Photosynthesis (SC/BIOL 4160 3.0)

Welcome to the Photosynthesis (SC/BIOL 4160.03, crosslisted as SC/BCHM 4160.03) course website. This is your central source for announcements, lab and lecture information (including course evaluations), past tests, useful links etcetera.


Announcements

9 April 2013: This will be the course website for the next offering of the course in the fall of 2013.

The course description includes past syllabi, course evaluations, and sample tests and assignments. The course evaluations include advice to prospective students and should give you a 'student-centric' view of the course. The lab exercises are mounted on a public Bio.Wiki website and should give you an idea about the nature of the lab component of the course.

18 April 2013: The tentative schedule for Photosynthesis labs is available (click on the image for a larger version). The lab manual is available online at Bio.Wiki.


18 December 2012: Photosynthesis in the News The Gates Foundation Sees the Light.

The Bill and Melinda Gates Foundation is most famous for providing funds in support of eradicating AIDS and malaria. But recently, they provided funds for research on photosynthesis. After all, we need photosynthesis to eat, and molecular biological tools for bioengineering photosynthesis to improve productivity have become very sophisticated in the past two decades. A news article from the News Gazette can be found [here]

18 December 2012: Useful resources for the Photosynthesis course can be found at Hansatech Instruments [link].

Hansatech Instruments (which specializes in measuring instrumentation for physiological research on photosynthesis) hosts digital textbooks accessible through Open Access in conjunction with the International Society of Photosynthesis Research [link]. They are by David Alan Walker, a very famous researcher in Photosynthesis (now deceased). One of these books is The Use of the Oxygen Electrode and Fluorescence Probes in Simple Measurements of Photosynthesis [link]. It provides a well-written overview of oxygen electrodes, fluorescence, and chloroplast isolation that should be very helpful to students for the lab component of the course.

17 December 2012: The 2013 Course Outline is available in draft form [pdf].

28 December 2011: Lab Exercises The lab manual has been mounted as a LabWiki at the following BioWiki website: [link].

9 June 2011: I have been asked by the University to remind students of the University Senate Policy regarding Academic Honesty. The policy can be found at the following [link]. The University provides additional resources for students at the following [link].


Course Description

A study of the process of photosynthesis at the biochemical, organelle and whole organism levels, including structure of the photosynthetic apparatus, primary light harvesting processes, electron transport, photophosphorylation, mechanism of carbon dioxide fixation in higher plants and algae, photorespiration.

Two lecture hours, three laboratory hours. One term. Three credits.

The Course Outline is available in draft form [pdf].

Cross-listed to: SC/BCHM 4160 3.0. Prerequisite: One of the following: (1) SC/BIOL 2021 4.00 or SC/BCHM 2021 4.00; (2) SC/BIOL 2021 3.00 or SC/BCHM 2021 3.00; SC/BIOL 2070 3.00.

Course Director: Roger Lew

Lab Demonstrator: TBA. Email: TBA

Schedule: Lectures (location: TBA) are on Monday and Wednesday (8:30 to 9:30 AM). The lab sections (Lumbers 106) are Monday and Tuesday (from 2:30 to 5:30 PM).

Textbook: Lawlor, D.W. (2001) Photosynthesis (3d edition). Springer-Verlag
(another good introductory textbook (not required) is: Blankenship, R.E. (2002) Molecular Mechanisms of Photosynthesis. Blackwell Science)


Assignments and Grading:

Students decided on the following breakdown for 2011/2012:
Lecture Component: 70%
Two Term Tests (40%): The lowest score is worth 10%, the highest worth 30% (of 40% in toto).
One Assignment (10%): Focussed on a popular description of some aspect of photosynthesis. (late penalty is 10% per school day)
Final Exam (20%): Comprehensive.
Laboratory Component: 30%
Participation (5%). Two lab reports on selected lab exercises, the lowest weighted 10%, the highest weighted 15% of the laboratory component (30% in toto).
In the event of a documented absence from a term test, 10% will be carried over to the final and the remaining term test will be worth 30%
Past grading schemes [png]

Other Information:
The mechanisms of photosynthesis are explored beginning with absorption of light and culminating in a survey of metabolic flux and assimilate partitioning in the whole plant.

Past Syllabi:

  • 2011 Syllabus [pdf]
  • 2008 Syllabus [pdf]
  • 2006 Syllabus [pdf]

    • Past Course Evaluations by the Students:

  • 2011 Evaluation (with advice from the class to prospective students) [pdf]
  • 2008 Evaluation (with advice from the class to prospective students) [pdf]
  • 2006 Evaluation [pdf]

    • Sample Tests:

  • 2011 exams (term tests and final) [pdf]
  • 2008 exams (term test and final) [pdf]
  • 2006 exams (term tests and final) [pdf]

    • Pathways

    The metabolic maps below were constructed by Donald Nicholson. They are useful for getting an overview of the photosynthetic process.

    Photosynthesis in Chloroplast (link to gif) Photosynthesis - Regulation (link to gif) both at IUBMB-Nicholson MiniMaps (from where you can download the maps in higher resolution pdf format)

    Readings

    These are not required reading. They provide entry points into various aspects of photosynthesis we explore during lecture.


    Bibliography
    David W. Lawlor: Photosynthesis (3d edition). Springer-Verlag (2001)
    A general textbook describing the mechanisms of photosynthesis and its physiological properties in photosynthetic organisms.
    		 Park S. Noble: Physicochemical and Environmental Plant Physiology. Academic Press (1991)
    A biophysical approach to cell and organismal physiology that includes useful chapters on all aspects of photosynthesis.
    T.W. Goodwin and E.I. Mercer: Introduction to Plant Biochemistry. Pergamon Press (1983)
    All aspects of plant biochemistry are presented, including the light and dark reactions of photosynthesis.
    		 Robert E. Blankenship: Molecular Mechanisms of Photosynthesis. Blackwell Science (2001)
    An introductory textbook describing the biochemistry of photosynthesis, history, and evolution.
    L.R. Milgrom: The Colours of Life. An introduction to the chemistry or porphyrins and related compounds. Oxford University Press (1997)
    An introduction to the remarkable diversity of porphyrins, which include the chlorophylls. The perspective is that of a Chemist.
    		 H-W. Heldt: Plant Biochemistry and Molecular Biology. Oxford University Press (1997)
    An introductory textbook describing plant biochemistry, including photosynthesis.

    Photosynthesis Wordle

    Archived Announcements

    5 December 2011: In last week's lecture, I mentioned Black Leaves, an idea proposed by the futurist Freeman Dyson as a means to enhance the quantum efficiency of light capture in photosynthesis. Here are direct quotes from Dyson's essay and a response from a Biochemist. [pdf].

    30 November 2011: I mounted the lecture notes for the ninth lecture (Metabolic Flux) on Moodle [link].

    28 nov 2011: NSERC USRA Awards

    NSERC USRAs are federally funded summer research awards for undergraduate students. Information about eligibility can be found at the NSERC website [link]. The internal application deadline is January 23, 2012. You can obtain more information by contactng your home departments.
    It is a wonderful (and paid) opportunity to be introduced to scientific research. You should be approaching professors about the possibility of working in their labs fairly soon.

    28 November 2011: I mounted the lecture notes for the eighth lecture (Dark Reactions) on Moodle [link].

    28 November 2011: The Final Exam is scheduled for Friday 16 December at 14:00 in CB (Chemistry Building) Room 115. The duration of the final is 3 hours. I expect the required time to be about 2 hours, but the additional time will be available to you as required.

    15 November 2011: Assignment Reminder: Current Topic in Photosynthesis. As detailed below, please don't forget your upcoming assignment!

    Update 3 (23 November 2011). I was asked about late penalties, and pulled my standard late penalties from another upper level course: A late penalty will apply: 10% after 4:30 friday (meaning that I find it under my door on the weekend), 20% for monday, 40% for tuesday ad infinitum. Please do hand it in on time!
    Update 2 (21 November 2011). I was asked about length and format of the assignment. It is a bit hard for me to 'metric' on this. But with a weighting of 10% of your grade, I think 6 to 10 pages (double spaced) should be reasonable. Bear in mind that I prefer hand-written. I like diagrams as a way to explain things, and diagrams are easier to dovetail into a handwritten assignment. Plus, I think hand-written encourages you to use your own voice, your explanation (rather than mimicking something written by someone else).

    9 November 2011: As promised, a sample work problem on Gibbs free energy [png].

    7 November 2011: I mounted the lecture notes for the seventh lecture (NADPH and ATP Production) on Moodle [link].

    7 November 2011: Reminder: Second Term Test next Monday 14 November.

    Update 2 The draft is finalized. At present, there are four (4) questions. I used the 2006 second term test as a template. The questions are different, but the coverage is similar. It's not cumulative. The questions are knowledge-based rather than analytical. The rules of engagement for the crib sheets are the same as last time: Both sides of two sheets of 8.5 by 11 inch paper. I hope you all do well!
    Update 1 The general format of the test will be similar to the second term test in 2006 [pdf]. More information to follow (after I write the questions!)
    The general idea is to change the format of the test from solely analytical (as in the first term test) to a mix of knowledge-based with some analytical.

    1 November 2011: I mounted the lecture notes for the sixth lecture (Reaction Centers) on Moodle [link].

    27 October 2011: Lab Exercises Here is an example of oxygen evolution in a whole cell suspension of Eremosphaera viridis that shows the effect of adding bicarbonate (that is, carbon dioxide for fixation) [png]. Note that dark causes oxygen consumption due to mitochondrial respiration.

    25 October 2011: Assignment: Current Topic in Photosynthesis.

    Update 1. I realized the due date was not announced. It is 4:30 pm on Friday 25 November
    Here are the general guidelines for the assignment. The basic objective is to give you an opportunity to communicate science to a reader who is not as knowledgeable as you. From my (pedagogical) viewpoint, this is a way to give you an opportunity to make science accessible to someone whose background is not science.
    Essentially, you will be describing some new or topical advance in photosynthesis, explaining what it is and what its impact could be. Please don't spend a lot of time reviewing basic photosynthesis, just assume that the reader has good general knowledge about the 'basic equations and processes' of photosynthesis, so that you can delve into your topic with minimal introduction.
    The rubric is, by the very nature of the assignment, fairly general. Described in order of descending importance: Mastery of the topic. That is, how well you understand the topic you are explaining. Then, your ability to explain the material effectively. That is, logical flow and clarity. Finally, writing is a craft. Your craftsmanship improves with experience, so grammatical skill and writing style will also be considered.
    The range of topics I provide on the website should give you a good entry into the possibilities. If you have questions (even as you write), please do ask me!
    I will need sources referenced. I am not requiring 'formal referencing', but I do need to be able to find the material you worked from when writing your assignment.

    24 October 2011: Photosynthesis in the News The End Is Near.

    An old news article reporting on a presentation at the American Association for the Advancement of Science highlights a long-standing concern of scientists, albeit with the excessive prose of the news media ("Combustion Leads to Eventual Suffocation"). Human consumption of resources, the burning of fossil fuels, the massive strain on global carrying capacity are real problems. The fact that The End Has Not Happened forty four years later may (or may not) be reassuring. It is all intertwined with photosynthesis.

    20 October 2011: Photosynthesis in the News Aurora | algae Enters the Commercialization Phase.

    Commercialization of photosynthesizing bioreactors is slowly becoming a reality, as this press release from Aurora | algae reveals. [link]. Aurora | algae is a company located in Alameda, California and West Perth, Australia that has been developing bioreactors to produce specialized products from algae.

    20 October 2011: Photosynthesis in the News Press Releases.

    I figured out that if I 'googled' photosynthesis and "press release", there were a number of top hits that might be a good starting point for the assignment:
    • Scientists probe the energy transfer process in photosynthetic proteins [link]
    • Elucidating the Mechanism behind Light-induced Water-splitting in Photosynthesis [link]
    • Artificial Photosynthesis versus Greenhouse Gas [link]
    • Photosynthesis - the most important chemical reaction on earth [link]
    • Mimicking Photosynthesis May Hold Key to Cheap Hydrogen for Fuel [link]
    • Could Black Trees Blossom in a World With Two Suns? [link]
    Feel free to explore more possibilities! [link]

    19 October 2011: Photosynthesis in the News Practical Artificial Leaves.

    Here is a press release from the American Chemical Society, describing recent advances in the engineering of an artificial leaf. "Placed in a single gallon of water in a bright sunlight, the device could produce enough electricity to supply a house in a developing country with electricity for a day, Nocera said. It does so by splitting water into its two components, hydrogen and oxygen." [link]. I don't know whether the work has been published, but if ACS thought it was news fit to print, then it might be a good subject for the assignment.

    19 October 2011: Photosynthesis in the News Global photosynthesis faster than thought.

    An international group of researchers took advantage of air samples collected over the past 30 years to obtain a fine-grained estimate of global photosynthetic rates. They relied upon isotopic ratios of water and oxygen, and discovered global rates of photosynthesis (usually extrapolated from laboratory measurements on leaves) were faster than previously thought [link]. The work was published in Nature [link].
    This might be a good subject for the assignment.

    18 October 2011: Lab Exercises Here are operating instructions for the Clark oxygen electrode [png] and chart recorder [png] (both will be provided as hardcopy for the oxygen evolution labs).

    Here is an example of the measurements and calculations for oxygen evolution from real data using algal cells, showing oxygen production in the light, and consumption in the dark (due to mitochondrial respiration, something that should not happen with chloroplasts) [png].

    12 October 2011: Term Test: Monday 17 October

    Update 4 (emailed 14 oct). The term test is finalized! The format is answer four of the following five questions.
    I'm not sure how much more guidance I can provide. I think the questions tend to be more thinking questions rather than a test of your comprehensive knowledge (more so than past tests). But answering them effectively will require a good understanding of the material we've covered so far.
    Update 3 (emailed 13 oct). The first draft of the term test is complete.
    There are four questions (I may add one more). They are drawn from each of the lectures (Evolutionary Photosynthesis, Bacterial Photosynthesis, Light, Pigments and Light Harvesting), and assume a familiarity with lab material (on fluorescence).
    Update 2 (emailed 12 oct). Crib sheets will be allowed (and will serve as a good way to review the material). The usual legalities apply: Two 8.5 by 11 inch sheets, both sides (four sides in total). Microscopes or other visualizing aids are not acceptable (in case anyone wondered).
    Students in the past have noted the usefulness of crib sheets, but have also commented that it is not a good idea to over-rely on them. The questions will emphasize integration and application, not rote recall.
    Update 1 (emailed 7 oct). Lecture notes are mounted ([link]). I'll be giving you guidance about the test soon (feel free to email suggestions for questions to Shahin). Past tests on the course website (www.yorku.ca/planters/photosynthesis) will give you an idea about the usual format.

    9 October 2011: Photosynthesis in the News Mapping Global Fluorescence.

    Fluorescence in photosynthesis is complex, but is an important metric of photosynthetic health. With the development of new imaging technologies, NASA has gotten into the act of measuring global fluorescence [link]. The work was published in Biogeosciences [link]. Cool movies of seasonal changes for ocean phytoplankton are available from the following NASA webpage [link]. All direct evidence of the Global Reach of Photosynthesis.
    This might be a good subject for the assignment.

    7 October 2011: I mounted the lecture notes for the fifth lecture (Light Harvesting) on Moodle [link].

    3 October 2011: I mounted the lecture notes for the fourth lecture (Pigments) on Moodle [link].

    26 September 2011: As promised, a taste of quantum tunneling. It's new, fascinating, and a bit incomprehensible to your prof!


    26 September 2011: I mounted the lecture notes for the third lecture (Light) on Moodle [link].

    19 September 2011: Here is the Assignments and Grading decided on by the students:

    Lecture Component: 70%
    Two Term Tests (40%): The lowest score is worth 10%, the highest worth 30% (40% in toto).
    One Assignment (10%): Focussed on a popular description of some aspect of photosynthesis. (late penalty will be 10% per school day)
    Final Exam (20%): Comprehensive.
    Laboratory Component: 30%
    Two lab reports on selected lab exercises (12.5% each) and 5% for participation (initialed lab notes) (30% in toto).
    In the event of a documented absence from a term test, 10% will be carried over to the final and the remaining term test will be worth 30%
    Term Test Dates:
    first term test 17 October 2011
    second term test 14 November 2011

    15 September 2011: See you in lab this afternoon! (Room 106 Lumbers).

    15 September 2011: I mounted the lecture notes for the second lecture (Bacterial Photosynthesis) on Moodle [link].

    12 September 2011: I mounted the lecture notes for the first lecture (Evolutionary Photosynthesis) on Moodle [link].

    This is a trial run. Should you run into any problems, please feel free to email me (planters@yorku.ca).
    Update:The lecture notes include readings (not required) which are part of my notes, provided for the sake of completeness. For students who are interested in the very current research on evolutionary photosynthesis, J. William Schopf (one of the 'controversial' (but respected!) scientists in this field) provides an update The paleobiological record of photosynthesis [link]. The take-home message for me is how new technologies revolutionize our understanding of very ancient times.

    11 September 2011: I mounted scans of overheads from the introductory lecture on Moodle [link].

    They should be useful as supplementary material.

    7 September 2011: I hope you get the opportunity to discuss possible grading and assignment schemes amongst yourselves fairly soon. The University deadline for 'announcing components of final grades' is 20 September.

    Don't forget that the first lab for the course is scheduled for next week (Thursday 15 September), which may be a good time to decide.

    20 August 2011: Photosynthesis in the News Eating Sunshine.

    Some science bloggers have been commenting on the phenomenon of photosynthetic animals. They do exist! Often in a symbiotic relationship, or as chloroplast thieves. It is not very common, raising the question why? Here is a link to commentary by "Dr. Dolittle" [link]

    15 August 2011:The moodle website for the course has been activated [link]

    Lecture Notes will be made available on Moodle during the term.

    10 August 2011 update:The textbook (David W. Lawlor: Photosynthesis 3d edition) (and lab manual) are available at the York Bookstore [png]

    19 June 2011: Photosynthesis in the News I thought students would be interested to know about the course they are taking from a broader perspective. It is not common to have a course on Photosynthesis at the undergraduate level, but there are Universities that do.

    Johns Hopkins University (Biology Department) offers a course entitled "Photosynthesis by Land and Aquatic Organisms" [link]
    MIT (Massachusetts Institute of Technology) offers an advanced biology undergraduate seminar entitled "Photosynthesis: Life from Light" [link].
    In both cases, the curricular contents are very similar to our course, but neither has an associated lab to provide experiential learning for the students.

    15 June 2011: Lab Exercises Here are operating instructions for the Clark oxygen electrode [png] and chart recorder [png] (both will be provided as hardcopy for the oxygen evolution labs).

    Here is an example of the measurements and calculations for oxygen evolution from real data using algal cells, showing oxygen production in the light, and consumption in the dark (something that should not happen with chloroplasts) [png].
    28 June 2011: And a further test of the lab exercises: Here are fluorescence excitation/emission scans of chloroplasts and chlorophyll (in acetone:water) run by Ira and me [png].

    3 June 2011: Here is a tentative schedule for lab exercises in the fall term (subject to change, as required) [png]

    8 February 2011: This will be the course website for the next offering of the course in the fall of 2011.

    The course description includes past syllabi, course evaluations, and sample tests and assignments.

    Thank you all for making this such an enjoyable course, and, best wishes on all your future photosynthetic endeavours

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