Thursday, September 12, 2019

A Brief Introduction to the Wonderful Life of Plants - Part I: The Plant Cell, Photosynthesis & Respiration, and Mitosis

Montaigne said, "to study philosophy, is to learn to die."
For botany, it can be said, "to study botany, is to learn to live."
Plants are everywhere, plants are ancient, and plants are vital for life. But as true as these statements are, as true is this: plants are messengers. Their evolution shows nature's unforgiving, but also its ability to create wonders through assiduous trial and error. However, this entry does not tell that story. No, this is a testament to its momentary conclusion! 
This is the beginner botanist's guide, in which we will explore what the interesting science behind botany. It is intended for the less scientific audience, who, while in love with the taxonomy of plants, may lack some of the understanding of what makes the plant tick. So, let us begin by studying what can be considered the atoms of the plants; its building block: the Plant Cell.

The Plant Cell


Fig 1: Diagram of Plant Cell
The plant cell (figure 1) is built much like an egg. While its shape and size may not be analogous, its structure most certainly is. Its "shell", the cell wall, exists with the purpose to protect the innards of the cells. On the inside of this shell is a membrane; in the cell this is known as the cell membrane. This substance is less rigid and serves a much more versatile purpose, such as nutrient transportation in and out of the cell and it acts as a primary vessel for "the white" of the cell that is the cytoplasma. Cytoplasma consists mostly of water, but it also suspends various nutrients and organic molecules, but most importantly, it houses the organelles, of which there are many, with different names and functions. Most notably there is "the yolk" of the cell, which is the nucleus. The word is derived directly from Latin and means "kernel" or "inner part". It is exactly that, and while it is unfair to devalue the importance of the other organelles, it serves a very important role in that it contains the genetic material of the cell. The genetic material is, in short, the blueprints needed to construct the cell, and this will show itself very important when we come to cell division.

Surrounding the nucleus, we have the endoplasmic reticulum or simply ER, of which there are two variants, the smooth and the rough. The smooth endoplasmic reticulum is used in the production of hormones and lipids (fats) that the cell uses for various purposes. The rough endoplasmic reticulum contains ribosomes which aid in the vital process of protein synthesis. The details of these processes, however, are for another time to discuss.

A typically very large organelle is the vacuole, which is a vessel with the primary objective of storing water inside of the cell. This vessel is more than just a biological canteen, though. It helps maintain the cell's turgor, which is the combined pressure of the cytoplasma of the cell and the vacuoles. This turgor helps maintain the structure and shape of the cell.

The Golgi apparatus or Golgi body packs proteins and lipids for transportation within the cell and outside the cell.

There are also lysosomes, which digest various compounds within the cell. Then, as the last important organelle before we introduce the two stars of the plant cell, are the peroxisomes, which aids in one of the key processes of the cell.

Fig 2: Diagram of chloroplast
The mitochondrion, of which there can be several (in which case it is mitochondria) is in the memories of many "the power house of the cell", and it can very well be viewed as such, as it plays a central role in the respiration of the cell. However, for now, we will leave it at that, and introduce the king of the plant cell, the chloroplast (figure 2). The chloroplast is the organelle that is primarily responsible for the process of photosynthesis.  The chloroplast is almost like a cell on its own; it contains a membrane, both outer and inner, and its own "cytoplasm" is called stroma, which plays an important role in photosynthesis, along with the chloroplast's main unit of interest: the thylakoid, of which every chloroplast is rich in number, and this is the main component of photosynthesis, because it contains the pigment chlorophyll, which reacts to sunlight. The thylakoids can arrange themselves in structure called grana (sing. granum), which are essentially stacks of thylakoids. They are connected by lamelles, formally denoted stroma lammealle. It is worth explaining the structures and properties of the thylakoid with a bit more resolution before we venture into the processes of the cell.

The Thylakoid, Chlorophyll and Visible Light


The thylakoid itself contains a membrane, in which a pigment is contained; these are the aforementioned chlorophyll. In reality, the chlorophyll is a very complex molecule, but to us it is simply a "device" that absorbs light. While we won't explore its properties of chemistry any further, we will briefly look into the physics of light.

For many years, physicists debated whether or not light should be considered a wave or a particle. Then Einstein came along and said that it could be both. That is called Wave-particle duality and it is definitely very interesting, but for our purposes, we will view light as a wave. As such, a natural property of light is a wavelength which is measured in nano-meters (nm), which is one-billionth of a meter! It denotes the length of a period of a wave, but to us it is just a number that represents a color.

Light is part of a larger concept called electromagnetic radiation, which exists on a spectrum.  What we consider as "light" and "color" is part of what is called the visible spectrum (figure 3).

Fig 3: Spectrum of Visible Light
We can see that the visible spectrum is roughly in the 400-750 nm range, where the lower end is blue and the upper end is red. German botanist, Theodore Wilhelm Engelmann, was the first to show the importance of color in the process of photosynthesis. In a type of algae called Spriogya, he saw that the algae produced the most oxygen (which is one of the criterion of succesful photosynthesis!) when exposed to blue and red parts of the spectrum. If we examine the figure above, we see that green and greenish light is in between these two parts of the spectrum. Light from the sun contains all wavelengths of the visible spectrum, as well as some outside of the visible spectrum, which causes it to be white. However, when sunlight hits the leaf of a plant, the blue and red wavelengths are absorbed by the chlorophyll, and the green wavelengths are reflected, which means it can enter our eyes and this is why plants look green! Bonus question: how come leaves turn red and brown during the autumn?

Now, the physics lesson is over. However, it is important for the botanist to understand how light reacts with the plant, and perhaps in a little more detail than the botanist will find use for (it may be of particular interest for indoor gardening with growth lights!). Nevertheless, we have established that the plant absorbs some types of light and reflects green light. So, what happens to this light once it is absorbed? This is where we will delve into the fascinating process of photosynthesis. 

Photosynthesis


Photosynthesis (Greek, paraphrased, "to make from light") is to many the subject of common knowledge. To refresh, the plant uses water, carbon dioxide and light to facilitate the synthesis of sugar and oxygen. With that in mind, we will go into more detail as to the processes which take place within the plant. For the sake of repetition, let us look at the equation of photosynthesis

6 CO2 + 6 H2O + light → C6H12O6 + 6 O2

Carbon dioxide and water goes in and sugar (glucose) and oxygen come out ... simple enough, right?Let us dive deeper into this process. 

Photosynthesis is split into two stages: the light stage, and the light-independent stage. These stages occur concurrently. i.e, in a "egg and the hen" scenario, the light stage comes first.


The light stage (figure 4) can be schematically shown as

Fig 4: Diagram of light stage in Thylakoid and Stroma (simplified)
A lot goes on in this picture, and as such we must somewhat structure our analysis of it. If we start from the left side and examine the entire area encapsulated by the gray membrane, we see the thylakoid in action. The inside of a thylakoid contains a proton pump, which supplies protons, schematically denoted as H+. They flow out of the thylakoid and react with free OH- groups, which are present in the stroma of the chloroplast. This creates water. The ⇌ symbol denotes an equilibrium, meaning that the reaction has no tendency to change with time.

Within in the thylakoid we also see something interesting, namely the presence of ADP and P. ADP is adenosine diphosphate, which is the baby-version of the energy molecule, ATP or adenosine triphosphate. When it reacts with phosphor, which the enzyme (protein that has a specialized task, like a worker) ATP synthase. These two compounds then exit the cell through a channel as useful, energy-rich ATP. This ATP leaves the process.

Let us look at the green spot around the center of the image, on the membrane of the thylakoid. This is the chlorophyll pigment (forget about the P680 and P700 designations for now). Notice how, when light reacts with it, it splits water (H2O), and this releases an electron (e-). We also notice that the water is split into a proton and oxygen (O2), which leaves the process. Yes, this is the part that creates oxygen, but more interestingly is that it takes place independently of any carbon dioxide (CO2) reactions.

The electron released from the water then goes into another important reaction. It should be noted that this reaction is greatly simplified, but for our goals, we must just understand that the electron turns the molecule NADP+ into NADPH, which then leaves the process.

This concludes this light stage, and we see that it has three purposes: create energy from ATP, split water into oxygen, and turn NADP+ into NADPH. Particularly the former and the latter are of interest to us now that we move on into the next stage.

The light-independent stage or the Calvin cycle (figure 5) is the process in which carbon dioxide is transformed into glucose. This series of reactions are not at all simple to understand, so we will try to understand it in the simplest terms possible and focus on getting the bigger picture.

Image result for calvin cycle
Fig 5: Diagram of Calvin Cycle (simplified)
If we view the diagram as a clock, let us start at 12 o' clock and go clockwise. At 12, carbon dioxide enters the cycle. Here it is led into the first stage called carbon fixation, which just means that we are taking inorganic carbon dioxide and making it into organic molecules (which of course contain carbon!) with the help of the enzyme RuBisCO. This process requires energy, so our ATP is expended and turned back into ADP, which leaves the cycle. At roughly 4 o' clock, during the second stage, reduction, these organic molecules are transformed further. Here the NADPH that was produced in the light stage is used up and leaves the cycle. Now we reach 7 on the clock. Here, some of the organic molecules that were created during the second stage go directly to the third stage, which, is what reacts with carbon dioxide to create these crucial organic molecules. Before this happens, however, some of these organic compounds are turned into sugar, the carbon-rich glucose (C6H12O6).

This concludes the light and light-independent stages, and thus photosynthesis. This process does not only exist only to serve humans though. The glucose created in the latter stage plays an important role in the next process worth of our investigation.

Respiration


Respiration is not a particularly foreign word, and should spark thoughts of breathing. Similarly to how animals inhale oxygen and exhale carbon dioxide, plants inhale oxygen via photosynthesis and exhale carbon dioxide in the respiration process. While not as extravagant as photosynthesis, it is nevertheless important for well-being of the cell. When examining the organelles of the cell, we were introduced to the mitochondrion. In a sense, these are the lungs of the cell. They convert glucose and oxygen into other compounds, as can be shown schematically

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy

The keen eye will see how it is reminiscent of photosynthesis, except that the "direction" of the reaction is reversed. For now, that thought can be entertained, however that is not entirely accurate, but due to the limited scope of this entry, we must leave it here. However, if one wishes further reading into the respiration of a cell, the Citric Acid Cycle or Krebs cycle (these are synonyms) are a good place to start. These are on the surface quite a bit more complex than the Calvin cycle, which takes place during the light-independet stage.

The important detail is how respiration uses  the glucose produced during photosynthesis. We have now covered the most important processes that occur within the cell during its life time. Now, let us look at what occurs at its end.

Cell Division


Most of us are familiar with how a plant starts as a simple sprout in the ground. Then, how does the plant grow into a magnificent bush or a grandiose tree? The answer is cell division. Before we get into the science, let us look at the math. A plant cell is somewhere between 10-100 micrometers in size. To clarify, 1 micrometer is one-millionth of a meter! That is small. So how do a few cells grow into a botanical masterpiece in a reasonable amount of time? Let us briefly delve into Indian folklore, and tell the story of the grain of rice that bankrupted a kingdom

(this part can be skipped)

One Grain of Rice

Long ago in India, there lived a raja who believed he was wise and fair, as a raja should be. The people in his province were rice farmers. The raja decreed that everyone must give nearly all of their rice to him. "I will store the rice safely," the raja promised the people, "so that in time of famine, everyone will have rice to eat, and no one will go hungry." Each year, the raja's rice collectors gathered nearly all of the people's rice and carried it away to the royal storehouses.
For many years, the rice grew well. The people gave nearly all of their rice to the raja, and the storehouses were always full. But the people were left with only enough rice to get by. Then one year the rice grew badly and there was famine and hunger. The people had no rice to give to the raja, and they had no rice to eat. The raja's ministers implored him, "Your highness, let us open the royal storehouses and give the rice to the people, as you promised." "No!" cried the raja. How do I know how long the famine will last? I must have the rice for myself. Promis or no promise, a raja must not go hungry!"
    Time went on, and the people grew more and more hungry. But the raja would not give out the rice. One day, the raja ordered a feast for himself and his court--as, it seemed to him, a raja should now and then, even when there is famine. A servant led an elephant from a royal storehouse to the palace, carrying two full baskets of rice. A village girl named Rani saw that a trickle of rice was falling from one of the baskets. Quickly she jumped up and walked along beside the elephant, catching the falling rice in her skirt. She was clever, and she began to make a plan.
    At the palace, a guard cried, "Halt, theif! Where are you going with that rice?"
    "I am not a thief," Rani replied. "This rice fell from one of the baskets, and I am returning it now to the raja."
    When the raja heard about Rani's good deed, he asked his ministers to bring her before him.
    "I wish to reward you for returning what belongs to me," the raja said to Rani. "Ask me for anything, and you shall have it."
    "Your highness," said Rani, "I do not deserve any reward at all. But if you wish, you may give me one grain of rice."
    "Only one grain of rice?" exclaimed the raja. "Surely you will allow me to reward you more plentifully, as a raja should."
    "Very well," said Rani. "If it pleased Your Highness, you may reward me in this way. Today, you will give me a single grain of rice. Then, each day for thirty days you will give me double the rice you gave me the day before. Thus, tomorrow you will give me two grains of rice, the next day four grains of rice, and so on for thirty day."
    "This seems to be a modest reward," said the raja. "But you shall have it."
    And Rani was presented with a single grain of rice.
    The next day, Rani was presented with two grains of rice.
    And the following day, Rani was presented with four grains of rice.
    On the ninth day, Rani was presented with two hundred fifty-six grains of rice. She had received in all five hundred and eleven grains of rice, enough for only a small handful. "This girl is honest, but not very clever," thought the raja. "She would have gained more rice by keeping what fell into her skirt!"
    On the twelfth day, Rani received two thousand and forty-eight grains of rice, about four handfuls.
    On the thirteenth day, she received four thousand and ninety-six grains of rice, enough to fill a bowl.
    On the sixteenth day, Rani was presented with a bag containing thirty-two thousand, seven hundred and sixty-eight grains of rice. All together she had enough rice for two bags. "This doubling up adds up to more rice than I expected" thought the raja. "But surely her reward won't amount to much more."
    On the twentieth day, Rani was presented with sixteen more bags filled with rice.
    On the twenty-first day, she received one million, forty-eight thousand, five hundred and seventy-six grains of rice, enough to fill a basket.
    On the twenty-fourth day, Rani was presented with eight million, three hundred and eighty-eight thousand, six hundred and eight grains of rice--enough to fill eight baskets, which were carried to her by eight royal deer.
    On the twenty-seventh day, thirty-two brahma bulls were needed to deliver sixty-four baskets of rice. The raja was deeply troubled. "One grain of rice has grown very great indeed," he thought. "But      I shall fulfill the reward to the end, as a raja should."
    On the twenty-ninth day, Rani was presented with the contents of two royal storehouses.
    On the thirtieth and final day, two hundred and fifty-six elephants crossed the province, carrying the contents of the last four royal storehouses--Five hundred and thirty-six million, eight hundred and seventy thousand, nine hundred and twelve grains of rice.
    All together, Rani had received more than one billion grains of rice. The raja had no more rice to give. "And what will you do with this rice," said the raja with a sigh, "now that I have none?"
"I shall give it to all the hungry people," said Rani, "and I shall leave a basket of rice for you, too, if you promise from now on to take only as much rice as you need."
"I promise," said the raja. And for the rest of his days, the raja was truly wise and fair, as a raja should be.

...a story about the inevitable folly of selfishness and finding true nobility among the ignoble, these are however not the modalities we will concern ourselves with. This story represents the concept of exponential growth, which is the idea that very little can become very much, as long as the quantity is constantly doubled. This is the crux of mitosis. One cell becomes two, and these two cells become two each, resulting in four additional cells, which then also divide into two cells each, resulting in eight new cells, and so on ...

Now that we understand the significance of this growth, we can look into the science. However, first we must answer to our promise that we made earlier and explain the nucleus in some further detail. In many ways, the nucleus is reminiscent of a planet. It has a crust, which is called the nuclear envelope, and similarly to how the Earth is partially porous, so this envelope. The pores are called nuclear pores. The mantle consists of chromatin, which is sort of the librarian of the nucleus if you will. It helps properly arrange and packing the DNA of the cell into chromosomes, which are very crucial to the cell division process. At its core, we have the nucleolus, and is made of DNA and RNA ("single-strand DNA"). During mitosis (figure 6), the entire nucleus is divided through different phases, which in chronological order are the interphase, (pre)prophase, metaphase, anaphase and telephase.

Fig 6: Diagram of Mitosis
The interphase (a) can be viewed as a default state of the cell; this is where the cell spends most of its life, and it would analogous of adulthood in human life. For us, it is not particularly interesting beyond that. Not shown is a process in which the preprophase band (b) is made. What is necessary to know is that this band acts as a scaffold for the rest of the cell division. It designates the "cutting site" if you will. It can be seen on the diagram in later stages. Once this has been done, the metaphase (c) commences, in which the chromosomes of the cell begin to divide with the assistance of mitotic spindle. In the telophase (d), we see two things happening: the formation of the cell plate, which will later become the cell wall that separates the cell into two new cells. Here, the mitotic spindle has arranged itself into a phragmoplast, which arises from the structures of the preprophase band, and now truly expresses itself as a scaffolding for the cell plate. At this stage, cytokinesis (d & e) takes place. Here, the cell formally begins to divide into two as the cell plate matures. Then we enter the early interphase (f), childhood if you will, and the divided nuclei now sit in their respective cells. The cycle then completes, and the cells enters a new interphase (g). However, it is important to notice that the sum of volume of the two new cells are roughly equal to the original cell. Therefore, cell enlargement (h), must take place. These new cells will now live their own life cycles, and if all goes well, they will also undergo mitosis eventually, and contribute to the growth of the plant.

***


This is but a foray into the vast science of botany. Much that could have been explained has been left out, and that is because it is sometimes better to say too little instead of too much. Curiosity comes from the unknown. A brief introduction, it has been.  We will explore the subject again another time, but for now, this is the end. 

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