Why Are Plants Green? or Why Aren't Plants Black

If I was hired as an engineer to design a machine whose job was to convert light energy into chemical energy I probably would not choose to use a green pigment. Instead, I would choose to use a black pigment because black pigments would absorb more energy because they would absorb all wavelengths of light. If you look at a field of plants you will notice that they are green (OK this doesn't work too well around Lubbock in the winter)and we have learned that chlorophyll, a green pigment, is the dominant photosynthetic pigment. What is going on?

Here is one theory about why chlorophyll is the dominant photosynthetic pigment in plants today. Early on there were photosynthetic bacteria with purple pigments (purple is a combination of red and violet). These aquatic bacteria had a very simple sort of cyclic electron flow that was able to convert light energy into energy in ATP (they didn't have non-cyclic flow or the Calvin Cycle).

Origin of chlorophyll- The purple pigment absorbed all wavelengths of light except for the reds and violets. Thus, any bacteria using purple pigments that lived deeper in the water than the purple bacteria on the surface would have no light to use because it had all been absorbed by the surface bacteris (exploitative competition). Because red and violet wavelengths pass through to deeper water, bacteria that contained a pigment that was able to absorb these wavelengths would be able to coexist with the purple bacteria. This was the origin of chlorophyll.

Competition purple and green photosynthetic pigments. Over time there was competition between organisms with purple photosynthetic pigments and green photosynthetic pigments. Obviously, the green photosynthetic pigments won this competition because chlorophyll is the dominant photosynthetic pigment today (there are still examples of photosynthetic bacteria with purple pigments, but they are limited to very harsh environments). Interestingly, chlorophyll came to dominate, not because it was a better at absorbing light energy, but rather because the cyclic flow machinery associated with chlorophyll was more efficient at producing ATP than the machinery associated with the purple pigment was. Thus, it is an evolutionary accident that modern plants are green.

Black Plants

It would be possible for modern plants to be black if they had enough accessory pigments to allow them to absorb all wavelengths of light. In fact, some red algae that live deep below the surface where light levels are low are basically black. Because the amount of light is not the factor that limits the rate of photosynthesis in most terrestrial plants, it is not worth the cost of producing extra accessory pigments. However, deep in the ocean where light levels are low, plants benefit from being able to absorb all wavelengths of light so deep marine algae have invested in extra accessory pigments.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss why terrestrial plants to not invest in the accessory pigments required to make them black

Factors LImiting the Rate of Photosynthesis

The graph above shows how the rate of photosynthesis is affected by irradiance (light level) and the concentration of carbon dioxide.

The rate of photosynthesis can be limited by a variety of environmental factors including

1) light
2) concentration of carbon dioxide
3) water
4) soil nutrients

Which factor most limits photosynthesis varies between environments.

Light- Can directly limit the rate of photosythesis by limiting the rate at which ATP and NADPH are produced.

Carbon dioxide- can directly limit the rate of photosynthesis by limiting the rate at which the Calvin Cyle takes place.

Water- can indirectly limit the rate of photosynthesis. When plants are water stressed they close their stomata (long before the concentration of water in the cell becomes too low for water to supply electrons to P680). Thus, the rate of photosynthesis is water stressed plants is directly limited by the amount of carbon dioxide in the leaf.

Soil Nutrients- Sometimes the rate limiting step in photosynthesis is the rate at which carbon dioxide + RuBP ==> PGA. This reaction is catalyzed by the enzyme RuBP carboxylase. Increasing the amount of RuBP carboxlyase in the cell can increase the rate at which this reaction occurs. Fertilizing plants with nitrogen will increase the amount of RuBP Carboxylase produced by the plant.

Expected Learning Outcomes

By the end of this class a fully engaged student should be able to

- discuss the factors that can directly or indirectly limit the rates of photosynthesis
- discuss how the most limiting factors should vary between environments
- discuss how the activities of farmers such as irrigation and fertilization can increase photosynthetic rates
- interpret the graph at the top of the post (irradiance measures light intensity and the three lines represent different concentrations of carbon dioxide)
- explain what why the graph shows that shape

Carbon Fixation

Technically, carbon fixation is defined as the first chemical reaction that incorporates carbon dioxide into an organic molecule (a molecule with more than one carbon atom).

In C3 photosynthesis the following step is considered to be carbon fixation-

carbon dioxide + RuBP ==> PGA

In CAM photosynthesis the following is considered to be carbon fixation-

carbon dioxide ===> malate

Note: CAM plants also have the reaction- carbon dioxide + RuBP ===> PGA, but in this case this step is not considered to be carbon fixation.

Sometimes people will loosely use the term carbon fixation to mean the production of glucose by photosynthesis. Be sure that you are aware of how different authors are using the term and you should attempt to use the term as precisely as possible in your own work.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- define carbon fixation
- identify carbon fixation in C3 and CAM photosynthesis

Stomatal Function and CAM Photosynthesis

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- describe patterns of stomatal opening in C3 plants
- describe CAM photosynthesis
- discuss why CAM photosynthesis is an adaptation in desert enviornments
- discuss why all plants do not use CAM photosynthesis


Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/c952faeba33546d3b8910e6e1bbf716c1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b



Powerpoint Presentation

http://www.slideshare.net/MarkMcGinley/stomatal-function-and-cam-photosynthesis

Leaf Structure

Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/c952faeba33546d3b8910e6e1bbf716c1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b




In most plants, leaves are the major sites of photosynthesis. Thus, we can think of leaves as "photosynthesis machines" and use our knowledge of natural selection to try to understand aspects of leaf structure.

Further Reading

http://micro.magnet.fsu.edu/cells/leaftissue/leaftissue.html

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss important differences between animals and plants in gas uptake
- diagram the cross section of a leaf
- discuss the characteristics and purpose of the cuticle, stomata, spongy mesophyl cells, and the palisade cells.
- explain the adaptive basis of leaf structure

Some Suggestions About How to Study About Photosynthesis

Photosynthesis is a complicated and complex process.  I find that many students focus so much on learning about the details that they lose focus on the big picture.

I suggest that you first review the powerpoint presentation I showed in class and then review the relevant material in the book. Next, I would look at the Expected Learning Outcomes in the blog posts on the Light Dependent and Light Independent reactions.  Make sure that you check out the animations. They all use a slightly different approach to cover the same process. You might also try some of the end of the chapter review materials.

 I suggest that you write out answers to all of the expected learning outcomes. Most of these are relatively short. After you have done this you should be able to answer the following three questions.

1) Describe the process of photosynthesis in only one sentence.

2) Describe the process of photosynthesis in only one paragraph.

3) Explain the process of photosynthesis in full detail.

In order to perform well on the test you should be able to explain the material to a fellow classmate.
I think that you can learn a lot by critiquing the answers of your fellow classmates and suggesting how to improve their answers (I find that it is always easier to critique someone else's work than it is to critique my own). Hopefully, the feedback you receive will help you to determine whether you have mastered the material at a deep level or not.

If you would like me to review your written answers to the Expected Learning Outcomes email them to me and I will take a look and get back to you.

Photosynthesis 2. Light Independent Reactions

Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/842d916401044c20a370989776ea66631d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


In the light independent reactions the energy stored in ATP and NADPH is converted to energy stored in glucose. This invovles a chemical cycle known as the Calvin Cycle.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss what links the light dependent and light independent reactions of photosynthesis
- describe the initial step of the Calvin Cycle
- describe the chemical reaction catalyzed by the enzyme RuBP carboxylase
- discuss some interesting characteristics of RuBP carboxylase
- define "carbon fixation" and identify the carbon fixation step in the different modes of photosynthesis
- diagram the Calvin Cycle (at the level of detail that I talked about in class)
- discuss where and why ATP and NADPH are required in the Calvin Cycle
- disucus where in the cell that the Calvin Cycle takes place

Reading From Textbook

pages 198-205

Powerpoint Presentation

Here is a link to the powerpoint presentation that I used in class.

http://www.slideshare.net/MarkMcGinley/light-independent-reactions-of-photosynthesis

Further Viewing

1) This is an excellent animation (narrated by a man with a perfect "announcer's voice"). This animation goes into the amount of detail you are required to know for this class. It even has its own quiz, so see how you do.

http://highered.mcgraw-hill.com/sites/0070960526/student_view0/chapter5/animation_quiz_1.html

2) I didn't know that photosynthesis was such a popular subject for musicians (I can't belive I gave up what would surely have been a lucrative career as a rock star to become a biologist- who knew I could have combined the two). The guy in the video seems like kind of a dufus, but the song is pretty cool, and I learned something from watching it.

http://www.youtube.com/watch?v=OYSD1jOD1dQ

3)Maybe you will find this animation to be helpful

http://www.science.smith.edu/departments/Biology/Bio231/calvin.html

Photosynthesis 1. Light-Dependent Reactions

Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/842d916401044c20a370989776ea66631d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


Photosythesis takes place in two steps. In the first step, known as the light dependent reactions, light energy is converted into chemical energy held in the bonds of ATP and NADPH.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- list the parts of a photosystem
- discuss the function of a photosystem
- describe where the light dependent reactions of photosythesis occur and discuss why these reactions occur in this location
- describe cyclc electron flow, be able to explain both the energetic result and what chemcical changes occur
- describe non-cyclic electron flow, be able to explain both the energetic result and what chemical changes occur
- describe the cause and the result of chemiosmosis
- answer the question- "why doesn't photosynthesis stop after the production of ATP and NADPH in the light dependent reactions

Readings From Textbook

pages 184 - 197

Further Reading

A simple introduction to the process of photosynthesis
Photosynthesis- http://www.eoearth.org/article/Photosynthesis

Here is a link to some fairly detailed info about photosynthesis (it contains some very good diagrams).
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html

Powerpoint Presentation

Here is the powerpoint presentation that I will use in class.

http://www.slideshare.net/MarkMcGinley/photosynthesis-light-dependent-reactions

Further Viewing

These videos contain animations that might help you to understand what is happening in the light dependent reactions. I encourage you to watch each of these videos.

1) This video has some great animations of what is going on in the light dependent reactions.

http://www.youtube.com/watch?v=hj_WKgnL6MI

2) This is a video of a woman with a very southern accent talking about photosyntheis with some decent animations.

http://www.youtube.com/watch?v=RFl25vSElaE&feature=related

3)Another explanation of light dependent reactions.

http://www.youtube.com/watch?v=BK_cjd6Evcw

Introduction to Energetics

Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/dfea523e65f54ad2af1a25fda81bd2f91d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


In order to understand the two important energetic processes taking place in living organims (photosynthesis and cellular respiration) it is useful to understand some basics of energetics.From a physics perspective, energy is required to do work. Because this is a biology class, we will focus on biological work. The three main types of biological work are (1) active transport, (2) biosynthesis, and (3) movement. The key point for this class is to realize that organisms require energy to do the biological work required to keep them alive.

Energetic processes follow the laws of physics. The two most important laws of physics that relate to energy are the First and Second Laws of Thermodynamics.

First Law of Thermodynamics

The total amount of energy in the universe is constant. Energy can not be created and existing energy can not be destroyed. Energy can only undergo conversion from one form to another.

Biological relevance- No living organisms are capable of creating their own energy so they must get it from another source.

Second Law of Thermodynamics

Left to itself, any system undergoes energy conversion to less organized form. Each time this happens some energy becomes so disorganized that it is no longer available to do work.

Entropy is a measure of the amount of energy that is so disorganized so that it can no longer do work. A simpler way of stating the Second Law of Thermodynamics is that entropy increases over time.

What does it mean when energy becomes disorganized? Another term for "organized energy" is "concentrated energy". Energy is only able to do work when it is concentrated enough to power a particular process.

Apparent Problem

The Second Law of Thermodynamics states that entropy should increase over time, yet life contains highly concentrated energy. How can this be?? They key phrase in the definition is "left to itself". It turns out that energetically, the earth is not left to itself; the earth receives a constant input of energy from the sun and it is this energy that is used to fight entropy.

Light

Light energy from the sun reaches the earth. Light is part of the electromagnetic spectrum. Different portions of the electromagnetic spectrum vary in their wave lengths. Forms of electromagnetic energy with shorter wavelengths (e.g., x rays and gamma rays) contain more energy than forms of energy with longer wave lengths (e.g, radio waves). Interestingly, light falls within the middle of the spectrum with wavelengths from about 400 - 700 nm. Different wavelengths of light have different colors. Ranging from the longest to the shortest wavelengths the colors are red, orange, yellow, blue, green, indigo, violet (some people remember this using ROY G BIV).

As you might recall from your physics class, light has characteristics of waves and of particles. Light energy is "packaged" in units known as photons and the amount of energy in a photon depends of the wavelength of that light.

Fusion reactions on the sun convert nuclear energy in to electromagnetic energy. The electromagnetic energy travels through outer space until reaches the earth. Unfortunately, we,and all other organisms can not directly use light energy to do biological work. Instead light energy must be converted into potential energy stored in the chemical bonds of molecules. This potential (stored) energy can then be used to power biological work.

What Happens When a Photon of Light Hits a Molecule?

Three things can happen when a photon of light hits a molecule- (1) the light can be transmitted (passed through), (2) the light can be reflected, or (3) the photon of light can be absorbed.

When a molecule absorbs a photon of light energy, the electromagnetic energy of light excites an electron in the molecule to a higher energy level (thus, giving the electron potential energy). The excited electron almost immediately falls back to resting stage and the potential energy in the electron is converted into heat (a form of electromagnetic energy) which is released to the atmosphere.

Pigments

When we think of pigments, we think of color. What determines an objects color? The color of an object depends on the wavelengths of light that are reflected back to our eyes. Thus, when you see red you are seeing the red wavelengths that have been reflected from the object that you are looking at. What happens to the other wavelength? They have been absorbed.

Different molecules absorb and reflect different wavelengths of light. A pigment is defined as a molecule that absorbs particular wavelengths of light. What is important to remember is that the color of a pigment is the color of light it reflects.

Absorption Spectrum

An absorption spectrum is a graph that plots how much light energy is absorbed (y-axis, usually measured as intensity or as a percentage) versus the wavelength of the ligh (x-axis, measured in nm). Take a look at the absorption spectrum shown below. You can see that this pigment absorbs mostly green wavelengths and reflects the red and violet wavelengths. When the red and violet wavelengths reach your eye it would appear to you as purple.

Can you draw the absorption spectrum for a red, green and blue pigment?



Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/dfea523e65f54ad2af1a25fda81bd2f91d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


Expected Learning Outcomes

By the end of the course a fully engaged student should be able to

- give examples of biological work
- list different forms of energy, give examples of the different forms, and give examples of energy conversions
- define the First and Second Laws of Thermodynamics and discuss why these laws are important for biologists
- discuss electromagnetic energy, including the wavelengths associated with different forms of electromagnetic energy and the relationship between wavelength and energy
- define a photon
- discuss the three things that can happen when a photon of light hits a molecule
- define a pigment
- draw and interpret an absorption spectrum

Further Reading

Electromagnetic radiation- http://www.eoearth.org/article/Electromagnetic_radiation