PLNT*6320 Metabolic Processes in Crop Plants

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The following description is for the course offering in Fall 2019 and is subject to change. It is provided for information only. The course outline distributed to the class at the beginning of the semester describes the course content and delivery, and defines the methods and criteria to be used in establishing the final grades for the course.

A comprehensive examination of the metabolic mechanisms and versatility whereby autotrophic organisms sustain themselves. Emphasis will be placed on our current understanding of the regulation and integration of metabolic processes in plants, and their physiological and agricultural significance including available research methodologies.

Prerequisite: one undergraduate course in biochemistry.

Restriction: no auditing without permission of Instructor.


Teaching Assistant:

Credit Weight:


Course Level:

  • Graduate

Academic Department (or campus):

Department of Plant Agriculture



Semester Offering:

  • Fall

Class Schedule and Location:

Please refer to Web Advisor for class schedule and location.


Learning outcomes:

By the end of the course you should be able to:

  1. Have a comprehensive understanding of the field of plant metabolism at a level that allows experimental implementation, including available methodologies and the historical development and current understanding of the field such that the interactions between various plant metabolic processes can be understood and appreciated
  2. Integrate the field of plant metabolism with other disciplines including other biological fields, chemistry, biophysics, environmental and social sciences, and agriculture to gain a greater appreciation for the potential of applying our knowledge of plant metabolism to improving humanity including global issues such as the food supply, sustainable energy, and climate change
  3. Apply our knowledge of plant metabolism to specific research problems associated with biological processes, agriculture, forestry, energy production, and medicine
  4. Have improved their skills in communication, literacy and numeracy, and have gained an understanding of forms of inquiry including hypothesis development through critical analysis of the relevant scientific literature coupled with oral presentations and writing

Lecture Content:

Topics to be covered in lectures include

Course Introduction/Introduction to Plant Metabolism

  • Discussion of the course outline, organizational aspects of the course, analysis of scientific papers.
  • Background knowledge assumed for this course.
  • Introduction to plant metabolism, including definition of sources and sinks, definition of 1o and 2o metabolic processes, interactions between metabolic and developmental processes, integration of metabolic processes and interactions between sources and sinks, consideration of flux rates, regulation in space and time, metabolic flexibility in plants.
  • Introduction to the components that affect the energy-use efficiency of photosynthesis.
  • Properties of sunlight, definition of photoautotrophy.

An Introduction to Source Metabolism in Plants​

  • An examination of how the biochemical components and reactions of solar energy capture and transduction (i.e. light reactions of photosynthesis) affect the energy-use efficiency of photosynthesis, including: (1) properties of light-absorbing pigments; (2) photons absorbed by the light harvesting complex; (3) quantum efficiency of photochemistry; and (4) conversion of light energy to ATP and NADPH.
  • Relationship between structure and function for the components involved in light capture and energy transduction.
  • An examination of how the components of C metabolism affect the energy-use efficiency of photosynthesis, including: (1) photorespiratory CO2 loss; (2) utilization of energy in ATP & NADPH to reduce CO2 to triose-P; (3) dark respiratory CO2 loss; and (4) sucrose and starch synthesis in source tissues.                                                                                                                                                                                

An Introduction to Sink Metabolism in Plants​

  • How C partitioning to sink tissues affects the energy-use efficiency of photosynthesis, including: (1) phloem loading and unloading of sugars; (2) C transport mechanisms; and (3) utilization of sugars in sink tissues.
  • Biochemical bases for sink limitations in plants.
  • Case study on modifying respiratory metabolism in Arabidopsis thaliana
Additional Course Information

Course Content                                                                                                                                     
This course is designed to provide a broad overview of plant metabolism with opportunities to explore specific topics in detail. It is a plant biology course that emphasizes integration of biological processes from the biochemical up to the whole plant levels. The exact topics to be covered will be dictated in part by the specific interests of students in the course.  The depth of study will go beyond the level of a 4th year undergraduate course on plant biochemistry and physiology, with the goal of approaching a level of understanding that allows experimental implementation. Emphasis will be placed on understanding the regulation and interaction between metabolic processes in plants at the molecular to whole-plant levels, and their physiological and agricultural implications. Detailed aspects of carbon, nitrogen, and sulfur metabolism are examined since collectively these processes contribute ~99% of the biomass in plants. An understanding of basic biochemical principles, components of the plant cell, the plant life cycle, and basic aspects of regulation of gene expression will be assumed.

Auditing versus Course Credit
Students are strongly encouraged to take PLNT 6320 for credit. Auditing requires written permission by B. Micallef, and non-registered attendance in the course is not allowed. Anyone auditing will be expected to give lecture and student-led scientific paper presentations, provide evaluations for student presentations, and participate in class discussions. It is assumed that all students registered in this course will physically attend classes on the Guelph campus.         

Method of Course Presentation
Students will be provided with the opportunity to examine specific metabolic processes in detail through critical analysis of the scientific literature, including a 50-min lecture presentation, and a student-led discussion of a scientific paper and associated written questions. Available research methodologies will be examined in detail, including genetic, biochemical, and physiological approaches.

The first 5 weeks of the course will involve an overview of metabolic processes in autotrophic organisms by B. Micallef, including an examination of specific scientific papers and methodologies. During Weeks 6-8, the course will consist of student lecture presentations on topics in plant metabolism, and subsequently during Weeks 9-12 there will be student seminars on specific scientific papers.  An opportunity to integrate material will be provided during the presentations and written assignments. Discussion and participation will be encouraged at all times in the course (20% of grade).

Lecture Topics

  • Introduction to Plant Metabolism
  • Introduction to Source Metabolism in Plants-Light Reactions of Photosynthesis
  • Introduction to Sourcde Metavolism in Plants-Photosynthetic C Metabolism
  • Introduction to Source Metabolism in Plants-N & S Metabolism
  • Introduction to Sink Metabolism in Plants


Labs & Seminars:
  • Student lecture presentations - Specific topics on source and sink metabolism in plants
  • Student-led discussions of scientific papers


Course Assignments and Tests:

Assignment or Test Contribution to Final Grade

Lecture Presentation


Outline for lecture presentation


Student-led scientific paper discussion


Designing and marking a question directed to the scientific paper


Answers to questions on scientific papers




Additional Notes:

Lecture Presentation on a Topic in Plant Metabolism (25% of final grade)

This assignment will provide students with an opportunity to deliver an advanced 50-min participatory/active learning lecture on a topic in plant metabolism. It is worth 30% of the final grade in the course (20% for the presentation and 5% for a lecture outline). Questions can be asked by the audience anytime during the lecture, and student presenters should anticipate 10 min for questions when designing the lecture. Your lecture presentation should provide an accurate representation of our present state of knowledge for the topic. In terms of the ‘big picture’, also attempt to address the relevance of the topic to plant physiology, and the practical relevance of the topic. The complete list of references used in preparing the Powerpoint presentation should be listed at the end of your Powerpoint presentation, and these references should be cited within the lecture presentation where appropriate. Detailed guidelines for the lecture presentation including the marking scheme are provided on Courselink.

Student-led Discussion of a Scientific Paper (25% of final grade)

This assignment will consist of two parts: (i) a 50-min student-led presentation and discussion of a scientific paper (20% of final grade); and (ii) the development and marking of a question directed to the scientific paper (5% of final grade). The goals of the student-led scientific paper discussion complement the lecture presentation, since the student-led paper discussion will require a greater emphasis on methodology, experimental design, and data analysis and interpretation, and it will be more focused overall. The general topic for the lecture and scientific paper presentations should be similar. Detailed guidelines for the student-led scientific paper presentation including the marking scheme are provided on Courselink. 

  1. Student-led Discussion of a Scientific Paper - Initially, students should find 2-3 scientific papers that they would like to discuss, and then in consultation with the instructor one of these papers will be selected for the student-led discussion.  The selected scientific paper will provide the basis for the discussion. The discussion will consist of two parts: (1) a Powerpoint presentation of the scientific paper that is no more than 20-min in length; and (2) a 30 min informal student-led discussion of the scientific paper. The 20-min presentation is to consist of the following items: (1) up to 4 introductory slides that provide the objective(s) of the paper, rationale for the experimental design, and any necessary background information; (2) a discussion of 5 key figures and/or tables from the scientific paper using up to 2 slides per figure or table, such that relevant methods, and the results and conclusions are provided; (3) no more than one slide providing the main conclusion(s) from the paper and future directions; and (4) a slide(s) providing the Literature Cited. Thus, the 20-min presentation should consist of no more than 15 well-designed slides + a Literature Cited slide(s). The 30-min student-led discussion can include any aspects of the scientific paper, including data not discussed during the 20-min presentation, and applications to the improvement of agriculture, forestry, etc. To encourage discussion, it is recommended that each class member prepares two questions for the discussion prior to class.
  2. Development and Marking of a Question Related to the Scientific Paper - A question directed to the scientific paper that is being presented in the student-led paper presentation will be developed by the presenter and provided to the instructor for posting on Courselink no later than two weeks prior to the student-led presentation.  The goal of this assignment is to encourage a detailed reading of the paper to be presented in the student-led discussion. Questions should foster an in-depth analysis of the paper and can include:
    • Queries as to the hypothesis being tested, and how the experiment(s)
    • allowed the hypothesis to be tested including the quality of the experiment(s);
    • Explanation of a methodology and how it was critical in addressing a scientific question;
    • Design of the next critical experiments to further the research area;
    • Analysis of data and methodology to assess limitations in the study;
    • Anything you think is appropriate.

Detailed guidelines for developing and marking the questions including the marking scheme are provided on Courselink. The quality of both the question and the marking of the question will be assessed by the course instructor for a total of 5% of the final grade.

Answering Questions Directed to Scientific-Paper Discussions (30% of final grade)

During Weeks 1-4, the course instructor will assign two questions directed to two separate scientific papers to be answered and handed into the instructor for marking. Each question will be worth 5% for a total of 10% of the final grade.

During Weeks 9-12, each student presenter will provide the class with one question directed to their student-led scientific paper presentation, and answers will be handed into the course instructor as a hard copy for marking by the student presenter. Only the best 4 marked answers will be used to calculate the final grade for these questions for a total of 20% (5% each). Thus, there is the option to answer only 4 questions or to answer more if you believe this will improve your overall grade.

Each answer will have a word limit of 1 double-spaced page per question (12-font, New Times Roman, 2.5 cm margins all). Answers are due just before the seminar presentation begins; they cannot be handed in at a later time. Detailed guidelines for answering the questions including the marking scheme are provided on Courselink.         

Class Participation (20% of final grade)

Level of class participation will be determined by the instructor through:

  • participation in class discussions;
  • the quality of evaluation of student presentations;
  • conforming to instructions; and
  • class attendance. 

Potential Topics for the Student Lecture Presentations

  1. Structure and function of the electron transport chain and light harvesting complexes, including potential applications to sustainable energy production.
  2. Bioenergetics of energy capture by plants.
  3. Synthesis of chlorophyll and carotenoids in the chloroplast and their importance to the electron transport chain and plant function (e.g. photoinhibition, reactive oxygen species) .
  4. Adaptations of the photosynthetic apparatus to high and low irradiance.
  5. Sensing of abiotic factors (e.g. light, temperature), including signal transduction pathways (e.g. photoreceptors, circadian clock); stress tolerance in plants.
  6. Photorespiration and variations in photosynthetic C reduction (e.g. C4 metabolism, CAM metabolism), influence of abiotic factors.
  7. Rubisco and its regulation in plants, modification of Rubisco.
  8. Sucrose and starch synthesis in source leaves, including nighttime starch degradation in chloroplasts; utilization of sucrose and starch in sink tissues.
  9. Modification of carbon metabolism in plants apart from Rubisco and photorespiration.
  10. Long distance transport processes in plants, including phloem loading and unloading.
  11. Biosynthesis of vitamin C and its physiological roles in plants.
  12. Mechanisms of cellular transport including H+/Ca2+-ATPases, co-transporters, and ion channels.
  13. Uptake and transport of water in plants, including the concept of water potential and the role of membrane transporters (e.g. aquaporins), stomates.
  14. Nitrogen and sulfur uptake, reduction, and assimilation, including biochemical aspects of Nfixation.
  15. Cell wall structure, function, and biogenesis, importance of cell walls in agriculture.
  16. Phenylpropanoid metabolism including primary and secondary metabolites, physiological roles and agricultural and nutritional importance
  17. Alkaloid compounds and their synthesis, including examples of mixed synthesis and interaction between biochemical pathways, relationship to medicine
  18. Starch, protein, or lipid synthesis in sink tissues including seeds.
  19. Terpenoid synthesis in sink tissues including primary and secondary terpenoids (e.g. Vit E, terpenoid-based plant growth regulators, volatiles, etc).
  20. Synthesis of N- and S-based plant growth regulators and their functions in plants.
  21. Signal transduction pathways associated with plant growth regulators (e.g. regulation of plant growth and development through ubiquitin-associated SCF complexes).
  22. Relationship between metabolic processes and signal transduction pathways in plants.
  23. Gene expression in plant organelles and its regulation in plants.
  24. The relationship between stress tolerance and plant metabolism (e.g. metabolic factors involved in temperature or drought tolerance).
  25. The relationship between metabolism and plant developmental processes (e.g. sugar sensing in plants, plant growth regulators, environmental interactions).
  26. Biochemical regulation of plant developmental processes (e.g. florigen protein).
  27. Plant-biotic interactions including interactions with pathogenic organisms.

Final examination:

There is no final exam for this course.

Course Resources:

Required Texts:

Not applicable

Recommended Texts:

Not applicable

Lab Manual:

Not applicable

Other Resources:

There will be numerous handouts on CourseLink, including selected papers from the scientific literature, other selected readings, and PowerPoint presentations.

Additional Useful Sources:                                                                                                                   

There are several journals that provide original scientific articles dedicated to plant biology such as Plant Physiology, The Plant Cell, The Plant Journal, Plant Molecular Biology, Plant and Cell Physiology, Journal of Experimental Botany, Plant, Cell and Environment, etc.  Wider-audience journals such as Science, Nature, Proceedings of the National Academy of Sciences, Cell, etc. also include many original articles in plant biology.

There are also several journals that publish review articles such as Annual Reviews of Plant Physiology and Plant Molecular Biology, Annual Plant Reviews, Trends in Plant Science, Current Opinion in Plant Science, Annual Reviews of Biochemistry, etc.

Field Trips:

Not applicable

Additional Costs:

Not applicable

Course Policies:

Grading Policies

For the Lecture Presentation, topics will be chosen in consultation with the instructor by the end of Week 2 to provide a complementary selection of topics. A detailed outline of the lecture presentation is to be handed into the instructor for marking no less than 2 weeks before the actual lecture presentation. The outline will constitute one-quarter of the presentation mark. The following should be provided to the instructor 4 days prior to the scheduled presentation for posting on Courselink: (1) a final version of the Powerpoint presentation in .ppt format; and (2) pdf copies of 3 relevant papers from the scientific literature.

Scientific papers will be chosen in consultation with the course instructor by the end of Week 4 to provide a complementary selection of topics. A pdf of the scientific paper will be posted on Courselink by the instructor once finalized.  A copy of the Powerpoint presentation in ppt format must be  provided to the instructor in class for posting on Courselink.

For questions directed to scientific papers presented by either the course instructor or student presenters, questions will be marked by the course instructor or presenting student, respectively. Answers are due in class as a hard copy before the seminar presentation occurs; they cannot be handed in at a later time. There will be 2 questions provided by the course instructor, and a minimum of 4 questions from student presenters must be answered and handed in for marking. Each answer will be worth proportionally the same % of the final grade (5% each) for a total of 30%. Regarding the questions marked by student presenters, the marked hard copies of the answers will be due to the instructor by Wednesday of the next week for final approval of the grade. The quality of both the question and the marking of the question will be assessed by the instructor for 5% of the final grade.

Each of the four components for Participation will constitute 5% of the final grade for a total of 20%, and participation components can overlap (e.g. if you miss a class, it will effect (i) and (iv) and it could effect (ii)).

If the lecture presentation or student-led scientific paper discussion must be missed at the scheduled date for a legitimate reason, the instructor should be told prior to class if possible, and an attempt will be made to reschedule the lecture in class at a later date. Supporting documentation for an absence may be requested by the instructor, particularly if the instructor is not informed prior to class.

Course Policy on Group Work:

Not applicable.

Course Policy regarding use of electronic devices and recording of lectures:

Electronic recording of classes is expressly forbidden without consent of the instructor, whether the instructor, a classmate or guest lecturer. When recordings are permitted they are solely for the use of the authorized student and may not be reproduced, or transmitted to others, without the express written consent of the instructor. Material recorded with permission is restricted to use for that course unless further permission is granted.

Other Course Information:

University Policies

Academic Consideration

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The Academic Misconduct Policy is detailed in the University Calenders:


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