Wednesday, May 22, 2013

Photosynthesis

The Evolution of Photosynthesis and How it Works

(This article can also be used as a follow-up to The Sun series - all about how the Sun works).

I just came back from a tour of four ecolodges in Costa Rica, my first experience being anywhere tropical, and my first introduction to an ecolodge. Around the world, forests and, perhaps surprisingly to some, oceans (phytoplankton) gather and turn sunlight into the kind of energy that supports almost every ecosystem on Earth, while regulating surface temperatures, cycling nutrients, especially nitrogen, providing a sink (storage) for carbon dioxide and supplying and maintaining oxygen in the atmosphere to breathe. Photosynthesis is absolutely essential to life on our planet. I dedicate this article to all the expertly trained natural guides and hosts I met in this jewel of a country which not only graciously invites travelers into their home - their ecosystem - but also reminds us that Costa Rica is our home too (as Canada is theirs). I may now be somewhere around 6000 km away once again but travel makes the world much smaller. Look for articles on ecoclodges and ecotourism to come in the future!

Introduction

All green plants use a process called photosynthesis to trap the Sun's energy and store it in a usable "container" - sugar bonds. For an easy introduction, click here. For a more detailed description, click on Wikipedia's page, here. Gardeners like myself know that we are simply guides; nature is dong the real work.

(various of my potted herbs from last year)
It is impossible to overstate the importance of photosynthesis. It evolved billions of years ago, changing Earth's atmosphere forever and establishing the foundation for almost every food web ever since. I've drawn a graph below of the timeline of Earth's oxygenation. The thin blue curved line traces the accumulation of oxygen gas in the atmosphere.


The vertical green line above marks the appearance of Earth's first photosynthetic machine, a tiny unicellular bacterium called cyanobacteria. These bacteria rapidly colonized ancient warm shallow waters, pumping oxygen gas into their environment. Nature's elegant invention for capturing and using the energy in sunlight hasn't changed very much since that time. In fact, as plant life evolved into more complex multicellular plans, it internalized these efficient little machines into sunlight-capturing organelles called chloroplasts. Almost every contemporary form of life on Earth relies on these tiny natural energy factories.

We exist because of photosynthesis. We eat the animals that ultimately get their energy from green plants and green algae and we eat the plants too. All of the energy our bodies need to reproduce, grow and live our lives can be traced back to photosynthesizing cells, and ultimately to the Sun itself. If you look at a food web, such as the one shown below, you will see that only plants, green algae and cyanobacteria (all of which are called producers or photoautotrophs in food webs) can directly use the Sun's energy. Trace the three black lines back to the Sun.

Thompsma;Wikipedia
There are a few exceptions to this rule. A few producers are not plants, green algae or cyanobacteria. These producers are called chemoautotrophs. These organisms, most of which are bacteria or archaea, obtain their energy from inorganic sources such as hydrogen sulfide, sulfur, iron and ammonia, rather than from the Sun. Like phytoautotrophs, chemoautotrophs form the basis of food webs, many of which exist deep in the ocean around thermal vents. Here, tube worms as well as species of clams and shrimp thrive without sunlight by consuming the bacteria. It's possible that phytoautotrophs evolved from an ancient chemoautotroph ancestor.

Photosynthesis = Energy

Photosynthesis is designed to harness energy. Energy is a word saddled with controversy these days. We need more and more energy to support and fuel our modern lifestyles and we are using up non-renewable energy resources in the process. Almost all climatologists now agree that our atmosphere is being permanently altered by the production and consumption of nonrenewable resources. These are energy sources like oil, coal and natural gas. Our current rate of energy consumption is unsustainable over the long term.

Have you considered that every nonrenewable energy source (nuclear energy is an exception) ultimately traces back to sunlight? Oil, gas and coal are made of energy-rich hydrocarbon bonds that began as living plants millions of years ago. Trees, plants, phytoplankton and zooplankton died over time, building up thick layers of detritus such as peat. Anaerobic bacteria present in the peat slowly digested the plant material and in time, sand, rock and clay covered these peat layers. Deep underground, pressure and heat chemically converted what was once cellulose, starches and sugars into hydrocarbons such as coal, oil and natural gas. What if we could find a way to get our energy directly from the Sun rather than through pollution-creating indirect sources? Are we ready to reverse engineer the brilliant energy-capturing machinery of plants?

Plants Create Useful High-Energy Molecules

To answer these questions, we must first explore how photosynthesis works. It is a sophisticated method to take abundant sustainable sunlight and turn it into a form that the plants and the organisms that eat them can use. Plant sugars, like related but more complex and carbon-rich hydrocarbons, store energy in chemical bonds. Breaking hydrocarbon bonds releases energy. This reaction is called combustion and it drives engines, generators, power plants, furnaces, etc. The general combustion reaction can be written like this:

CnH2n+2 + (3n+1)/2O2 → (n+1)H2O + nCO2 + Energy

Our bodies also act like engines, except that we accomplish the same goal in two steps rather than one and it is carried out in a much more controlled way. We split apart carbohydrates and starches in the plants we eat, including grains, seeds, roots, leaves, flowers and nuts, using a reaction called hydrolysis. To carry out hydrolysis, our digestive system uses special proteins called enzymes to cleave the bonds into simple sugars such as glucose, which our cells can take in and use directly. Inside our cells, the glucose is "burned" using oxygen, into water and carbon dioxide, releasing useful energy in the process. This cell reaction is called cellular respiration and it works much like combustion, except that rather than using a high temperature to trigger the reaction all at once, our cells use various enzymes to get the reaction to proceed over various steps at a much more controlled rate.

Enzymes act as catalysts in biological reactions. They lower the activation energy of reactions. Many reactions, while thermodynamically favourable (the products have less potential energy then the reactants), don't happen because the activation energy barrier must be overcome in order to start them off. Think of how you must strike a match in order to get the flame. You are adding energy in the form of friction (heat) so that you can overcome the potential energy barrier of the combustion reaction. Inside cells, such barriers are overcome by the action of enzymes, so that they may then proceed spontaneously. Unlike the friction example, enzymes don't add energy to the reaction. Instead, they lower the energy barrier itself.

The concept of a series of chemical reactions that are activated and rate-controlled by enzymes can be carried over from the release of plant energy (as fuel in engines and in our cells) to the creation of plant energy (photosynthesis).

The Story of Photosynthesis Begins with Cyanobacteria

Nature's first "leaf" prototype evolved more than 3.5 billion years ago, in an environment that would not seem conducive to life at all. This was the Archean period. Earth then might have looked like the NASA artist's concept below.


The planet was still releasing tremendous internal heat left over from its formation, resulting in extreme volcanic activity, as meteorites pummeled the surface. There was no oxygen to breathe. Instead the atmosphere consisted of a toxic blend of methane, ammonia, carbon dioxide and other gases. Wave ripple marks on ancient stone in Australia indicate there was also liquid water present and chemical analysis of this stone suggests that the water was warm, somewhere between 26°C and 35°C. The young Sun at this time was only about 70% as bright as it is today. It shouldn't have had enough energy to keep surface water liquid, let alone warm (despite young Earth's great release of internal heat). This startling finding is called the faint young Sun paradox. Some experts believe that the high concentration of greenhouse gases (such as methane and carbon dioxide) may have helped to keep radiant solar energy in, but the paradox is far from being solved. The preceding link lists alternative hypotheses as well.

Despite the violence and chaos of the Archean era, Earth had all it needed to allow photosynthesis to make its grand entrance - warm water, organic nutrients and sunlight, and this incredible evolutionary breakthrough came in the form of an unassuming microscopic blue-green alga called cyanobacteria. Below is a microscopic view of a genus of cyanobacteria called Tolypothrix. Long (colonial) threads of rectangular bacterial cells coated in a protective gelatinous sheath are visible. This genus thrives on aquatic pants and stones and survives occasional dry periods outside the water.

Matthew Parker;Wikipedia
Many types of cyanobacteria have changed very little since they first evolved, and yet they remain abundant and can be found in almost every ecosystem. They are the most successful organisms on Earth. When these simple unicellular organisms first appeared, they formed extensive colonies in shallow water. Among these colonies were large rocklike structures called stromatolites, composed of sand cemented together by biofilms of cyanobacteria. The cyanobacteria protected themselves from deadly ultraviolet radiation (the protective ozone layer did not exist them) by secreting a thick gel. They also secreted calcium carbonate. These two secretions together with sand created cement-like dome structures that ranged from small delicate fingers to domes several meters high and wide. Their size depended on their age, as it can take a stomatolite 100 years just to grow 5 cm. Stromatolites still live in some parts of world such as Shark Bay in Australia, shown below.

Paul Harrision;Wikipedia
Cyanobacteria are ubiquitous and tenacious. These simple organisms have survived massive atmospheric changes, meteorites, volcanoes, periods of hot temperatures and stretches lasting millions of years in which Earth was covered in ice and snow. You can find cyanobacteria living as individual organisms or in colonies that form filaments, sheets or even hollow balls. Some colonies are able to differentiate into different cell types, which include tough-walled climate-resistant spores.

Cyanobacteria In Sponges and Lichens

They inhabit almost every terrestrial and aquatic ecosystem, and some even live inside other organisms as endosymbionts, inside lichens and sponges for example, where they provide energy for the host. One example of endosymbiosis is the freshwater sponge shown below, called Spongilla lacustris. The particular sponge below was found in Washington State. You can even find this sponge growing in waterways here in Alberta.

Kirt L. Onthank;Wikipedia
Sponges such as these turn vivid green in sunlit waters thanks to millions of both green algae and cyanobacteria living within their tissues as endosymbionts.

Many endosymbionts are obligate, which means that either the host or the endosymbiont cannot live without the other. While most sponges can live without their green guests by filtering nutrients from the water, other organisms, such as many lichen species, are obligate. Lichens are composite organisms made up of a fungus and a photosynthesizing partner, either green algae or cyanobacteria. While the cyanobacteria and algae appear to be able to live independently, many lichen-forming fungi cannot. Their partnership with algae or cyanobacteria allows them to thrive in some of the harshest environments on Earth, such as frozen arctic tundra and hot dry desserts. They thrive on leaves and branches in rain forests as well as on gravestones. Below, familiar orange lichens colonize a stone wall.

Roantrum;Wikipedia
Although most evidence suggests that many different lichens evolved independently from each other, fossilized lichens date back at least 400 million years, meaning that they were some of the first photosynthetic land colonizers. Cyanobacteria even live in sloth fur, helping to camouflage the animals in their tree canopy habitat. A Costa Rican two-toed sloth is shown below right. If you look closely you can see a green tinge to its back fur. I wasn't lucky enough to see one of these gentle animals myself but luckily a Wikipedia user got a great photo.

Leyo;Wikipedia
Cyanobacteria Oxygenated Earth

Cyanobacteria multiplied into such great colonies that they singlehandedly oxygenated Earth's atmosphere, setting the stage for cellular aerobic respiration, an evolutionary milestone of tremendous importance. Many ancient bacteria living alongside cyanobacteria died because for them oxygen was poisonous. This set off one of Earth's most significant extinction events. They are called anaerobic (meaning no oxygen) bacteria. Many anaerobic bacteria still thrive in various oxygen-poor environments such as inside our intestines, where they make vitamins for us and ferment undigested carbohydrates into energy-rich fatty acids. They all carry out respiration without using oxygen.

Eventually, unicellular bacteria evolved that could not only tolerate oxygen but they could harness its chemical bond energy as well and these are called aerobic bacteria. The process of harnessing oxygen's energy is called aerobic respiration. It marks an enormous breakthrough in evolution. All organisms that breathe or use gills or absorb oxygen through their skin evolved long ago from aerobic bacteria.

Meanwhile, cyanobacteria, though primitive and simple, are still going strong on Earth, continuing to contribute significant oxygen to the atmosphere. In fact, some studies have them accounting for about a third of all photosynthetic activity, and more than half of the photosynthesis in the oceans today. The total rate of solar energy converted into chemical energy by cyanobacteria is calculated to be around 450 TW. TW is a trillion watts (joules/second). To put this number into perspective, the entire world consumed 15 TW of electrical energy in 2008, just 1/30th of the chemical energy that was stored in Earth's cyanobacteria.

Evolution Boosts ATP (Energy) Production

Every organism, plant or animal, needs energy, whether it is sunlight or ingested as food. The cells themselves, however, cannot directly utilize sunlight or food. They must use a specific kind of chemical energy to carry out their functions. Adenosine triphosphate, or ATP, evolved as the universal cell energy molecule. Plant cells, animal cells and even bacteria use it. To create ATP, organisms use cellular respiration. Anaerobes strip electrons off of iron, hydrogen sulfide, or other compounds and use that bond energy to create ATP through a series of reactions called anaerobic respiration. When oxygen flooded the atmosphere, cells evolved that could make use of its energy and greatly enhance their ATP production. The evolution of aerobic respiration afforded life much more energy to work with.

By this time, unicellular organisms were diversifying into different niches and they interacted with each other as they did so. Some organisms engulfed other organisms and instead of digesting them, they took advantage of new assets that came along with their internal guests. A modern example of this kind of symbiotic relationship is a type of coral called stony coral. These corals are considered by many biologists to be living fossils. Based on fossil evidence, their body plan has not changed since the Cambrian period, half a billion years ago. They live in nutrient-poor clear waters, building skeletons of calcium carbonate sequestered from the water. Coral is a colony of individual multicellular organisms called polyps (http://en.wikipedia.org/wiki/Polyp), which are related to jellyfish. Below left, polyps of the stony coral, Favites flexuosa, are extending their tentacles in the evening to feed.

Nick Hobgood;wikiped
Polyps use stinging tentacles to capture fish larvae and zooplankton and then digest their food in a primitive tube-like gut, but this is not enough to sustain these corals. They also harbor unicellular green algae within their tissues, which supply the high-energy products of photosynthesis to their host, while enjoying protection within their limestone fortress.

Green algae are considered to be the ancestors of all multicellular green plants. They all contain chloroplasts. Biologists can trace living examples of these organisms from simple unicellular organisms to macroscopic seaweeds to special pondweeds (Charales), shown below right, which are fresh water algae that demonstrate the tissue differentiation you see in higher plants. Higher plants include mosses, ferns, flowering plants and conifers. They all contain cell walls that contain cellulose, and this sets them apart from green algae.

Christian Fischer;Wikipedia

The algae in stony corals are particular about their temperature and sunlight needs. If the water gets too warm, too shallow or too deep, the algae will either depart the host polyps or die, leaving the coral bleached. Coral can survive only temporarily in this bleached state before the polyps also die. By sequestering energy into a nutrient-poor environment, these endosymbiotic algae are sometimes called the rain forests of the sea. They form the foundation for incredibly productive reef ecosystems around the world.

These coral algae, called Zooxanthellae, are all photosynthetic but many types also contain pigments of different colours in addition to green. The coral polyps themselves also produce a variety of protein-based pigments. This is why stony coral reefs are so amazingly colourful. A New Guinea reef is shown below.

Brocken Inaglory;Wikipedia
Chloroplasts, mitochondria and other cell organelles likely evolved in a similar kind of symbiotic way, offering energy to their hosts while receiving a protective home. Cyanobacteria are considered to be the ancestors of chloroplasts inside plant cells. The endosymbiosis of cyanobacteria probably took place somewhere between 600 and 1600 million years ago.

By playing host to other smaller cells with specific attributes, cells could grow in complexity and efficiency. Both modern chloroplasts (in plant cells) and mitochondria (in both plant and animal cells) function as ATP factories, greatly boosting energy production. A typical plant cell is shown below. Notice all the organelles it contains, including a nucleus, mitochondrion and chloroplast. Each organelle, like a division in a company, supplies its own unique product or service to the cell.

LadyofHats;Wikipedia
A real cell, such as the moss cells shown below left, may contain many chloroplasts and mitochondria; the amount of which usually depends on the cell's role. Here, dozens of green chloroplasts are visible inside each moss cell.

Kristian Peters;Wikipedia
Plants Cells are Eukaryotic Cells

Plant cells not only undergo photosynthesis, but they also respire, using oxygen to break down sugars into carbon dioxide and water, releasing energy in a process that is, in many ways, opposite to photosynthesis. However, like photosynthesis, the reactions used are redox, or reduction-oxygenation, reactions. We will explore how these biologically important reactions work later on. The redox reactions take place through an electron transport chain located on an inner membrane within the cell. This means that, during these reactions, electrons are transferred from one molecule to another down a line of molecules, and this too will be explored in more detail later on.

Inside the mitochondrion, the inner membranes where cell respiration reactions take place are called the cristae, and they are quite similar to the inner membrane inside chloroplasts, called the thylakoid membrane. We will explore redox reactions, thylakoid membranes and energy shortly. These more complex cells, containing organelles and a membrane-bound nucleus, are called eukaryotes. Every multicellular organism, from bees, to mushrooms, carrot plants, and bison evolved from eukaryotes.

The Origin of Plant Photosynthetic Machinery

As we've learned, photoautotrophs, such as cyanobacteria, green algae and green plants, convert solar energy into chemical energy through a process called photosynthesis. Most of us have seen a simple diagram of it like the one shown below right.
At09kg;Wikipedia

It's a good starting point, but to really appreciate the beauty of photosynthesis we need to dig deep into the details of what is going on. The redox reactions I just mentioned portray an incredible elegance that is worth understanding. So, how do plants make sugars, carbohydrates and cellulose? You can't just bubble carbon dioxide through a beaker of water and come out with sugars and oxygen gas. The reaction, by itself, will not happen on its own. Cyanobacteria developed an ingenious method to drive this reaction by using the energy of sunlight as the driver.

To undergo photosynthesis, special proteins embedded in the cell membrane of cyanobacteria gather light. To maximize sunlight absorption, the membrane is tightly folded inward into sheets called thylakoids, shown in the diagram of a cyanobacterium below.

Kelvinsong;Wikipedia
Notice that this cyanobacterium contains DNA but no membrane-bound nucleus to house it in. The lack of a membrane-bound nucleus defines cyanobacteria as a prokaryote. Bacteria and Archaea are prokaryotes. (Archaea used to be classified as bacteria but research shows they have a unique evolutionary path and unique biochemistry that sets them apart)

Prokaryotes are simpler smaller cells than eukaryotic cells and we can call them more primitive as well because there is good evidence that eukaryotes evolved from prokaryote ancestors. Despite, or perhaps because of, their primitive simplicity, prokaryotes are extremely successful organisms. Right now, for example, your body contains at least ten times more prokaryotic cells than eukaryotic cells. Our bodies are biomes for these tiny organisms, and many of them are essential. Most of these organisms (especially Archaea) also live in extreme environments where eukaryotes can't.

The evolution of plants marks a trade-off. While plants do not generally have the adaptability of cyanobacteria to extreme environmental changes, their complex cells, brimming with mitochondria and chloroplasts, maximize the energy they receive from sunlight.

In plants, photosynthesis takes place in specialized organelles called chloroplasts. A plant cell will have anywhere between 10 and 100 of these organelles within it. Inside each chloroplast, thylakoids are stacked like flattened disks within the fluid (called stroma). The membranes of the thylakoid disks are where complexes of light-capturing proteins are located. The diagram below shows how a typical chloroplast is arranged.

SuperManu; Wikipedia
We won't worry about all the labels here, but if you'd like a guide to them, click here. Notice some similarity between a cyanobacterium and this chloroplast, and that is because the chloroplast very likely evolved from a cyanobacterium. The first organisms to contain chloroplasts were probably green algae, mentioned earlier. Green algae are a large group of unicellular and colonial organisms, most of which are microscopic but some, such as seaweeds, grow very large. Chloroplasts in green algae are bound by double membranes in contrast to the single-membrane chloroplasts found in higher plants, suggesting that these more primitive organisms retain a vestige of the endosymbiosis of a cyanobacterium.

Sunlight-Capturing Equipment

The process of aerobic photosynthesis in all photoautotrophs is carried out by coupling two systems, called photosystem II and photosystem I. Under anaerobic conditions (no oxygen), cyanobacteria can switch to just photosystem I and use hydrogen sulfide or other molecules as electron donors, rather than water. In addition, most cyanobacteria can even make energy in the dark without oxygen by reducing sulfur. They pull this off by resorting to components of the respiratory electron transport chain, rather than using the photosynthesis electron transport system. We will explore what photosystems are in a moment

The ability to adapt to various conditions by using different types of photosynthesis, or even none at all, has made cyanobacteria very successful. Under aerobic (oxygen) conditions, they can reduce both carbon dioxide and nitrogen by oxidizing water molecules. This makes them great nitrogen fixers to the benefit of all higher plants, which need nitrogen in a usable form to grow. In chemistry, "oxidize" means to lose an electron, while "reduce" means to gain an electron. These words stem from an outdated understanding of these reactions, which together are called redox reactions, where chemists thought that oxygen is always involved. In this case, water is split and the oxygen loses an electron. In other words, it is an electron donor. You will see how important an electron donor is to photosynthesis soon.

While cyanobacteria's photosynthetic machinery is located on the inner folds of the cell membrane only (the thylakoid sheets), both the thylakoid sheets and the outer membrane house anaerobic respiration machinery.

Sun-Capturing Pigments

Photoautotrophs use a variety of protein complexes to capture light. Cyanobacteria use a protein complex called phycocyanin, which contains a bluish pigment and it gives the cells their blue-green colour. Phycocyanin complexes are embedded in the thylakoid sheets, which are formed by folding the cell's outer membrane inward.

The thylakoid membrane in cyanobacteria contains light-harvesting antennae called phycobilisomes. Below, a model shows how these antennae are organized.
User:Vojtek.dostal;Wikipedia

The antenna core is made of a protein called allophycocyanin and the rods are stacked disks of the pigment-protein complexes called phycocyanin that I mentioned earlier. These pigment-protein complexes absorb visible sunlight and then they transfer the light energy to chlorophyll, a green pigment that is essential to photosynthesis. Chlorophyll also absorbs light energy just as the phycocyanin pigments do, but it absorbs it in a different part of the visible sunlight spectrum. The primary chlorophyll pigment, chlorophyll-a, absorbs photons of light between 650 and 700 nm. Cyanobacteria's phycocyanin pigments absorb light in the 500-650 nm range. This helps cyanobacteria utilize more of the sunlight spectrum because longer wavelengths don't tend to penetrate the water column where many of these bacteria exist (and where they likely first evolved).

The phycobilisome antennae arrangement is amazingly efficient, boasting a 95% efficiency of energy transfer. The two photosystems that cyanobacteria use each consist of a phycobilisome antennae arrangement as well as another protein-pigment complex called a reaction centre. Chlorophyll acts as part of the reaction centre at the heart of the photosystem. Both the reaction centre and the light-harvesting complexes (the phycobilisome antennae) are membrane protein complexes. Light energy is directly absorbed at two places - by chlorophyll and by phycocyanin - where the energy is then passed to the chlorophyll-containing reaction centre.

The antennae and the reaction center capture light energy through a series of electron and proton transfers. These transfers take place through oxidation-reduction (redox) reactions, which ultimately end at an electron acceptor molecule. Chloroplasts and cyanobacteria have two types of reaction centres. One absorbs light at 680 nm and the other absorbs light at 700 nm. Both of them work together in a complementary fashion to extract electrons from water and create oxygen as a byproduct.

Besides cyanobacteria and chloroplasts, there is a third kind of photosynthesis. Certain bacteria, such as purple bacteria, use a different kind of photosystem called a bacterial reaction centre. These bacteria are found in hot springs and in stagnant water where they carry out photosynthesis, but instead of producing oxygen, they produce sulfur as a byproduct.

Chloroplasts and cyanobacteria use photosystem I as well as photosystem II to capture light energy. The diagram below shows how each system is arranged across the thylakoid membrane. This looks fairly complicated but notice that both PS I and PS II (the two green coloured complexes) absorb light energy. Notice also that there is a redox reaction chain (blue doted line) from PS I to PS II that functionally connects them.
Tameeria;en.wikipedia
You will see also that no phycobilisome antennae are present associated with the chloroplast membrane. In cyanobacteria, these structures would be attached to the PS I and PS II reaction centres, shown above. The existence to these additional light-absorbing structures increases the efficiency of light absorption in cyanobacteria. The diagram above is specific to chloroplasts. In chloroplasts (inside green plants and green algae), part of the chlorophyll P680 and P700 reaction centers act as internal antennae instead. Each chloroplast reaction centre contains a pair of chlorophyll-a molecules (this pair together is called P680) and sometimes it also contains an accessory chlorophyll, called chlorophyll-b, as well (chlorophyll-b is yellow and it absorbs blue light). In plants, chlorophyll molecules transfer resonant energy in the internal antennae complex to the reaction centre where one of two other specific chlorophylls - called P680 and P700 (same names) - are found.

Photosystem II is the first protein complex in these light reactions (I was named "I" because it was discovered first). Below is a computer model of what this complex looks like. Chlorophyll-a is the green net-like embedded structure that makes up part of the internal antenna complex of the reaction complex. Again, this is what PS II looks like in a chloroplast, not cyanobacteria.

Neveu,Curtis (CS1004);Wikipedia
Photosystems look extremely complicated but they are simply designed to carry out one important function, and that is to act as an enzyme. Photosystems, like all enzymes, are highly selective catalysts that accelerate the rate of the redox reactions by lowering their activation energy. I will explain what this means in a moment.

Cyanobacteria capture photons through chlorophyll and the phycobilisome antennae. The photons excite electrons in the photosystem. The excitation state is transferred through a series of coenzymes (enzyme helpers) and cofactors (inorganic molecules that increase the reaction rate) to ultimately reduce a molecule called plastoquinone to plastoquinol. Along the way, excited electrons oxidize water into hydrogen (H+) ions and oxygen molecules, supplying the electrons that will reduce plastoquinone to plastoquinol. Plastoquinol is then used to reduce important molecules called NADP+  to NADPH. Meanwhile, the protons (H+) released create a proton gradient that is used by the enzyme ATP synthase to create ATP, the energy molecule of the cell. In the thylakoid membrane diagram above, ATP synthase is the large orange structure on the right. ATP is the single most important energy-carrying unit in any living cell.

The system, though complex, is a beautifully elegant method to take sunlight energy and store it in chemical bonds in a thermodynamically favourable (and spontaneous thanks to the enzymes, etc.) way. Each photosystem II unit, for example, contains at least 99 cofactors, 35 chlorophyll molecules, and various other accessory molecules, all to do one job - get visible photon energy into a molecule where it can be used to do work.

The trick is to find a way to take lower energy molecules and make higher energy ones out of them in a way that is, overall, energetically favourable. Oxygen evolution, the process of splitting water into oxygen molecules and providing both electrons and protons to drive photosynthesis, is the most important life-dependent reaction on Earth, even though most people have never heard of it and it is still not completely understood even by experts. Enzymes, coenzymes and cofactors of the photosystem complex not only lower the activation energy of various reactions so that they can proceed spontaneously but they also couple some reactions together so that thermodynamically unfavourable reactions will take place because they are coupled to (higher-energy) favourable reactions. In this way, the overall energy of the system decreases and useful work can be done at the same time, such as creating ATP and NADPH, which are both high-energy molecules. These are the cell's energy currency, and they can be used to both drive cell functions as well as reactions that allow the cell to create longer-term energy storage units called sugars, starches (such as cellulose) and carbohydrates. We will look at these ATP/NADPH reactions in a moment.

Photosystem I follows photosystem II. A computer model of the protein complex of photosystem I is shown below.
Curtis Neveu;Wikipedia
As you can see, this system, which is also present in all phytoautotrophs, is complex. It uses many of the same proteins as photosystem II does, with a slightly different version of antennae structure, reaction center, intermediate redox carriers and a reducing molecule (electron acceptor). Cyanobacteria and green plants both use photosystem I and II, but cyanobacteria use slightly different versions of the various proteins used.

ATP and NADPH: Two Very Important Molecules for Life

Cyanobacteria are bacteria after all, not plants per se, so they make ATP by oxidative phosphorylation, the same way other bacteria do. As I mentioned earlier, other bacteria besides cyanobacteria carry out photosynthesis, purple bacteria and green sulfur bacteria for example, but only cyanobacteria create oxygen as a result of the process, like plants do.

You often see the photosynthesis reaction shown as it is below.
There is nothing inaccurate about this reaction but it is a simplification used to show a balanced chemical equation. A generic 6-ring sugar is used to show that the reaction balances, but what actually happens is a complex cascade of interconnected reaction cycles. Now that we have an idea of how the light-dependent reactions work for phytoautotrophs, we can write a more complex reaction, shown below (Pi stands for inorganic phosphate).

2 H2O + 2 NADP+ + 3 ADP + 3 Pi + light → 2 NADPH + 2 H+ + 3 ATP + O2

Instead of a generic sugar product we have two energy-rich molecules - NADPH and ATP. We can combine the two photosystems, PS I and PS II, into one single scheme called the Z-scheme, shown below.

Remember the blue dotted line connecting PS II with PS I in the previous thylakoid membrane diagram? That is the Z-scheme. It shows the non-cyclic electron flow between the two systems. What's most important here is that you end up with two molecules, NADPH and ATP, that have more potential bond energy than the molecule you start with, water. The Z-scheme shown above is for green algae and green plants. The molecules differ slightly for cyanobacteria but the general scheme is the same.

Notice too that we have not yet talked about how carbon dioxide contributes carbon to create sugars (see CO2 and C6H12O6 in the generic photosynthesis reaction above). Now we are ready to explore light-independent reactions. These are collectively called the Calvin cycle. The generic reaction above (the one in the coloured boxes) is actually a combination of both light-dependent and light-independent reactions in plants.

The Calvin Cycle

An enzyme called RuBisCO in plants captures CO2 from the atmosphere and ultimately releases 3-carbon sugars, called triose phosphate or G3P, shown below at the bottom of the Calvin cycle.

Mike Jones, Wikipedia
Again, it looks complex and it is, but generally this is what happens: CO2 combines with a 5-carbon sugar (ribose 1,5-biphosphate or RuBP) to ultimately make two G3P molecules. Most of the G3P made gets recycled to make new RuBP, but one out of every six of G3P made condenses into a hexose phosphate. This is a 6-ring proto-sugar that can then be reduced into sucrose, for example, as well as starches and cellulose. The sucrose can be used as fuel for cellular respiration. The molecular diagram of sucrose is shown below. It is a dimer made of a six-ring sugar called glucose (left) and a five-ring sugar, called fructose (right).


Plant cells use the same reactions for their cellular respiration as animal cells do, but animals get their sugars from eating and breaking down the carbohydrates in plants, while plants make their own. Sucrose (or glucose, a single sugar unit) can also be fed into other metabolic reactions that make new amino acids (to make proteins) and lipids for the plant as well as starches and cellulose that are used as plant building blocks.

Notice in the Calvin cycle diagram above how much ATP and NADPH go into the cycle. Cleaving a phosphate group from ATP creates ADP. Free energy (about 11 kcal/mol) is released to the cell when this anhydride bond is broken. ADP is then re-phosphorylated in the light-dependent reactions we explored earlier. NADPH is a coenzyme and a reducing agent. It powers the biosynthetic reactions in the Calvin cycle that take carbon dioxide from the air and fix that carbon into sugars, carbohydrates and cellulose in plant cells. Like ADP, NADP+ is then "recharged" in the light-dependent reactions.

For the light-independent reaction in plants, we can now write the following equation.

3 CO2 + 9 ATP + 6 NADPH + 6 H+ → C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O

The high-energy molecules created in the light-dependent reactions are now fueling the light-independent reactions. These molecules ultimately fuel all the metabolic processes the plant needs in order to grow, live and reproduce. And, because almost all other organisms consume plants or those that eat plants, these reactions - the process of photosynthesis - fuel almost all life on Earth. This is how we are all connected to the Sun's energy.

Now that we have a general idea of how cyanobacteria and later on how all plants evolved to take advantage of the Sun's ample energy, let's dig even deeper and investigate exactly how pigments capture the energy, because this is really where all the magic happens. Remember that in cyanobacteria, the light harvesting antennae (called phycobilisomes) capture photon energy and the pigment, chlorophyll, in the reaction center transfers it in addition to capturing more energy as well. From here on we are going to focus on green plants. The light-capture system in green plants is more widely studied than that in cyanobacteria so we will look at how light capture works inside chloroplasts.

Light-capturing pigments, such as chlorophyll, act as chromophores. Chromophores are atoms or molecules that give a molecule or complex of molecules a specific colour by reflecting (and absorbing) visible light of particular wavelengths. Plants actually have several different kinds of pigments but we will focus on chlorophyll here. A chromophore absorbs certain wavelengths of visible light and reflects others. In order to do this, there must be a part of the chromophore molecule where there is a difference in energy between two molecular orbitals that exactly matches a wavelength in the visible spectrum. This is how it works: A photon of visible light strikes the chromophore and excites an electron in one of its atoms from ground state to an excited state. This affects the energy of one or more chemical bonds in the molecule. A chemical bond is a molecular orbital. A bond between two atoms forms by sharing two atomic (electron) orbitals of those atoms. The atoms form hybrid orbitals (shared between the two electrons) in order to make the bond possible, and this hybrid bond is called a molecular orbital. It will have a specific energy that falls between that of the two original atomic orbitals. To learn more about how molecular bonds and bond hybridization works, check out Atoms Part 4C. When an electron is excited, this increases the energy of the molecular orbital, the chemical bond.

Chlorophyll, for example, contains a resonant carbon ring structure that surrounds a central magnesium atom. The resonant ring, called a chlorin ring, is a very stable structure held together by hybrid bonds, which are hybrids between double and single molecular bonds. These special bonds can absorb the exact energy of particular visible photons. This means that certain wavelengths of sunlight are absorbed and converted into a slightly higher resonant energy in the molecule's hybrid bond ring. There are two main kinds of chlorophyll in green plants - chlorophyll-a (left) and chlorophyll-b (right) - shown below. Their different functional groups are circled in red.


The long hydrocarbon tail anchors the chlorophyll molecule to the thylakoid membrane of the chloroplast inside the plant cell. The two chlorophyll types differ only by a side chain group but this small difference allows them to absorb different wavelengths of sunlight.

In the electromagnetic spectrum, visible sunlight spans between about 400 and 700 nm, as shown below.
Philip Ronan;Wikipedia
Neither of the two chlorophyll molecules absorb light well between 500 and 600 nm. Sunlight of these wavelengths is reflected instead, and that is why plants look green. See the two absorption spectra below right (chlorofil is Polish for chlorophyll).

Mix321;Wikipedia
Once light energy is captured by a chlorophyll molecule, the energy, now in the form of chemical resonance energy, is easily transferred from one molecule to the next (in the chorin rings) until it reaches a chlorophyll molecule in the reaction center. This transfer process is called Förster resonance energy transfer. In order for this process to work efficiently, the donor and acceptor molecules must be right next to each other. Normally, an excited electron emits a photon as it returns to its ground state. Here, the radius of the interaction is much smaller than the wavelength of light that would be emitted. Instead, the excited chromophore emits a virtual photon that is immediately absorbed by the receiving chromophore, exciting it in turn, and in this way energy is transferred from one chromophore to the next. This is a quantum electromagnetic effect that operates in a way similar to how near fields work (as in radio antennae):

According to Maxwell's equations for electromagnetism, an electromagnetic (EM) field)) (a radio signal, or visible light for example) decays away from the source at a rate of 1/r with r being the distance from the source. That's how a far field works. But for a near field, which means you are much closer to the source, closer than one single wavelength of the EM radiation, the rate of decay works differently, 1/r2 and even 1/r3 if you are very close to the source. And the near field is carried by virtual photons (as in how magnetism is "carried") while the far field is carried by real photons (the radio signal). You can get a near-field-like energy transfer using virtual photons between two molecules that are very close, closer than the wavelength of the light that was absorbed, and this is how the chromosphores exchange energy.

Energy now reaches the special chlorophyll molecule in the reaction center. These chlorophyll molecules are special excitonic dimers. This means they act as one single unit.  They are excited as one big molecule either by the input of resonance energy from other chlorophyll molecules, which we just explored, or directly from a photon striking them. Now, in the reaction center, excitation energy and resonance energy is transferred to redox energy. The first electron carrier molecule in the electron transfer pathway is oxidized, and that molecule is either pheophytin for photosystem II or an iron-sulfur protein cluster for photosystem I. These are the primary electron donors for the electron transport chain to follow. The molecules pass electrons to start a series of redox reactions where electrons are donated and accepted across the thylakoid membrane. This sets off a proton gradient across the membrane. This proton gradient stores the energy that fuels the synthesis of ATP and NADPH.

Electron transport chains form the foundation of all living systems. They are the basis for all kinds of metabolic functions in plant cells, animal cells and in bacteria. They carry out a series of redox reactions (electron donation and acceptance) that build up gradients across membranes. The difference in potential energy between the reactants and the products is what ultimately drives every electron transport chain, and the resulting gradient, when released (for example, when a proton is allowed to travel back across the membrane) does work for the cell. The gradient energy can enable mechanical work to be done (such as rotate a flagellum for example) or it can it create chemical energy (such as making ATP).

This basic energy system as well as the energy molecule, ATP, is found across all known life forms. Perhaps it will come as no surprise to you that ATP synthase, the enzyme used to synthesize ATP is one of the most highly conserved molecules of life. This means that the DNA coding for it is the same in us as it is in all other animals, plants and even bacteria. Nature knows when to hold on to a good thing.

Photosynthesis is one of Nature's grandest designs. I think it is well worth the effort to really look into how it works and how it developed over time. Its evolution set the tone for all life on Earth to follow. We are all children of light capture technology.

Now, could we build a photosynthesis-like mechanism to harness the Sun's energy for our energy needs? Could we build an artificial leaf? Look for an article exploring this possibility, to come.

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