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Abstract/Syllabus:
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Weigele, Peter, and Yongting Wang, 7.343 Photosynthesis: Life from Light, Fall 2006. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 09 Jul, 2010). License: Creative Commons BY-NC-SA
Photosynthesis is carried out by many different organisms, ranging from plants to bacteria. (Image by Dr. Peter Weigele.)
Course Highlights
This literature-based seminar features a full set of readings, as well as summaries of each topic in the lecture notes.
Syllabus
Course Description
The biological conversion of solar energy to chemical energy forms the basis of life as we know it. Knowledge of this fundamental process is critical to our understanding of the biogeochemical cycles that mitigate global warming. In this course, you will journey through the web of physical, chemical, and biological reactions that collectively constitute photosynthesis. We will begin with light harvesting and follow photons to the sites of primary photochemistry: the photoreaction centers. A molecular-scale view will show in atomic detail how these protein complexes capture and energize electrons. Then we will follow the multiple pathways electrons take as they carry out their work. Consequent reactions, such as the synthesis of ATP and the reduction of CO2 during the synthesis of carbohydrates, will also be discussed in structural detail. Lastly, we will delve into the evolution of these systems and also discuss other photosynthetic strategies, such as light-driven proton pumps and anoxygenic photosynthesis. The course will include a visit to an electron microscope to allow students to directly observe proteins involved in photosynthesis.
Course Format
During the typical class session, we will analyze two papers in a discussion-based format. Everyone should read both papers before class, and each student should be prepared to raise and answer questions. At the beginning of each class, we will have a question and answer period in which the instructors and the rest of the class will respond to any specific questions that the students may have thought of while reading the articles. We will spend the remainder of the class discussing the data presented in the article by analyzing each figure and table and the resulting conclusions. Each class will conclude with a brief outline of the following session class by the instructors.
Expectations
Students are expected to attend every class meeting and turn in all assignments on time on the date they are assigned. The major focus will be on discussion and interpretation of scientific papers, so student attendance and participation is essential. Other than Ses #1, there will be no lectures and students should come to class prepared to participate in a discussion of the assigned papers. Missing a class should occur only in extreme circumstances. If a student knows he/she must miss a class, he/she must contact the instructor in advance and receive permission for the absence. Students who have been allowed an excused absence will be asked to complete a written assignment concerning the papers discussed during the missed class session.
Grading and Evaluation
There are no exams. The class has a pass/fail grading system. There will be two two-page written assignments and a project. The first assignment will be a project and will involve creating a graphic representation of a protein involved in photosynthesis using 3D-structural coordinates from the Protein Data Bank (PDB). The goal of your protein modeling is to highlight and visually present a feature of the protein important to its function. Protein illustrations should be completed in class in Ses #4. For the second assignment, students will be given an abstract from a scientific paper and will be asked to design a set of experiments that would support the conclusions presented in it. This assignment will be due by 5:00 pm in Ses #6. The final assignment will coincide with an oral presentation and will involve presenting an original research proposal to the rest of the class followed by a critique. Students should contact the instructors to discuss ideas and topics. The written research proposal should be handed in before 5:00 pm in Ses #12. Students will be expected to rewrite their proposals incorporating any changes deemed necessary by the instructors and hand-in rewritten documents at the final class meeting. The proposal presentations will take place in class in Ses #15.
Prerequisites
As the goal of this course is to familiarize students with the reading and critical evaluation of the primary literature (research papers) in the field of photosynthesis, students are expected to have completed 7.03, 7.05, 7.06 or 7.08.
Calendar
Calendar table.
SES # |
TOPICS |
KEY DATES |
1 |
An Introduction to Photosynthesis |
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2 |
The Emergence of Oxygenic Photosynthesis |
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3 |
Anoxygenic Photosynthesis |
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4 |
Light Harvesting |
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5 |
Primary Photochemistry of Photosystems II |
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6 |
Primary Photochemistry of Photosystems I |
Abstract assignment due |
7 |
Structure of Photosystems II and I |
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8 |
Electron Transfer |
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9 |
Production of ATP |
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10 |
Carbon Fixation- Ribulose 1,5-Bisphosphate Carboxylase |
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11 |
C-4 vs. C-3 Photosynthesis Pathways |
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12 |
Project Day: TEM of Phycobilisomes |
Draft of research proposal due |
13 |
Bacterial Proteorhodopsin and "Extreme" Photosynthesis |
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14 |
Nanotechnology of Photosynthesis |
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15 |
Proposal Presentations |
Final version of research proposal due |
Course Description
In this course, you will journey through the web of physical, chemical, and biological reactions that collectively constitute photosynthesis. We will begin with light harvesting and follow photons to the sites of primary photochemistry: the photoreaction centers. A molecular-scale view will show in atomic detail how these protein complexes capture and energize electrons. Then we will follow the multiple pathways electrons take as they carry out their work. Consequent reactions, such as the synthesis of ATP and the reduction of CO 2 during the synthesis of carbohydrates, will also be discussed in structural detail. Lastly, we will delve into the evolution of these systems and also discuss other photosynthetic strategies, such as light-driven proton pumps and anoxygenic photosynthesis. The course will include a visit to an electron microscope to allow students to directly observe proteins involved in photosynthesis.
This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.
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Further Reading:
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Readings
Readings table.
SES # |
TOPICS |
READINGS |
1 |
An Introduction to Photosynthesis |
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2 |
The Emergence of Oxygenic Photosynthesis |
Dismukes, G. C., V. V. Klimov, S. V. Baranov, Y. N. Kozlov, J. DasGupta, and A. Tyryshkin. "The Origin of Atmospheric Oxygen on Earth: The Innovation of Oxygenic Photosynthesis." Proceedings of the National Academy of Sciences of the United States of America 98, no. 5 (2001): 2170-2175.
Xiong, J., W. M. Fischer, K. Inoue, M. Nakahara, and C. E. Bauer. "Molecular Evidence for the Early Evolution of Photosynthesis." Science 289, no. 5485 (2000): 1724-1730.
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3 |
Anoxygenic Photosynthesis |
Post, A. F., and B. Arieli. "Photosynthesis of Prochlorothrix Hollandica Under Sulfide-Rich Anoxic Conditions." Applied and Environmental Microbiology 63, no. 9 (1997): 3507-3511.
Griesbeck, C., M. Schutz, T. Schodl, S. Bathe, L. Nausch, N. Mederer, M. Vielreicher, and G. Hauska. "Mechanism of Sulfide-Quinone Reductase Investigated Using Site-Directed Mutagenesis and Sulfur Analysis." Biochemistry 41, no. 39 (2002): 11552-11565.
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4 |
Light Harvesting |
Liu, Z., H. Yan, K. Wang, T. Kuang, J. Zhang, L. Gui, X. An, and W. Chang. "Crystal Structure of Spinach Major Light-Harvesting Complex at 2.72 A Resolution." Nature 428, no. 6980 (2004): 287-292.
Li, X. P., O. Bjorkman, C. Shih, A. R. Grossman, M. Rosenquist, S. Jansson, and K. K. Niyogi. "A Pigment-Binding Protein Essential for Regulation of Photosynthetic Light Harvesting." Nature 403, no. 6768 (2000): 391-395.
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5 |
Primary Photochemistry of Photosystems II |
Barry, Bridgette A., Ian B. Cooper, Antonio De Riso, Scott H. Brewer, Dung M. Vu, and R. Brian Dyer. "Time-Resolved Vibrational Spectroscopy Detects Protein-Based Intermediates in the Photosynthetic Oxygen-Evolving Cycle." Proceedings of the National Academy of Sciences 103, no. 19 (2006): 7288-7291.
Groot, M. L., N. P. Pawlowicz, L. J. van Wilderen, J. Breton, I. H. van Stokkum, and R. van Grondelle. "Initial Electron Donor and Acceptor in Isolated Photosystem II Reaction Centers Identified with Femtosecond Mid-IR Spectroscopy." Proceedings of the National Academy of Sciences of the United States of America 102, no. 37 (2005): 13087-13092.
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6 |
Primary Photochemistry of Photosystems I |
Rajagopal, S., N. G. Bukhov, H. A. Tajmir-Riahi, and R. Carpentier. "Control of Energy Dissipation and Photochemical Activity in Photosystem I by NADP-Dependent Reversible Conformational Changes." Biochemistry 42, no. 40 (2003): 11839-11845.
Poluektov, O. G., S. V. Paschenko, L. M. Utschig, K. V. Lakshmi, and M. C. Thurnauer. "Bidirectional Electron Transfer in Photosystem I: Direct Evidence from High-Frequency Time-Resolved EPR Spectroscopy." Journal of the American Chemical Society 127, no. 34 (2005): 11910-11911.
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7 |
Structure of Photosystems II and I |
Ben-Shem, A., F. Frolow, and N. Nelson. "Crystal Structure of Plant Photosystem I." Nature 426, no. 6967 (2003): 630-635.
Ferreira, K. N., T. M. Iverson, K. Maghlaoui, J. Barber, and S. Iwata. "Architecture of the Photosynthetic Oxygen-Evolving Center." Science 303, no. 5665 (2004): 1831-1838.
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8 |
Electron Transfer |
Maiti, S., G. C. Walker, B. R. Cowen, R. Pippenger, C. C. Moser, P. L. Dutton, and R. M. Hochstrasser. "Femtosecond Coherent Transient Infrared Spectroscopy of Reaction Centers from Rhodobacter Sphaeroides." Proceedings of the National Academy of Sciences of the United States of America 91, no. 22 (1994): 10360-10364.
Kurisu, G., H. Zhang, J. L. Smith, and W. A. Cramer. "Structure of the Cytochrome b6f Complex of Oxygenic Photosynthesis: Tuning the Cavity." Science 302, no. 5647 (2003): 1009-1014.
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9 |
Production of ATP |
Abrahams, J. P., A. G. Leslie, R. Lutter, and J. E. Walker. "Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria." Nature 370, no. 6491 (1994): 621-628.
Stock, D., A. G. Leslie, and J. E. Walker. "Molecular Architecture of the Rotary Motor in ATP Synthase." Science 286, no. 5445 (1999): 1700-1705.
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10 |
Carbon Fixation- Ribulose 1,5-Bisphosphate Carboxylase |
Esquivel, M. G., T. S. Pinto, J. Marin-Navarro, and J. Moreno. "Substitution of Tyrosine Residues at the Aromatic Cluster Around the betaA-betaB Loop of Rubisco Small Subunit Affects the Structural Stability of the Enzyme and the in Vivo Degradation Under Stress Conditions." Biochemistry 45, no. 18 (2006): 5745-5753.
Desimone, M., A. Henke, and E. Wagner. "Oxidative Stress Induces Partial Degradation of the Large Subunit of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase in Isolated Chloroplasts of Barley." Plant Physiology 111, no. 3 (1996): 789-796.
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11 |
C-4 vs. C-3 Photosynthesis Pathways |
van Ginkel, L. C., G. Bowes, J. B. Reiskind, and H. B. Prins. "A CO(2)-Flux Mechanism Operating Via pH-Polarity in Hydrilla Verticillata Leaves with C(3) and C(4) Photosynthesis." Photosynthesis Research 68, no. 1 (2001): 81-88.
Yuan, J., J. Sayegh, J. Mendez, L. Sward, N. Sanchez, S. Sanchez, G. Waldrop, and S. Grover. "The Regulatory Role of Residues 226-232 in Phosphoenolpyruvate Carboxylase from Maize." Photosynthesis Research 88, no. 1 (2006): 73-81.
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12 |
Project Day: TEM of Phycobilisomes |
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13 |
Bacterial Proteorhodopsin and "Extreme" Photosynthesis |
Beja, O., E. N. Spudich, J. L. Spudich, M. Leclerc, and E. F. DeLong. "Proteorhodopsin Phototrophy in the Ocean." Nature 411, no. 6839 (2001): 786-789.
Beatty, J. T., J. Overmann, M. T. Lince, A. K. Manske, A. S. Lang, R. E. Blankenship, C. L. Van Dover, T. A. Martinson, and F. G. Plumley. "An Obligately Photosynthetic Bacterial Anaerobe from a Deep-Sea Hydrothermal Vent." Proceedings of the National Academy of Sciences of the United States of America 102, no. 26 (2005): 9306-9310.
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14 |
Nanotechnology of Photosynthesis |
Das, R., P. J. Kiley, M. Segal, J. Norville, A. A. Yu, L. Wang, and A. S. Trammell, et al. "Integration of Photosynthetic Protein Molecular Complexes in Solid-State Electronic Devices." Nano Letters 4, no. 6 (2004): 1079-1083.
Steinberg-Yfrach, G., J. L. Rigaud, E. N. Durantini, A. L. Moore, D. Gust, and T. A. Moore. "Light-Driven Production of ATP Catalysed by F0F1-ATP Synthase in an Artificial Photosynthetic Membrane." Nature 392, no. 6675 (1998): 479-482.
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15 |
Proposal Presentations |
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