How does photosynthesis work? (part 3): Photorespiration, C4 and CAM

So the final installment of this thread of posts is about one of the big problems of C3 photosynthesis, and also how alternative methods of photosynthesis help plants overcome this problem.

As previously mentioned, the enzyme responsible for the whole shebang is Rubisco - it captures CO2 in the first place, and allows the chloroplasts to do their thing. The problem with this system is that Rubisco also has an affinity to Oxygen (particularly at higher temperatures or low CO2 levels), meaning when the temperature of a leaf increases less photosynthesis is achieved. The process of Rubisco fixing O2, rather than CO2, is called photorespiration and can slow plant growth by reducing the rate of photosynthesis by a significant amount.

Photorespiration is a particular problem in the tropics, as the temperature is usually high (and this also causes problems with waterloss). This has lead to the evolution of a different form of photosynthesis, that allows the plant to separate the absorption of CO2 either temporally or spatially, hence reducing photorespiration by limiting Rubisco's access to O2.

The first alternative to C3 photosynthesis is called C4. This is because it involves the CO2 being fixed into a 4-Carbon sugar at the first stage. For the initial absorption of CO2, C4 plants use a different enzyme called PEP Carboxylase. This then delivers the CO2 to the photosynthetic part of the leaf by the 4-C sugar breaking down and releasing the CO2 directly to the Rubisco.
The whole process works well because C4 plants have a slightly different leaf anatomy to C3 - they have specialised cells that surround the veins in the leaves, called bundle-sheath cells (this is known as Kranz anatomy). These are packed with chloroplasts, and photosynthesis takes place here rather than in the mesophyll. So by spatially separating the initial capture of CO2 and the Rubisco, photorespiration is significantly reduced. However this form of photosynthesis is also more energetically costly, requiring more ATP than C3. This means it is less efficient that C3, and only occurs in areas where the benefit of reducing photoresipration and waterloss outweigh the larger energy cost, such as the tropics and some arid zones.

The second alternative to C3 photosynthesis is CAM photosynthesis. CAM photosynthesis (Crassulacean Acid Metabolism photosynthesis) was named after the family of plants in which it was first discovered, Crassulaceae (a family of succulents). It tends to occur in arid plants, like cacti, and works by separating the CO2 capture and photosynthesis temporally. This again reduces photorspiration, however perhaps more substantially reduces waterloss. It works in two stages, at night when it is cooler and waterloss is less severe, the plant opens its stomata. It stores the captured CO2 as a 4-Carbon acid, Malate, and then breaks this down back to CO2 during the day to feed back to the Rubisco so photosynthesis can occur. This allows the plant to keep its stomata closed during the day, when it is hot and dry, helping it avoid waterloss and photorespiration.
I also have a healthy admiration for CAM plants, as they can also use this system to do what other plants cannot. During times of extreme stress, such as a severe drought, they can 'CAM-idle'. This means they can keep their stomata closed during the day and the night, and use the CO2 released through respiration at night for photosynthesis during the day and the O2 released from the photosynthesis during the day for respiration at night. Which is pretty cool. But they can't do this indefinitely, and will eventually need to open their stomata to start the photosynthetic process up again. It does, however, allow them to survive long periods of water stress, and also to recover quickly when water again becomes available.

So that, in 3 long posts, is how photosynthesis works. Perhaps next time I'll discuss talking trees, or some other thing that isn't physiology related ;)

How does photosynthesis work? (part 2): Light and dark reactions and the Calvin cycle

The basic reaction of water + CO2  (catalyze with sunlight) ------> H2O + O2 is explained in more depth below, mostly because I get sick of the 'add CO2 and water and sunlight and.... magic happens!' explanation ;)
Photosynthesis is a rather complicated process, and I'll try to keep this simple.

Within a leaf there are cells that specialise and become functionally different from each other. As previously discussed, in leaves one of the major cell types are known as mesophyll, and this again differentiates into 2 types with different functions.
However it's not just plant tissues that specialise, they do it at the cellular level too, and even the sub-cellular level! (I told you it gets complicated).
Within the cells that make up mesophyll tissue, there are organelles that are called chloroplasts (these are what make leaves appear green). This is where the photosynthetic process actually happens.

So the mechanisms of photosynthesis are best discussed if you split them along the conventional lines and talk about them in two parts. The first part is known as the 'Light reactions' as it takes place in direct sunlight, and the second part is the 'Dark reactions' which do not need direct sunlight (although they usually take place during the day).

Light reactions occur in the membrane of the chloroplasts (which remember are within the plant cells). When light is available, it causes a chain reaction that converts chemicals in the chloroplast to ATP (adenosine triphosphate) and NADPH (Nicotinamide adenine dinucleotide phosphate), two molecules that are basically the universal fuels of cells. The ATP acts to move energy to where it's needed, and the NADPH allows phosphorous and more importantly Hydrogen ions to move to where they're needed for photosynthetic reactions.
So once these molecules are generated in light reactions the ATP and NADPH can be used to make sugars in the Dark reactions.

The Dark reactions are where the carbon dioxide is converted into sugars by the plant, in a process known as the Calvin cycle (because it was discovered by Melvin Calvin, James Bassham, and Andrew Benson). For a diagram of this cycle, use your favourite search engine - wikipedia is more than a little complex for this one. Or for a written explanation, keep reading below ;)
So the ATP and NADPH generated in the Light reactions are essential to the turning of this cycle, which is a rather complicated piece of molecular-energy transfer. It occurs in 3 stages, known as Carbon fixation, Reduction and Regeneration.

In Carbon fixation, CO2 is incorporated into a 5-carbon sugar, called ribulose biphosphate, via the enzyme Ribulose-1,5-bisphosphate carboxylase oxygenase (aka Rubisco). Rubsico is an important enzyme, not only as it allows CO2 to be captured and converted into a sugar, but also as it has an affinity to Oxygen, which can cause problems with something called photorespiration (I'll discuss why photorespiration is a problem and how plants deal with it in the next post). So at this point if the Rubisco has fixed CO2 as it should (and not O2), the sugar has 6 Carbon units in it. However this is only an intermediate product and it is then split into two 3-carbon sugars.

The next stage, Reduction, uses the ATP and NADPH from the light reactions to alter the structure of the 3-carbon sugars (this is where the chemistry will take over this post, so I'm keeping it simple here!) and turns them into the precursor to glucose. This can then be used to generate the 6-carbon sugars for the plant. The remaining 3-C sugars continue within the cycle, and enters the next stage, Regeneration. For this, more ATP is used to convert the 3-C sugar from this pool back into the original 5-C sugar that is used to capture the CO2, and the cycle can begin again.

So in summary, while a complicated process, each turn of the Calvin cycle will actually only capture just a single additional Carbon, so for a 6-C glucose molecule to be generated it will require 6 turns of the cycle. This involves 12 photons hitting the chloroplasts and generating 18 ATP and 12 NADPH molecules in the light reactions, which can then be used for 6 turns of the Calvin cycle in the Dark reactions to fix 6 CO2 molecules to end up with a single 6-Carbon sugar. In a nutshell, the light reactions provide the energy required for the dark reactions to fix carbon, and this is how basic C3 photosynthesis works (so called C3 as it's based on 3-Carbon sugars).

However some plants run into trouble with maintaining water balance, or with excessive light or temperatures. As such they've evolved to cope with this by photosynthesising in a different way. There are 2 main alternatives to C3 photosynthesis: C4 or CAM photosythesis, and I'll discuss these (along with photorespiration) in the next post...

How does photosynthesis work? (part 1): Leaf anatomy

Ok, so I took a week off - ah the hassles of PhD life!
I also sort of lied, as upon reflection perhaps it is better to discuss basic leaf anatomy before going on to how the process of photosynthesis actually works. But I'll make it a long post to make up for it ;)

So there are a few basic components to leaves, that are common to all no matter what species of plant we're talking about. I'll list these, along with their function below:

Cuticle - A waxy layer that sits on the surface of the leaf, it's main role is protecting the leaf from attack from pathogens and to prevent water loss.

Epidermis - This is a single cell layer that surrounds the outside of the leaf (cuticle sits on this layer). It functions much like our skin, in the sense that it prevents nasties from getting in, and water and the insides of the leaf from escaping. There are openings called stomata within this layer, that allow gases to move in and out of the leaf. These pores are controlled by the plant, which can open and close them as it needs. Some plants also have hairs arising from their epidermis, and these have multiple functions (protect from predation, reflects excess light, help reduce water loss through the creation of cool and humid microclimates around the stomata) although which function they perform varies with species.

Vascular tissue - Much like our veins and arteries, this is made up of Xylem tissue, which conducts water and it's associated dissolved nutrients, and Phloem tissue which carries photosynthates (ie the sugary products of photosynthesis) around the plant.

Mesophyll tissue - This is where it gets interesting. Mesophyll is a tissue that is usually found in 2 forms in leaves (although to be fair some leaves only have one type).
The first is Palisade mesophyll (also known as palisade parenchyma), and is composed of elongated, block-like cells that are usually stacked along the sun-side of the leaf. These cells collect light and are full of chloroplasts. You guessed it, they're the photosythetic cells in the leaf. However CO2 is also needed for photosynthesis, and that's where the second type of mesophyll comes in.
Spongy mesophyll (or spongy parenchyma) is (surprise surprise) called such because it is full of air-spaces and so looks like a sponge. The airspaces allow gases to pass in and out of the leaf easily whilst minimizing water loss.

So those are the basic tissue types (there are sometimes others, such as fibers for structural support or other specialized cells in various different plants), however their arrangement within a leaf can vary dramatically.
Basically the aim of any leaf is to photosynthesise, whilst not losing too much water, so the tissues within the leaf will be arranged to best accomplish this in the environment that the plant grows in.
For example, a plant that grows in a hot, dry climate is more likely to have a thick cuticle and less spongy mesophyll than a plant that grows in cooler wetter environments, as it will need to conserve water whereas the cool climate plant won't.

Perhaps the best example of changing the arrangement of tissues within a leaf to suit the environment, is to compare a typical European plant, such as a privet leaf, to an Australian plant adapted for hot dry environments, such as a Eucalyptus leaf.
Pictures below (I don't have access to a camera that I can take micrographs on at the moment, so the sources were: http://sols.unlv.edu/Schulte/Anatomy/Leaves/PrivetLeaf.jpg for the privet and http://www.sciencephoto.com/media/98433/enlarge for the Eucalyptus)

 Here (left) we have the typical leaf. Along the top is that palisade mesophyll, and this is the side of the leaf that would be in the sun. The leaf is held parallel to the ground (known as a dorsoventral leaf), meaning the sun always hits the upper surface of the leaf no matter what time of day it is. So to sum up it makes sense to pack that side with the light-collecting palisade mesophyll, and have the spongy on the cooler side of the leaf that is   permanently shaded.

And this one (right) is of the Eucalyptus leaf. You can see there is lots of palisade mesophyll, but hardly any spongy. The big red bit in the middle is a vascular bundle - the reason it's so huge is that it's the central vein in the leaf - and the white holes are actually oil glands. But the mesophyll is what we're interested in here ;)
It's arranged like this (ie palisade is packed on both sides of the leaf) because Eucalyptus species have their leaves hanging downwards, perpendicular to the ground. This is known as an isobilateral orientation, and helps reduce waterloss and photodamage during the hot part of the day. Because the leaf hangs downwards, during the morning and afternoon (when the sun is cooler) the light hits one side of the leaf. As it moves overhead at midday and becomes hotter, there is very very little leaf exposed to the sun (sort of like a person - in the morning and afternoon the sun will strike your whole body when you're standing up, but at midday only the top of your head will be hit by the sun). And in the afternoon the other side of the leaf is in the sun. This system helps keep the leaf cool, but means that stomata and palisade mesophyll are needed on both sides of the leaf.

So that, in a nutshell, is basic leaf anatomy. There are minor differences between monocotyledon and dicotyledons (for definitions of those types of plants, see wikipedia), and of course different types of plant may have different specialisations, but for your general C3 plant, that's what it looks like. C4 are slightly different, but for a proper explanation of what the hell C3 and C4 even mean, and how they're different, you'll have to wait for the next post ;)

Problems with photosynthesis (part 2): Photodamage and the xanthophyll cycle

Right, so again a slightly late post (whatever happened to Monday updates?!) regarding more problems with photosynthesis.
Last time we dealt with problems arising from water stress, and how plants can deal with them. This time it's light, again an essential part of the photosynthetic process, but also one that if taken in excess will cause damage to the plant.

Photodamage occurs in the photosynthetic tissues of plants when light and/or heat is in excess and damages these delicate organs. Basically plants use a chain reaction to transfer energy from sunlight into carbohydrates (through an electron transport chain - a series of proteins that can pass on electrons and hence form a chain - a process known as the Calvin cycle - will discuss the exact mechanisms in a later post), however an excess of this energy can begin to damage the proteins that are used to convert this energy. If the amount of sunlight doesn't decrease (ie it's a hot summer day), the plants do need some way of releasing or absorbing this energy before they become photodamaged.
Luckily for them, they've evolved such a system.

A nifty piece of evolution known as Xanthophyll pigments evolved to deal with this problem. These are a series of 3 pigments that have the capacity to absorb some of this excess energy before it can damage the photosynthetic parts of the leaf, and these are found in the thylakoid membrane that makes up the surface of the chloroplast (where photosynthesis occurs - more on this next week). To explain how the system works, a little chemistry is needed (sorry).

The first pigment in the cycle is violaxanthin, and this contains two double-bonded Oxygen (for a good image of the pigments and their conversion process, go to wikipedia). When violaxanthin absorbs some of this excess energy, one of the oxygen atoms breaks away to form a water molecule, and the pigment becomes known as antheraxanthin. The same process can then occur again, and once the pigment has lost it's second Oxygen, it becomes known as Zeaxanthin. The whole process is reversible, which means during the day each violaxanthin molecule can absorb two excess electrons, and by loading the thylakoid membrane of each chloroplast with these pigments, the plant can prevent quite a lot of photodamage.
However there is a limit, and if excess light continues to fall on the leaf, photodamage will eventually result (and is more often than not  irreversible).
During the night is when these pigments usually convert back to the lowest energy state (violaxanthin), and the plant can prepare it's defenses for the next day.

The xanthophyll cycle is just one way plants can deal with light stress, but it is I think by far the coolest ;) Other ways can be to preferentially grow in shadier areas (although the plant will acclimatise and produce fewer xanthophyll pigments - afterall, why produce them if you grow in the shade and won't need them?) and also via leaf alignment (as in the Eucalyptus example in the previous post). Why this protective mechanism is so important will be the subject of the next post - how does photosynthesis work?

Problems with photosynthesis (part 1): Maintaining water balance

As promised, a (slightly late) post about photosynthesis, and some of the problems that plants face when they try to do it. Because these can get complicated, I'll split it into 3 posts. Firstly we'll deal with maintaining water balance, and then photodamage caused by excess light (including the xanthophyll cycle - a really cool bit of evolution involving photosynthetic pigments). The last post will be an introduction to the actual process of photosynthesis at a molecular level, and the development of different kinds of photosynthesis to suit different environments (known as C3, C4 and CAM photosynthesis), and subsequently why higher CO2 levels are not necessarily a useful thing for most plants.

So, as every year 7 student can tell you, plants take up carbon dioxide from the atmosphere, water from the soil and absorb sunlight to magically produce sugars. The process is really a marvel of evolution, and involves complex chain-reactions at a molecular level. However for this to even begin, the basic ingredients (CO2, sunlight and water) need to be collected. Most plants use their leaves to obtain the first two, and roots to gather water (by the mechanisms discussed in the previous post!), although of course there are exceptions to this rule (some plants photosynthesise in only their stems, others are parasitic and get water from their hosts rather than root systems, but you get what I mean).
However one of the biggest problems plants have while trying to photosynthesise is maintaining a balance of all 3 requirements, and particularly maintaining enough water to survive (how well they do this is known as their Water Use Efficiency - WUE).

The means by which plants take-up CO2 is through the pores in their leaves known as stomata (singular: stoma). Plants have direct control over these pores, and can open and close them when they need. Opening stomata to uptake CO2 allows the absorption of carbon necessary for photosynthesis to occur, however it also allows water (and oxygen) to escape the leaf, and the plants have little control over this. Consequently in times of water-stress, plants must close their stomata and cease photosynthesis or they will lose valuable water. However allowing water to evaporate from the leaf in hot weather can also assist in cooling the leaf down, as excess light can heat the leaf and damage the photosynthetic organs within it (the other mechanisms to deal with this problem will be discussed in the next post).

Because this is a big problem, many adaptations to low-water environments have evolved (although usually perennial plants in low-water systems are deep-rooted as well). Three of the most common dry-climate adaptations include:

1. Reduced leaf area: This allows for fewer stomata to lose water per unit leaf area, and consequently a greater WUE, although as it does decrease the rate of absorption of CO2 these plants are usually slower-growing than plants without this adaptation. Often leaves are fleshy and succulent as well, and store fluids even in dry times. In some plants, such as cacti, the leaves are so reduced they became spines, and photosynthesis occurs in the stem, while the spines protect the valuable photosynthetic stem from herbivores.

2. Light colouring/hairs on leaves: Many species have a woolly coating on their leaves, intended to reflect excess light. If a leaf remains cooler, less water will be driven from it through evaporation, and the chances of damaging photosynthetic structures is lower. Saltbush and many other arid species are examples of plants that use this protective mechanism.

3. Sunken/hairy stomata: This is really quite cool - many plants have pits and/or hairs in the leaf surface that create a cooler, more moist microclimate around each stoma, reducing water loss but still allowing CO2 to enter the leaf. Banksia species often show this sort of adaptation, particularly those found in the drier regions of Western Australia.

Other plants have more simple mechanisms to deal with waterloss, such as members of the Eucalyptus genus that have leaves that hang downwards, rather than holding them horizontally. This ensures that during the morning and afternoon when the sunlight is cooler the leaves are exposed to it, but when it is overhead and hot at midday the thin edge of the leaf is the only part exposed. This simple anatomical re-arrangement dramatically reduces water loss and allows the trees to grow easily in hot, dry environments (now go find a gumtree and see what I mean!)

So to sum up, plants (like all living things) need to maintain their internal water levels to survive, but also have to balance collecting the ingredients required for photosynthesise. They have evolved many different ways to achieve this, while maintaining a capacity to collect sunlight for photosynthesis. Stay tuned for the next post on the nifty mechanisms used to deal with excess (hence potentially damaging) sunlight.