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DA Discussion 3
===Question #2 Photosynthesis and Bio-fuels By: Quaternary Structure ===

**Photosynthesis: ** Photosynthesis is a process used by plants and numerous microorganisms to convert the sun's rays into chemical energy. To begin our discussion of photosynthesis, we first explored the questions offered in the photosynthesis notes provided by Rachel. We also linked back to Microbiology in order to connect our previous knowledge. As we learned more about photosynthesis, we were able to discuss the role of photosynthetic organisms in the production of bio-fuels. Here are some of the interesting facts we learned!


 * Chlorophyll: **

We first discussed chlorophyll as a pigment used by many photosynthetic organisms. Chlorophyll is very similar to the heme porphyrin of the blood protein hemoglobin. While the heme porphyrin allows oxygen to be distributed to our bodies, chlorophyll is vital for photosynthesis as it allows photosynthetic organisms to absorb the sun's rays to be converted into chemical energy through other processes. (Watson 2010) Both molecules are essential for life!

//Figure 1: A side-by-side comparison of hemoglobin and chlorophyll. // //http://wheatgrasstherapy.webs.com/ //

Along with being an essential molecule for plants, chlorophyll has some health properties in humans as well. Among these health properties are: blood production, protection from cancer and radiation, wound healing, intestinal regularity, reducing cholesterol, detoxification and deodorization. (Handel 2010)

After learning about the structural properties of chlorophyll, we dove into the physical properties, in particular the wavelengths of light at which the pigment is absorbed. Using 2 helpful figures, we were able to see at what depths of water chlorophyll would be present. This would be an indicator of what photosynthetic organisms produced which pigments in varying bodies of water. Chlorophyll a would be would be used between approximately 0-100 feet. Chlorophyll b would be used up to approximately 275 feet. Carotenoids would be used up to about 100 ft. Cyanobacteria, or blue-green algae, is a phylum of photosynthetic organisms that use both chlorophyll a and b and are found at varying depths of water, and therefore produce these different pigments.

//Figure 2: Wavelengths of light absorbed by photosynthetic pigments.// //http://www.uic.edu/classes/bios/bios100/lecturesf04am/lect10.htm// //Figure 3: Wavelengths of light absorbed at varying depths of water.// //http://science.kennesaw.edu/~jdirnber/limno/LecPhy/LecPhy.html//

As we learned about the light absorbance of chlorophyll, we took a look at one of nature's wonders, the color changing leaves of autumn and their relation to chlorophyll and other natural pigments.

<span style="font-family: 'Comic Sans MS',cursive;">The leaves of trees and other plants contain three main pigments: carotene, anthocyanin, and the photosynthetic pigment, chlorophyll. As the most abundant pigment, chlorophyll is what gives leaves their green hue in spring and summer. Another chemical in leaves, auxin or indole-3-acetic acid, controls a special band of cells at the base of each leaf stem, called the abscission layer. During the growing season, auxin prevents this layer from fully developing and blocking the tiny, internal tubes that connect each leaf to the rest of the tree’s circulatory system. (Moran et. al. 2012)

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">//Figure 4: The abscission layer in leaves.// <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">//http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Auxin.html//

<span style="font-family: 'Comic Sans MS',cursive;">In fall, however, cooler and shorter days trigger an end to auxin production, allowing the abscission layer to grow and cut off the circulation of water, nutrients and sugar to the leaves. When this happens, chlorophyll disintegrates rapidly, letting carotene shine through as the yellow in maple, aspen and birch leaves. Anthocyanin, meanwhile, provides the oranges and reds of maples, sumacs and oaks. The pigments other than chlorophyll are considered accessory pigments. Carotene is part of the larger family of carotenoids that contain a large amount of conjugated double bonds that allow them to absorb light. Caroteniods absorb the blue region of the spectrum the best so they are red, yellow, and brown. (Moran et. al. 2012)

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">//Figure 5: The varying color, anthocyanin, and carotene levels of sumac leaves.// <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">//http://www.warrenphotographic.co.uk/01766-sumac-leaf//


 * <span style="color: #008000; font-family: 'Comic Sans MS',cursive;">Photosynthesis Processes: **

<span style="font-family: 'Comic Sans MS',cursive;">At this point, we took a turn in our discussion to look more at photosynthesis itself rather than photosynthetic pigments. We first need to look at the net formula describing photophosphorylation, an energy-producing process in photosynthesis, before discussing how it works.

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">NADP+ + ADP + Pi +H2O --> NADPH + 1.5 ATP + ½ O2 + H+

<span style="font-family: 'Comic Sans MS',cursive;">This reaction shows the overall production of photosynthesis in the form of reducing power (NADPH), ATP, oxygen, and protons. (Watson 2010) We were prompted with the challenge to compare and contrast the source of electrons for photosynthesis with the source of electrons for respiratory electron transport.

<span style="font-family: 'Comic Sans MS',cursive;">What we found was that in photosynthesis, the electrons come from the splitting of water into O2 and are transferred to NADP+ while in respiratory electron transport electrons come from NADH and are transferred to Q, or ubiquinone. Both reactions involve reducing power, NADH and NADPH. But in respiratory electron transport, reducing power is consumed where as in photophosphorylation reducing power is produced. The reaction of the catabolism of glucose is just the opposite of the carbon fixation reaction which is used to make glucose for various things, one of them being human consumption. The NADPH and ATP produced are used in the Calvin Cycle, or carbon fixation, to produce glucose. (Watson 2012)

<span style="display: block; font-family: 'comic sans ms',cursive; text-align: center;">Catabolism of Glucose: <span style="display: block; font-family: 'comic sans ms',cursive; text-align: center;">C6H12O6 + 6O2 → 6CO2 + 6H2O <span style="display: block; font-family: 'comic sans ms',cursive; text-align: center;">Carbon Fixation: <span style="display: block; font-family: 'comic sans ms',cursive; text-align: center;">6CO2 + 6H2O (+ light energy) → C6H12O6 + 6O2 <span style="display: block; font-family: 'comic sans ms',cursive; text-align: center;">(Watson 2012)

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">Triose phosphates are also products of the Calvin Cycle. These can be converted to starch and sucrose. Starch is made in the chloroplasts in the day time when photosynthesis is going strong, and ATP molecules accumulate within the chloroplast. After it gets dark the starch is used as a source of carbon and energy for the plants. This is done by starch phosphorylase cleaving the starch molecules to produce glucose-1-phosphate. Another fate of starch is that it can be hydrolyzed by amylase to dextrin then to maltose and finally to glucose. Sucrose is a energy form that can be easily transported around the plant. Sucrose is created in the cytoplasm of cells that contain chloroplasts. Once created the sucrose can then enter the plants vascular system so that non-photosynthetic cells can use it for energy. (Horton 2006)

//<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">Figure 6: Starch and sucrose synthesis. // //<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">http://www.scribd.com/doc/85643442/Taiz-Plant-Physiology-3e-Sinauer-2002 //

<span style="font-family: 'Comic Sans MS',cursive;">Another important process in photosynthesis is electron transport. Noting that electron transport in photosynthesis is very similar to respiratory electron transport, we can look at the cytochrome b6f complex in photosynthesis and compare it to the cytochrome bc1 complex, or complex III, in non-photosynthetic electron transport. The cytochrome b6f complex evolved from the cytochrome bc1 complex. (Moran et. al. 2012) Both complexes contain Fe-S clusters. The biggest difference between the two seems to be that in the b6f complex there is a third heme group (in addition to bH and bL) between the bH and Qi (quinone reduction) sites. ( Darrouzet 2004)

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: center;">//Figure 7: Cytochrome bc1 complex (left) and cytochrome b6f complex (right).// //<span style="font-family: 'Comic Sans MS',cursive;">http://www.chem.missouri.edu/cooleylab/rcaps_bookfigure.jpg // **<span style="color: #008000; font-family: 'Comic Sans MS',cursive;">Bio-fuels: ** <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">Finally armed with our extensive knowledge of photosynthesis, we were able to discuss photosynthetic organisms in the production of bio-fuels. But first, we should note the many other types of bio-fuels being produced and researched today. (FAO 2009) <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">Bio-fuels are fuels produced directly or indirectly from organic material (biomass) including plant materials, microorganisms and animal waste. Bio-fuels can be solid, gaseous or liquid, even though the most often used bio-fuel is liquid. A primary bio-fuel consists if fuelwood, or wood chips and pellets, organic materials that are used in an unprocessed form of heating and cooking. As for secondary bio-fuels, these result from processing biomass and consist of liquid bio-fuels such as ethanol and biodiesel. (FAO 2009) <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">The alcohol type of liquid bio-fuel that is produced using any feedstock containing a large amount of sugar or starch is ethanol. The fermentation of the sugar compounds converts this liquid into alcohol; similar to making wine or beer. Pure ethanol is obtained by distillation. The use of ethanol is like a form of gas for engines. It can be blended with petrol to help improve the combustion performance. (FAO 2009) <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">Ethanol production using corn has been considered one of the major alternatives to fossil fuels irregardless of the very energetically intensive processes that are used to generate a large enough crop of corn to ensure that there is an acceptable fuel yield. It is difficult to consider ethanol as a viable alternative to energy requirements in today's world when you consider the use of nonrenewable resources that must be used in the production and generation of ethanol. "Industrial corn-ethanol cycle” relies on mining the nonrenewable fossil fuels and the environment. The fossil energy inputs into corn farming include: nitrogen, phosphate and potash fertilizers, calcinated lime, herbicides and insecticides, machinery, genetically-modified hybrid seeds, irrigation, electricity, diesel fuel and gasoline, and methane and LPG for drying and power generation. The fossil energy inputs into ethanol production are fuels for corn processing, fermentation, distillation, and ethanol dewatering, as well as transportation. The cycle outputs are heat, ethanol, which is burned to obtain useful work, as well as depleted soil, water and air, all contaminated with the chemical byproducts of use of the nonrenewable resources. (Patzek 2004) <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">Combing vegetable oil or animal fat with an alcohol produces biodiesel. Biodiesel is traditionally created with adding diesel fuel or being burned in its pure form in compression ignition engines. Biodiesels have a wide range of oil derivatives such as soybean, palm, coconut or Jatropha oils. These fuels result in a greater variety of physical properties than ethanol. (FAO 2009) <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">A second-generation bio-fuel, cellulose, provides us with another way of creating combustion. Cellulose is broken down into two processes. First it is broken down into sugars which secondly are then fermented to obtain ethanol. The lack of commercial viability has inhibited the production of cellulose-based second-generation bio-fuels. However, cellulose bio-fuels have the potential to become a bid source of energy. (FAO 2009) <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">Here is a link to a 3 minute video explaining how bio-fuel is produced: <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">3 min Animation on BioFuel Production <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">//Note: This video may be biased towards bio-fuels and against fossil fuels because it is produced by a commercial algal bio-fuel company. However, this video is a helpful learning tool.//


 * <span style="color: #008000; font-family: 'Comic Sans MS',cursive;">Microorganism Production: **

<span style="font-family: 'Comic Sans MS',cursive;">Now that we know about the different types of bio-fuels, we can look at microorganisms in the production of bio-fuels. Cyanobacteria, or blue-green algae, is a phylum of microorganisms commonly used for bio-fuels.

<span style="font-family: 'Comic Sans MS',cursive;">Cyanobacteria and microalgae as bio-fuel producers is that they can be used to produce bio-ethanol, bio-hydrogen, biodiesel, bio-methane, and other non-fuel co-products used in other industries. (pharmaceuticals, cosmetics, fertilizer, etc.) Biodiesel seems to be the most efficient use of algae in fuel production. As stated Parmar et. al. in 2011: “Producing biodiesel from algae provides the highest net energy because converting oil into biodiesel is much less energy-intensive than methods for conversion to other fuels. This characteristic has made biodiesel the favorite end-product from algae.” (Parmar et. al. 2011)

//<span style="font-family: 'Comic Sans MS',cursive;">Figure 8: The many pathways cyanobacteria/microalgae can use for fuel production. (Parmar et. al. 2011) //

<span style="font-family: 'Comic Sans MS',cursive;">The other types of bio-fuels made by cyanobacteria seem to be much more cost and labor intensive. For example, using algae as biomass to produce bio-gas includes cultivating, harvesting, de-watering, drying, and separating the algae. All of these processes can both take a long time and also cost a lot of money.

//<span style="font-family: 'Comic Sans MS',cursive;">Figure 9: The different steps that must be taken to produce bio-fuels and co-products. (Parmar et. al. 2011) //

<span style="font-family: 'Comic Sans MS',cursive;">Another economic point to look at is the ways these algae can be grown. The traditional way is in outdoor ponds but this method involves loss of resources through evaporation and not being able to collect all the products from the algae. Closed ponds and bio-reactors (expensive machines that support biological environments) have proven to be very expensive, but more efficient. Additionally, algae require specific nutrients such as: NaCl, NaNO3, MgSO4, CaCl2, KH2PO4, citric acid and trace metals. The most efficient medium to grow the algae on seems to be seawater because many of these nutrients are already found there. However, algae can still grow on a variety of media including: fresh, brackish, seawater and wastewater. So they are flexible in that way, but still require those nutrients.

<span style="font-family: 'Comic Sans MS',cursive;">Cyanobacteria and microalgae can also be genetically engineered to produce more bio-fuel. Specifically, over expression of specific enzymes in the lipid metabolism process can yield high bio-fuel efficiencies and an increased production of triacylglycerols (TAGs). One example is the over expression of acetyl-CoA carboxylase, which is the enzyme involved with the reaction acetyl-CoA --> malonyl- CoA. Another enzyme that leads to increased lipid content is gylcerol-3-phosphate dehydrongenase. With regards to biodiesel production, thioesterases are important because of the specificity of chain length which is 12-14 carbon chains. Acyl-ACP-thioesterase is known to be successful in making chains of this length. Smaller chains can be used in the production of gas and jet fuel. (Radakovits et. al. 2010) A negative surrounding this idea is the possible spread of unnatural, engineered algae into natural environments and therefore contaminating those ecosystems. There are also human health concerns with these engineered algae. (Parmar et. al. 2011)


 * <span style="color: #008000; font-family: 'Comic Sans MS',cursive;">Conclusion: **

<span style="font-family: 'Comic Sans MS',cursive;">With all of this information, we were able to discuss the potential economic repercussions of the use of microorganisms in the production of bio-fuels. In the end, using photosynthetic organisms in order to produce bio-fuels is becoming a very promising idea however, it will take much more research and development in order to produce enough bio-fuel to compete with the amount of fossil fuels consumed each day. As stated by Newman from //How Stuff Works//:"Algae production has the potential to outperform other potential biodiesel products such as palm or corn. For example, a 100-acre algae biodiesel plant could potentially produce 10 million gallons of biodiesel in a single year. Experts estimate it will take 140 billion gallons of algae biodiesel to replace petroleum-based products each year. To reach this goal, algae biodiesel companies will only need about 95 million acres of land to build biodiesel plants, compared to billions of acres for other biodiesel products. Since algae can be grown anywhere indoors, it's a promising element in the race to produce a new fuel." (Newman 2012) Additionally, in an article in //Water Environment Research// it has been concluded that the cost can be very expensive and a considerable amount of land and water is required to grow the microorganisms and produce bio-fuels. (Yuan et. al. 2012)


 * <span style="color: #008000; font-family: 'Comic Sans MS',cursive;">Source Analysis: **

<span style="font-family: 'Comic Sans MS',cursive;">Sources 1, 7, 9, and 12 are scholarly, peer-reviewed journals. This means that these journals have been published to disseminate knowledge. The purpose of these journals is to educate. The funds for these journals come from academic entities, not industrial or commercial sources. They also provide both sides to the argument on bio-fuels. Therefore, they are unbiased and can be used as credible sources.

<span style="font-family: 'Comic Sans MS',cursive;">Sources 4 and 5 are biochemistry books published by Pearson. Pearson is an academic publisher that publishes a wide variety of textbooks for the academic world. This source is not bias. These textbooks are purely for education.

<span style="font-family: 'Comic Sans MS',cursive;">Sources 8, 10, and 11 are from professors of UC Berkeley and the University of Wyoming (UW). While these professors may have specific biases, a focus on engineering at UC Berkeley and a focus on microbiology at UW, these sources are still academic and credible.

<span style="font-family: 'Comic Sans MS',cursive;">Source 2 is from the Food & Agriculture Organization. This source was used to explain the different types of bio-fuels. This is not a scholarly source. While it seems to be credible, this organization has a bias towards production through agriculture. So, they may have a bias towards the production of ethanol because this increases the production of corn and helps the agricultural world.

<span style="font-family: 'Comic Sans MS',cursive;">Source 3 is a health magazine. This source was used to discuss the potential health benefits of chlorophyll. This source is definitely biased towards natural health resources. However, they used credible scholarly sources to write the article regarding chlorophyll. In that regard, this source is still credible even though it is not academic.

<span style="font-family: 'Comic Sans MS',cursive;">Source 6 is a website called How Stuff Works. This website is funded by the Discovery channel so the bias there is having a commercial audience. This source was used to describe how algae bio-fuels are produced. So this website only presents the positives of algal bio-fuel production. This source does not show the negatives about bio-fuels. However, the information used was credible.

<span style="font-family: 'Comic Sans MS',cursive;">All figures were either from credible sources or have been evaluated to make sure they are correct.

**<span style="color: #008000; font-family: 'Comic Sans MS',cursive;">References: **

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(1) Darrouzet, E., Cooley, J, Daldal, F. The cytochrome bc1 complex and its homologue the b6f complex: similarities and differences. //Photosynth Res.// 2004; 79: 25-44. <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(2) Food & Agriculture Organization ([|FAO]) The State of Food and Agriculture, Biofuels: Prospects, Risks and Opportunities. //Green Facts//. 2009. <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(3) Handel, J. Chlorophyll. //Healing Our World.// 2010. 30(3): 32-33. Web. http://www.hippocratesinst.org/magazines/30-3_screen.pdf. <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(4) Horton, M.S. 15.4 Fixation of CO2: The Calvin Cycle: 464-473. //Principles of Biochemistry. 4th ed.// New Jersey: Pearson; 2006. <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(5) Moran, et. al. Ch. 15: 447, 456. //Principles of Biochemistry. 5th ed.// New Jersey: Pearson; 2012. <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(6) Newman, S. How Algae Biodiesel Works. //How Stuff Works//. 2012. Web. http://science.howstuffworks.com/environmental/green-science/algae-biodiesel.htm. <span style="font-family: 'Comic Sans MS',cursive;">(7) Parmar, A., Singh, N., Pandey, A., Gnansounou, E., & Madamwar, D. 2011. Cyanobacteria and microalgae: A positive prospect for biofuels. //Bioresour.Technol.//, 102(22): 10163-10172.

<span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(8) Patzek, T. W. Sustainability of the corn-ethanol biofuel cycle. //Diss. U.C. Berkeley: Department of Civil and Environmental Engineering,// 2004. 12 May 2004. Web. <http://www.birrenbach.com/GSE/EtReportMain.pdf>. <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(9) Radakovits, R., Jinkerson, R.E., Darzins, A., Posewitz, M.C. [|Genetic Engineering of Algae for Enhanced Biofuel Production]. //Eukaryot Cell.// 2010 April; 9(4): 486–501 <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(10) Watson, R. Photosynthesis_2010. 2010. //MOLB 3610, University of Wyoming.// <span style="display: block; font-family: 'Comic Sans MS',cursive; text-align: left;">(11) Watson, R. Lectures 8-11: Metabolism. 2012. //MOLB 2021, University of Wyoming.// <span style="font-family: 'Comic Sans MS',cursive;">(12) Yuan, X., Wang, M., Park, C., Sahu, A. K., & Ergas, S. J. 2012. Microalgae growth using high-strength wastewater followed by anaerobic co-digestion. //Water Environ Resear.// (10614303), 84(5): 396-404. <span style="display: block; height: 1px; left: -40px; overflow: hidden; position: absolute; top: 4783.5px; width: 1px;">