have a lot in common. They have their entities marked and preserved by a barrier, wall or membrane. The wall of the Tower defended it from invaders, enabled traffic through its gates, served for observation of exterior environments. The cell membrane performs all of these functions and in addition, in some cases even more. It can act as a kitchen, a place where new substances are being synthesized and the biological energy can be produced. Within the Tower stand a few buildings of various functions. Similarly, the fortress-cell has a variety of subcellular structures – organelles – surrounded by their own membranes. The cell is packed with these structures so densely as houses in medieval town (take the Shambles of York, for example). The crowdie compartmentalized nature of the cell interior is a crucial feature of life design. Divide et impera or ‘divide and rule’: that was the key strategic doctrine of the Roman Empire. In other words, segregation makes things better organized and controlled, hence it allows a certain kind of order to be established.
The way cellular compartments are organized and their work is coordinated is remarkable. The emperor is obviously the cell nucleus, sending various messages and directives to all cellular compartments, it holds the information needed to build the cell structures. Compartmentalization also takes place on the level of individual organelles and their components. Membranes divide compartments and components and enable formation of gradients of various substances: molecules, ions, protons, electrons and even electric fields. The gradients accumulate potential energy, which when transformed into kinetic energy can produce work and directionality, leading to formation of biological matter and establishment of those functions characteristic for an organelle or entire cell. Order emerges as a result. Barriers also serve to separate those types of molecules that otherwise would interact with each other producing unwanted substances that may harm the cell and create chaos. But what enables the membrane to possess such a variety of functions supporting the life of the cell, tissue, organ and organism? The answer is membrane proteins and their complexes with lipids and other functionally important cofactors, like ions and relatively small organic molecules.
2.3 Membrane Components: Fundamentals of Proteins
The membrane is not much less complex and, by all means, not less fundamental than the cell itself. In order to fulfil all those functions described in the previous paragraph it must possess some specialized features. These features first of all, are represented by membrane-associated proteins. Proteins in the membrane play a central role in enabling the biological functions on a molecular level. Membrane proteins are a special class of proteins, which are amongst the most difficult to study, mostly because the membrane is their natural environment from which they cannot be harmlessly liberated without consequences for their intactness. The membrane protein environment is amphiphilic (see Figure 2.2).
The presence of proteins in the membrane not only defines its functions but also significantly changes its physicochemical properties, including temperature stability and permeability to various molecules. Different biological membranes contain various amounts of proteins. Myelin, a membrane that insulates nerve fibres has low protein content (~18%). Relatively pure lipids are good insulators. In contrast, the plasma membranes of most other cells are much more metabolically active and hence require more specialized molecular apparatus. These membranes contain many pumps, channels, receptors and enzymes: all proteins. The protein content of some plasma membranes is typically 50%. However, biological energy-transduction membranes, such as the internal membranes of mitochondria and indeed photosynthetic membranes have the highest content of protein, typically 75% and even more in some cases. Figure 2.3 displays electron microscopy pictures of the fragments of photosynthetic membrane from higher plants containing two types of proteins or rather protein complexes, photosystem II (PSII) and light harvesting complex II (LHCII). It shows that proteins of different type and function can have different density in the membrane. Whilst PSII particles positioned relatively far one from other (more then a particle diameter), the LHCII particles look like a crowd of proteins, tightly interacting with each other. This simple observation could be indicative of the different functional roles of the two types of membrane proteins.
Figure 2.3Different densities of two types of membrane proteins. Freeze-fracture electron microscopy image of the photosystem II (left) and LHCII particles.
Whilst membranes of specialized cells often contain only a few types of proteins, membranes of metabolically active cells and organelles normally contain a large variety of protein types, structures and sizes. These proteins can also vary in the way they interact with or are positioned within the membrane. Typically membrane proteins span the whole width of the membrane having a hydrophobic membrane-spanning (transmembrane) domain and two hydrophilic domains protruding into water phase (see Figure 2.2). These proteins are called integral membrane-spanning proteins. There are, however, proteins, that are integral but do not span the whole membrane depth. They are called integral non-spanning membrane proteins. The other type of proteins does not even interact with the hydrophobic lipid interior of the membrane. They are simply bound to the hydrophilic domain of other membrane proteins via most commonly ionic interactive forces and hydrogen bonds. This type of interaction is relatively strong and normally these proteins are fixed permanently in their binding site and do not move around, whilst integral membrane proteins display a certain degree of mobility (this will be discussed in detail later). The ability of membrane proteins to move in the membrane plain allows them to interact with each other, regroup, oligomerize and form domains, thus giving the membrane a heterogeneous character. All this enables a broad range of adaptations of the membrane structure and function suited to various metabolic and environmental changes and requirements.
Figure 2.4Order versus disorder of membrane protein assemblies. Freeze-fracture electron microscopy image of the photosystem II-containing membrane. Courtesy of Matt Johnson.
One important feature of membrane proteins is that they very often form relatively stable superstructures: complexes of several subunits (sometimes dozens of subunits). The molecular weight of these complexes can reach hundreds of thousands and even a few millions of Daltons. Those who work on the evolutionary aspects of membrane protein functions are often puzzled by the question of how at all such complex, cooperatively built and functioning molecular machinery could evolve? What is even more intriguing is that whilst some of these structures took a relatively short time to evolve, they have been then preserved in nature for hundreds of millions of years.
Another interesting aspect of the superstructural character of many membrane proteins is that since they are very large (sometimes 10 or even 30 nm in diameter) there are not so many of them in the biological membranes of organelles, in particular, to treat their behaviour (movements and interactions) with random statistics, there are simply too few of them and they do not behave any more as billions of small molecules obeying the laws of classical molecular thermodynamics. There only are about 200 PSII complexes in the area of 400 × 700 nm of the photosynthetic membrane presented in Figure 2.4. Hence, it is not surprising to see otherwise improbable, nearly perfect transient ordering of membrane supercomplexes as displayed here. The behaviour of such system cannot be correctly described by statistical molecular physics. It would require N-body modelling approaches used in the studies of dynamics of stellar clusters in the Universe, a totally unexpected turn in the research of a nanoworld of the biological membrane. Indeed, for such a large structure as the PSII complex factors like symmetry (or indeed asymmetry), sensitivity to environment, ability to interact via various types of weak forces (see the Figure 2.2 caption) could be major determinants of 2D diffusion and, hence, positioning. Therefore, the conventional statistics of molecular behaviour are replaced in the membrane by a more deterministic control resulting in predictable collective dynamics and simple control over function, and in this way establishing order in the nanoworld of cell processes, an ultimate goal of life.
Figure 2.5Functional classification of membrane proteins.
2.4 Functional Classification of Membrane Proteins
Proteins in the membrane play a number of vital cellular and organellar functions. These functions can be divided into the three major groups: transport, signalling (reception) and metabolism (enzymes).
Transport proteins are the largest and the most versatile in functions and structure group (Figure 2.5). It consists of photosynthetic light harvesting antenna complexes, which ‘deal’ with the tiniest particle, the ‘photon’ that carries the energy needed to drive the photosynthetic reactions. The second group of transport proteins is light driven proton pumps. The typical example of this group is bacteriorhodopsin, a protein that captures light energy and converts it into the energy of a proton gradient across the membrane it is located in. Hence, this is a complex transporter that deals not only with photons but also much larger particles, protons. The next group of transporters are light-driven electron transport complexes. These are represented by reaction centre complexes of various photosystems of prokaryotes to eukaryotes. The role of these complexes of proteins is to convert the energy of excited by light electrons into the energy of moving electrons that are donated into the chain of reactions of reduction and oxidation that supply the cell with NADPH and ATP. Another group of transporters is electrochemical potential transporters. Typical representatives are proton-drive ATPases that transform energy of the proton gradient across the membrane they are inserted in to synthesize ATP from ADP. Relative to them is a group of transporters that work in reverse, hydrolysing ATP in order to transport various ions across the membrane (calcium ATPase). The other group of transporters is essential for channelling ions (ion channels). Next group of transporters is capable of transporting molecules of various sizes actively (porters) or passively (porins).
Functions of transport membrane proteins span from primary to metabolic energy generation, from work, communications to cellular homeostasis. A remarkable feature of transport proteins is that they are capable of handling the particles of matter that vary in sizes by more than 10 orders of magnitude (mass of a moving photon is ~10-33 g, mass of electron is ~10-27 whilst the mass of glucose is ~3.10-22 g). This is yet another feature and advantage of a nanoscale design of life.
The second class of membrane proteins are various receptors that form systems of cellular communication and signalling (G-protein coupled receptors (GPCRs), gamma-aminobutyric acid (GABA) receptors). Here, we see a very similar feature to transporter proteins: ability of receptor proteins to ‘handle’ particles of nature from photon of light and ions to large organic molecules and even proteins.
The third class of membrane proteins are enzymes. A typical example is prostagandin H2 synthase that catalyses the first step in prostaglandin synthesis. The enzyme is an integral but nonspanning membrane protein. Its active centre must be located within the hydrophobic environment, since the substrate is a fatty acid (arachidonate). The hydrophobicity of the substrate simply dictates the design and location of the metabolic enzyme, not in the water phase but in the 2D space of the membrane interior.
Reference
Feynman, R. (1960) There’s Plenty of Room at the Bottom. Caltech Engineering and Science, 23, 22–36.
Bibliography
Berg, J.M., Tymoczko, J.L. and Stryer, L. (2012) Biochemistry. Basingstoke: W.H. Freeman and Company.
Branden, C. and Tooze, J. (1991) Introduction to Protein Structure. New York and London: Garland Publishing.
Luckey, M. (2008) Membrane Structural Biology (With Biochemical and Biophysical Foundations). Cambridge: Cambridge University Press.
Nicholls, D. and Ferguson, S.J. (2002) Bioenergetics. London: Academic Press.
3
The Photosynthetic Membrane: Outlook
‘In thy house or my house is half the world’s hoard…’
Rudyard Kipling
3.1 Knowledge of the Pre-Atomic Structure Era: Organization of the Photosynthetic Membrane System
Let us consider the photosynthetic membrane of the higher plants. Figure 3.1(a) shows typical evenly green young spinach plants. Spinach has been a model plant for research in photosynthesis spanning from studies of primary processes to experiments on carbon assimilation in isolated chloroplasts. They can be visualized even without preparation in the intact cell using the modern confocal scanning fluorescence microscopy (see the next chapter for details). Figure 3.1(b) shows a confocal fluorescence microscopy image of round spinach chloroplasts, a very high resolution optical microscopy, whilst Figure 3.1(c) displays an image of isolated chloroplasts obtained by conventional optical microscopy. It is easy to detect the intact chloroplasts, which show much better contrast to the broken organelles, which loose their shape and appear rather flat. Both images, however, reveal the presence of grained structures with higher intensity of absorption/fluorescence inside of the chloroplast. They can be numerous and are called granae. The medium they are embedded into is called stroma. The granum is a very structured particle that can be explored in detail only by a higher resolution microscopy, like transmission electron microscopy (EM). EM images in Figure 3.1(d) and (f) display numerous grana in the chloroplast and a single granum that exhibits a clear lamellar structure. Figure 3.1(e) shows a schematic simplified presentation of the structure of granum. It is basically a stack of flattened often round vesicles called thylakoids. Vesicles are surrounded by membranes, which, in fact, are the photosynthetic membranes of higher plants. The volume insight the thylakoid is called the lumen. Its space is very narrow, only about 10 nm wide. The physiological reasons for the existence of the lumen space, that is, a closed volume surrounded by the photosynthetic membrane, will be explained later.
Stacking of thylakoids into granae is known to depend upon the presence of divalent cations of magnesium, Mg2+. Monovalent cations of potassium, K+, are also effective though at higher concentrations than Mg2+ (100 mM of K+ vs 5 mM for Mg2+). It is generally accepted that positively charged cations bind to negatively charged groups exposed on the membrane surface therefore compensating electrostatically the screening repulsive forces between membranes assisting thylakoid stacking. As will be shown later, membrane proteins play crucial role in this process undergoing a radical lateral cooperative regrouping in the thylakoid membrane system. Still, there are also thylakoids in chloroplasts that are not involved in formation of granae called intergranal or unstacked thylakoids. Together with granae they form the chloroplast thylakoids, a site where the whole light phase of photosynthesis takes place. Thylakoids can be isolated relatively easy from chloroplasts and have been the subject of studies for a number of decades. Some of them will be mentioned later in this book. However, first of all it must be said that the thylakoid system is the site in chloroplasts that plays a direct part in the absorption of sunlight and, hence, the trapping photons. What is interesting is that the area of these photosynthetic membranes is extremely large. Let us do a simple rough calculation.
Take 1 cm2 of the average spinach leaf. Its area in micrometres would be 108 µm2. The average cell size is about 20 × 40 µm, therefore the area is 800 µm2. Hence, one cell layer of the 1 cm2 of leaf will contain 125 000 cells. Each cell can carry ~50 chloroplasts (in shade-grown plants). Each chloroplast can easily contain 100 granae with around seven stacked thylakoids, each having two membrane surfaces. The average thylakoid diameter is 0.5 µm, which corresponds to ~0.2 µm2. Using these numbers we can calculate the total area of only granae membranes in the one layer of cells of 1 cm2 leaf area. It yields approx. 20 cm2, more than an order of magnitude higher than the leaf area itself. Remarkably, this is achieved despite the total chloroplast volume is being only ~1/10 of the cell volume. Taking into account that the average leaf can contain around 20 cell layers we can see that the total grana membrane of the leaf of 1 cm2 can be about 400 cm2, that is, 20 × 20 cm. For a leaf with 10 cm2 area, this will be 4000 cm2 or nearly a half of a square metre! This is a truly remarkable achievement of a compact character of the nanoscale organization of the chloroplast cell compartment reflecting Feynman’s famous remark about the significant amount of space the nanoworld potentially possesses (see the previous chapter). By making light harvesting take place in a very thin two-dimensional system, the membrane, it is possible to compact a large membrane area into a relatively small three-dimensional space. This space in the case of the photosynthetic membrane area is well-utilized in the processes of adaptation to the light environment that involve alterations in leaf, cell and chloroplast morphology. This is a well-documented fact that plants acclimated to low light accumulate more chloroplasts per cell, grana per chloroplasts and thylakoids per grana. This type of acclimation results in a one or even two orders of magnitude increase in the light interception and photosynthetic capacity of the plant, overall. The changes in the ‘macroworld’ of the plant also take place during light acclimation manifesting in alterations in the leaf area, and so on. However, those occur on much smaller scale than the changes in the structure on the level of organelles.
Figure 3.1Origin and organization of the photosynthetic membrane of higher plants. (a) Spinach plants – a common model for mechanistic photosynthesis research. (b) Fluorescence confocal image of chloroplasts in the intact leaf showing clearly separated fluorescing dots – granae. Bar is 5µ m (courtesy of Tomasz Goral and Conrad Mullineaux). (c) Isolated chloroplasts in the incubation medium. Bar is 10µ m. (d) Electron micrograph of a single chloroplast showing dark elongated granae and large white starch granulae (centre). Bar is 1 mm. (e) Schematic presentation of thylakoid system structure of the chloroplast. (f) Electron micrograph of a single grana stack (centre). Bar is 200 nm. (g) Freeze-fracture electron micrograph of a single thylakoid membrane from grana showing photosystem II particles. Bar is 100 nm. (h) Freeze-fracture electron micrograph of grana thylakoid membranes displaying photosystem II as well as light harvesting complex particles (LHCII). Bar is 200 nm.(See Plate 3.1 in colour plate section.)
Another interesting feature of the efficiency in light interception by the leaf cell is that chloroplasts can move and adopt positions to maximize or indeed minimize light interception. The elements of structure such as cell walls and vacuoles scatter light effectively in the leaf so that it can propagate virtually in any direction reaching optimal numbers of chloroplasts and their thylakoids. Figure 3.2, left, displays even redistribution of chloroplasts in the spinach cell grown under low light environment. Figure 3.2, right, shows the effectiveness of oak leaves absorption of sunlight. The second layer of leaves shaded by the first layer still receives some light, whilst the third remains in very shaded environment. As it will be shown in a later chapter, filtration of light by leaves in diverse and stratified ecosystems alters significantly spectral quality of light available for plants that live under canopy of others and therefore demands and, indeed, results in development of important light adaptation strategies by the photosynthetic membrane.
Figure 3.2Scattering and absorption of light by oak leaves. Left: 1, 2 and 3 order of leaves facing light. Right: chlorophyll fluorescence confocal image of the leaf cell showing even redistribution of chloroplasts. Bar is 5 micrometers (Photo on the right is courtesy of Tomasz Goral and Conrad Mullineaux).(See Plate 3.2 in colour plate section.)
3.2 Composition of the Photosynthetic Membrane
3.2.1 Lipids
Lipids are essential components in the photosynthetic membrane. First, their amphipathic properties direct the self assembly process leading to the formation of biological membranes (see Chapter 2). Thylakoid lipids make up to 50% of a total membrane mass. Also, this figure depends on the plant growth conditions and the stage of chloroplast development and can often be rather smaller. Second, they are essential components of the membrane protein complexes, helping to shape protein structure and function (see the next section). There are four major classes of lipids present in the thylakoid membrane of plants. These include two classes of galactolipids, mono- and digalactosyldiacylglycerides (MGDG and DGDG, respectively). They are the major lipids in the thylakiod membrane, occurring at the ratio of MGDG to DGDG ~2 : 1 and constituting up to 75% of the total lipid content in spinach membranes. The remaining lipids of the thylakoid membrane are made up of phosphatidylglycerol and sulfolipids, occurring in approx. 2 : 1 ratio. Structure of all thylakoid membrane lipids is based upon glycerol, esterified by two fatty acids to carbons 1 and 2 (Figure 3.3
