Photosynthesis (SC/BIOL 4160 3.0)

Reaction Center poster 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

15 August 2014: As a backup to the Lab Manual (Bio.Wiki), here is an html backup: Lab Manual (Static HTML)

4 December 2013: Thank you all for making this such an enjoyable course, and, best wishes on all your future photosynthetic endeavours!


9 June 2011: I have been asked by the University to remind students of the University Senate Policy regarding Academic Honesty: Both the University Policy and additional resources for students.


Course Description

reflectance spectroscopy poster

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 [pdf] is available, as is the Syllabus [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: Christopher Powe. Email: cpowe@yorku.ca

Schedule: Lectures (location: Life Sciences Building 101) 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)


solar spectrum

Assignments and Grading:

Students decided on the following breakdown for 2013/2014:
Lecture Component: 70%
Two Term Tests and the Final Exam (comprehensive) (60%): The lowest score is worth 15%, the middle worth 20% and the highest worth 25% (of 60% in toto).
One Assignment (10%): Focussed on a popular description of some aspect of photosynthesis. (late penalty is 10% per school day)
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, 15% will be carried over to the final and other term test (lowest score worth 27.5%, highest worth 32.5%)
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:

  • 2013 Syllabus [pdf]
  • 2011 Syllabus [pdf]
  • 2008 Syllabus [pdf]
  • 2006 Syllabus [pdf]
  • Past Course Evaluations by the Students:

  • 2013 Evaluation (with advice from the class to prospective students) [pdf]
  • 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:

  • 2013 exams (term tests and final) [pdf]
  • 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

    diatom poster

    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. (Library reserve link)
    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. (Library reserve link)
    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. (Library reserve link)
    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

    photosynthesis wordle


    Archived Announcements

    16 December 2013: I have finalized the draft of the final exam. The format is similar to previous final exams. You will be asked to answer FIVE of the SIX questions in the exam booklet provided.

    The questions cover the full range of topics covered in the course. I expect that students will be able to complete the exam in two (2) hours.
    Crib sheets details: For the final exam, you can have four pages (letter size), both sides (for a total of eight sides). Typed is fine. They should be handed in with your exam.
    The exam is being held in CB 115 from 7:00 PM. Don't forget that goSAFE is available should you require it.

    27 November 2013: I've mounted the lecture notes for the Dark Reactions on Moodle.

    The next lecture will be on Bioengineering. Recent overviews are provided by Raines (2011) Increasing photosynthetic carbon assimilation and Hanson et al (2013) Chloroplast transformation.

    25 November 2013: Lab Exercises Here are the gel digests (in case you were unable to download them from Moodle).


    18 November 2013: Tests will be returned to you during Wednesday's lecture. We will be continue to 'track the carbon' in the Calvin Cycle.

    11 November 2013: Photosynthesis in the News Photosynthetic Machines

    wavelet diagram There will be a Public Lecture (Tuesday 26 November at 7:30 pm) by the 2012 NSERC Polanyi Prize Winner Gregory Scholes: Photosynthetic Machines: Why Nature is Astounding. He will be introduced by Nobel Laureate John C. Polanyi.
    "Photosynthetic solar energy conversion occurs on an immense scale across the earth, influencing our biosphere from climate to oceanic food webs. These are amazing solar cells!
    Fronds in kelp forests, crustose coralline algae and purple bacteria show interesting properties that are helping reveal the chemical physics involved in the ultrafast energy transfers of light harvesting. This talk introduces the incredible processes that initiate photosynthesis in the first picoseconds after light is absorbed."
    Scholes is very well known for his research on the initial exciton transfers after light absoprtion, where quantum effects are now known to occur even at room temperature. It's strong evidence that Biology discovered Quantum Physics more than 3500 million years ago!.

    12 November 2013: Lab Exercises restriction digest of chloroplast genome Here's the digest from Monday's lab. You should be able to compare the digest band sizes with the restriction map mounted at the Bio.Wiki.


    10 November 2013: Term Test: Monday 18 November

    The format is likely to be answer three of the following four questions. I don't expect to include questions on carbon dioxide fixation.
    The questions are not likely to be cumulative, but answering them effectively will require a good understanding of the material we've covered so far. So, you may want to review past material while focussing on the material since the last term test.
    Update (13 November 2013) The test questions are focussed on the lectures on Reaction Centers and NADPH and ATP Production.
    Crib sheets details: For the second term test, you can have three pages (letter size), both sides (for a total of six sides). Typed is fine. They should be handed in with your test (and will be returned to you). I expect that you will be re-using them for the final exam --with an added sheet.

    4 November 2013: I mounted the ATP and NADPH production lectures on Moodle. We are now commencing the Dark Reactions of photosynthesis. The textbook provides good coverage in Chapter 7 (The Chemistry of Photosynthesis).

    Update: Here is an example of a worked bioenergetics problem [png].

    25 October 2013: Photosynthesis in the News Liquid Fuel

    leaf network of veins The New Yorker magazine published an article entitled Liquid Fuel, from the Sun, highlighting research coming from the Joint Center for Artificial Photosynthesis (JCAP). This is a heavily-funded research center whose mandate is "the development of an artificial solar-fuel generation technology". Most of the research is on the engineering side, but the biochemical-side of photosynthesis can provide some ideas, proven to work for 3500 million years!.


    21 October 2013: I will be finishing up the lectures on Reaction Centers this week (I will update the lecture notes on Moodle when finished). The next lecture will be on ATP and NADPH production. I don't have a 'source' for this lecture. The textbook provides good coverage of both Electron and proton transport (Chapter 5) and Synthesis of ATP: photophosphorylation (Chapter 6). The lectures are relevant to the lab exercises you will be doing this week and next week (Labs 06 and 07), where you will be introduced to the Oxygen Electrode, a favorite tool of researchers studying chloroplasts (and mitochondria).

    14 October 2013: Term Test: Wednesday 16 October

    The term test is finalized! The format is answer three of the following four questions.
    The questions tend to be more thinking, but answering them effectively will require a good understanding of the material we've covered so far.
    I don't think I ever memorialized the crib sheets details: two pages (letter size), both sides (for a total of four sides). Typed is fine. They should be handed in with your test (and will be returned to you). I expect that you will be re-using them for the next test --with an added sheet.

    8 October 2013: Assignment I have updated my list of some examples of TIPS articles that might be suitable for your assignment [txt].

    Update 14 October: Here is a link to general guidelines for your assignment [html].

    The lecture notes for Light Harvesting have been mounted on Moodle.

    2 October 2013: Assignment Students decided to have an assignment in which they explained a recent photosynthesis topic to first year science students. The due date will be Monday 4 November (before 5:00 PM). The best approach is to have students select an article from a Trends journal. I ran a quick search on two of the Trends journals (Trends in Biochemical Sciences and Trends in Plant Sciences) using PubMed. The search strings were:

    • http://www.ncbi.nlm.nih.gov/pubmed/?term=photosynthesis+trends+in+plant+sciences
    • http://www.ncbi.nlm.nih.gov/pubmed/?term=photosynthesis+trends+in+biochemical+sciences
    with more recent hits from TIPS. You should be able to find some good possibilities, and I will highlight some that I think would work well for the assignment over the next couple of weeks [txt]. You can check your selection with me to ensure it will work effectively as an assignment topic.


    2 October 2013: Lab Exercises chloroplast isolation chloroplast isolation Here are before and after shots of chloroplast isolation from the green alga Eremosphaera viridis, courtesy of Knika's lab group. The highly birefringement chloroplasts in the lower panel indicate a high percentage of intact chloroplasts. To the right are leaves in situ. The chloroplasts are crescent-shaped (right panel).


    2 October 2013: I've mounted the lecture notes for the fourth lecture topic (Pigments) on Moodle. The next lecture will be on Light Harvesting. I don't have a 'source' for this lecture. The textbook provides good coverage in Chapters three (Light Harvesting and Energy Capture) and four (Architecture of the Photosynthetic Apparatus).

    26 September 2013: Photosynthesis in the News Oxygenic Photosynthesis gets Older

    oxygen molecule Canadian news sources have picked up on some recent research that has a national connection (UBC scientists). It's geological evidence for 'elevated' oxygen levels much earlier than previously thought (by 700 million years!). (CBC coverage). It's based on indirect metrics for oxygen levels (traces of oxidized chromium isotopes in old rocks) and predicts oxygen levels of about 0.002% (much lower than our present 20%). I think the finding will face scepticism. Like all evidence of early oxygenic photosynthesis, the data are frustratingly indirect. The sciency article was published in Nature.


    24 September 2013: I've mounted the lecture notes for the second and third lecture topics (Bacterial Photosynthesis and Light) on Moodle. The next lecture will be on Photosynthetic Pigments. I don't have a 'source' for this lecture. The textbook provides good coverage of both Light (Chapter 2) and Light Harvesting (Chapter 3 --including pigments).

    15 September 2013: I've mounted the lecture notes for the first lecture topic (Geological Photosynthesis) on Moodle. The next lecture will be on Bacterial Photosynthesis (anaerobic). The major objective is to introduce you to the diversity of photosynthetic mechanisms, highlighting alternative carbon dioxide fixation pathways. The long-term relevance is bioengineering. I don't have a 'source' for this lecture. A relatively recent overview is provided in an article by Bryant and Frigaard (2006) entitled Prokaryotic photosynthesis and phototrophy illuminated.

    12 September 2013:reflectance setup Just a reminder for the labs on Monday and Tuesday. The reflectance spectroscopy uses fiber optic cables. Overbending the cables can damage the optical fibers. So handle them gently (don't force them to bend) during the labs.


    10 September 2013: The first lecture topic (tomorrow) will be on Geological Photosynthesis. We will be exploring the different kinds of evidence supporting the appearence of photosynthesis in geological time. My source for this is a review by J. William Schopf (The paleobiological record of photosynthesis). His paper was part of a special issue of the journal Photosynthesis Research on the Evolution of Oxygenic Photosynthesis. An overview is available in your textbook (Chapter 1).

    20 August 2013:Reflectance plants Reflectance plants Preparations for the Photosynthesis course are ongoing, including growing crops in the greenhouse to provide plants (and chloroplasts) for the lab exercises (online at Bio.Wiki). Students will select which kind of plants they want to use for their experiments. We've got beans, basil, sunflower, cucumber, corn and many other possibilities!

    Update (14 September 2013): More recent snapshots of the plants to the right, the beans are already flowering!


    13 August 2013:textbook The textbook for Photosynthesis is available at the York Bookstore. The lab manual is available online at Bio.Wiki.


    5 August 2013: Photosynthesis in the News Photosynthesis at the Microscale (CERL-30)

    Rather than news, this is a solicitation for research proposals (I received it via email, so no links). The Environmental Chemistry Laboratory (ECL) at CERL (Construction Engineering Research Laboratory) is currently interested in addressing the need for supplying energy at the microscale for powering portable or remote fieldable devices. With the ongoing revolution in our scientific understanding of photosynthesis in plants, the interest is to develop artificial photosynthesis to provide power at a high efficiency. Who is interested in funding this kind of research? Mostly the US Military (US Army Engineers in this example). DARPA is interested; on the civilian side, DOE has been interested for a long time. In this particular solicitation (CERL-30), proposals are sought to address each step in the photosynthetic process. This includes but is not limited to the following:
    • self assembled constructs that mimic one or more parts of photosystem II: photon capture, electron transfer, charge separation and water oxidation steps
    • membrane systems with selective passive transport of protons
    • immobilized hydrogenase mimic for reduction of protons to hydrogen or enzymes for CO2 conversion to biofuel.
    It's an example of the tremendous importance of photosynthesis (and a good reason to teach a course on the subject!)

    22 July 2013: Photosynthesis in the News X-rays Illuminate Oxygen Evolution.

    x-ray fluorescence techniqueTo see what happens during water splitting in photosystem II, you need to look fast and with extraordinary spatial resolution at physiologically relevant temperatures. That's where femtosecond x-ray pulses come into play: combining x-ray spectroscopy and x-ray diffraction. The work was done at the SLAC National Accelerator Laboratory in Menlo Park California. It revealed changes in the electronic structure of the Mn4CaO5 cluster that is central to the water-splitting reaction --light-driven oxidation that sequentially removes electrons (and hydrogen) from water, to eventually produce the oxygen byproduct. The sciency article was published in an April issue of Science Magazine. It's a good indication of how fast things are happening in the photosynthetic revolution.


    25 June 2013: Photosynthesis in the News Algae Airships.

    algal airshipsThe BBC World News highlights futuristic visions of cities in a recent article, including an idea from the architect Vincent Callebaut: who proposed 'algae airships', using hydrogen-creating seaweed which allows the structures to float above the ground. There is a lot of interest in hydrogen-producing photosynthetic organisms. The idea of algal airships is a bit 'up in the air' (pun decidedly intended).


    21 June 2013: Photosynthesis in the News Photosynthesis Goes Quantum.

    There has been an ongoing scientific controversy about unusual quantum effects in photosynthesis: Coherence and entanglement. Coherence is when the photon (excition) exists in multiple places simultaneously. Entanglement is when the fate of one exciton affects the fate of another exciton. Physicists get excited about this sort of stuff (pun intended). Biologists are a bit more practical (these kinds of effects are normally demonstrated at super-cold temperatures, well below biologically relevant ones). Still, the physicists won't give up. The latest is a news article in BBC News that highlights a recent paper in Science.

    18 April 2013:lecture calender 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.


    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.
    Update (14 July 2013): The lecture room will be Life Sciences Building Room 101.

    light reaction diagram 18 December 2012: Useful resources for the Photosynthesis course can be found at Hansatech Instruments.

    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. 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. 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.


    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. Here is a news article from the News Gazette.

    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 BioWiki website.

    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 [pdf] from Dyson's essay and a response from a Biochemist.

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

    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. 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.

    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.

    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 [pdf] in 2006. 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.

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

    news article 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. 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: Feel free to explore more possibilities!

    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.

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

    quantum equation26 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.

    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".

    15 August 2011:The moodle website for the course has been activated.

    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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