Principles of physiological and metabolic processes in agriculture

A.Y. 2021/2022
Overall hours
AGR/13 AGR/16
Learning objectives
The course will provide students the basic knowledge of the fundamental biochemical and physiological processes of plants, with the general objective of understanding mechanisms most involved in the determination of crop plant yield, also in unfavorable environments.
The course also proposes to provide the fundamental notions concerning Agro-Ecological Microbiology and basic microbiological techniques for the analysis of environmental and food samples.
These skills will be acquired both through lectures and classroom exercises concerning the resolution of biochemistry problems, and through laboratory exercises related to biochemical and microbiological analyses aimed at defining the quality of agricultural-food products.
Expected learning outcomes
The student will acquire the knowledge of the mechanisms regulating energy transfer and carbon metabolism in plants and in microorganisms, and of the biochemical and physiological factors underlying the productivity in the agro-food sector, even in unfavorable environments. At course completion, the acquired knowledge will be useful to face practical problems in agricultural contexts, also through the application of basic biochemical and microbiological techniques for the analysis of agro-food samples. Participation in classroom exercises, laboratory activities, and oral or written assessment methods will contribute to the development of communication skills. Furthermore, the use of diversified study tools (manuals, on-line material made available by the Teachers, personal notes, on line resources) will help to develop the ability to find independently information and useful ideas for future job activities.
Course syllabus and organization

Single session

Lesson period
First semester
More specific information on the delivery modes of training activities for the academic year 2021/2022 will be provided over the coming months, based on the evolution of the public health situation.
Course syllabus
The Course describes the fundamental biochemical and physiological processes of higher plants, whose knowledge is mandatory for understanding the main mechanisms involved in the determination of crop plant yield, also in unfavorable environments.

In synthesis, the Course syllabus foresees the following topics: 1) Bioenergetics and thermodynamics (0.5 CFU). 2) Enzyme catalysis (0.5 CFU). 3) Energy metabolism: Glycolysis, fermentation, TCA cycle, other pathways of carbon metabolism. Oxidative phosphorylation (1 CFU). 4) Photosynthesis: light reactions and assimilation reactions, ecophysiology of photosynthesis (1.25 CFU). 5) Plant-water relations. Transpiration, stomata regulation, water transport in the xylem (1 CFU); 6) Translocation of photosynthates (0.25 CFU). 7) Mineral nutrition. Chemical and electrochemical potentials, solute absorption and assimilation (1 CFU). 8) Phytoregulators and stress adaptations (main issues; 0.5 CFU).
Principles of bioenergetics and thermodynamics. Thermodynamic systems and their environments. I and II thermodynamics laws. Entropy and free energy. Exo- and endo-ergonic reactions; energetically coupled reactions. ATP and phosphor group transfer. Other high energy compounds. Carbon redox states in compounds of biological interest. Oxy-reduction potential. Relationship between delta E and delta G. Oxy-reduction coenzymes. Redox reactions of biological interest (0.5 CFU).
Thermodynamic and kinetic aspects of enzymatic catalysis. Michaelis-Menten's equation. Inhibition and regulation of enzyme-catalyzed reactions (0.5 CFU).
Metabolic reations: the concepts of catabolism and anabolism. Carbon metabolism: degradation of storage polysaccharides (starch). Glycolysis and lactic and alcoholic fermentation. Energy yield of anaerobic glucose degradation. The Krebs cycle. Electron flux and oxidative phosphorylation. Mitchell's chemiosmosis theory. Energy yield of glucose aerobic degradation. Other mechanisms of O2 consumption in plants. Other pathways of glucose degradation: the pentose-P pathway. Basic aspects of the metabolism of storage lipids: energy yield of fatty acids degradation. Basic aspects of storage lipid degradation in plants: the glyoxilate cycle. (1 CFU).
Photosynthesis. The electromagnetic spectrum. Energy content of different wavelength radiations. Photosynthetically Active Radiation. Absorption and action spectra. Photosynthetic pigments: excitation and de-excitation phenomena. Photosystems, light-harvesting complexes, reaction centers. Energy transfer from the light-harvesting complexes to the reaction center. Accessory pigments. Photosynthetic electron flow and phosphorylation: the Z scheme. Non-cyclic and cyclic photophosphorylation. Herbicides disrupting the photosynthetic electron transport. Photooxidative damage. Carbon assimilation: C3 and C4 cycles, CAM metabolism. Photorespiration. Responses to light and temperature: light compensation point, CO2 compensation point. (1.25 CFU).
Plants and water. Definition of water potential and factors contributing to it in the plant cell: pressure, temperature, presence of solutes. Components of water potential in the plant cell: solute potential, matric potential, pressure potential. Osmotic phenomena: Van't Hoff's law. Isotonic, hypotonic, hypertonic solutions. Plasmolysis, cell turgor. Expansion growth. The soil-plant-atmosphere continuum. Water absorption by roots: the apoplastic and symplastic pathways. Transpiration. The driving force for the ascent of the xylem sap in the xylem. Loss of water through the stomata, regulation of stomata opening. (1 CFU).
Photosynthate translocation in the phloem. Osmotically generated pressure flow. Role of active transport of H+ in sucrose loading and unloading. "Sinks" and "sources" (0.25 CFU).
Mineral nutrition. Plant nutrient requirements: micro- and macronutrients. Nutrient availability and plant growth. Solute transport in plant cells. Cell membranes and the plasmalemma: their role in cell physiology. Selective permeability. Chemical and electrochemical potentials and their role in determination of the direction of solute flux. Diffusion, active and passive transport. The Nernst's equation. Carriers and ion channels. Role of the PM H+-ATPase in generating the transmembrane electrochemical proton gradient and its role in secondary active transport. Absorption and assimilation of N, S and P. Micronutrient absorption: the case of Fe. Heavy metal toxicity: the case of Al. Mechanism of resistance to heavy metals: exclusion and detoxification. (1 CFU).
Plant growth regulators. General description of their peculiar characteristics. Evaluation of biological activity: biological tests. Auxins, gibberellins, cytokinins, abscisic acid and ethylene: description of a few specific physiological effects and of a few related agricultural practices. Stress physiology. The concepts of stress. Abiotic stresses: low temperature stress, water stress, soil acidity stress, oxidative and radiation stresses. Biochemical and physiological aspects of plant responses to stresses. (0.5 CFU frontal lesson).
Specific topics will be broadened by exercises in the classroom.

The course provides fundamental notions regarding morphology, physiology, metabolism and function of micro-organisms in nature, with reference to their use in agricultural biotechnologies concerning environmental protection, animal and plant production, food processing.

In summary, the Course syllabus includes the presentation and the discussion of the following topics:
1) Morphology and cytology of prokaryotes (0.25 CFU). 2) Microbial growth, its evaluation and control (0.25 CFU). 3) Microbial metabolism and microbial nutritional groups (0.75 CFU). 4) Bacterial viruses (0.15 CFU). 5) Genetics of prokaryotes (0.25 CFU). 6) Microbial ecosystems: interactions between microorganisms, animals and plants (0.75 CFU). 7) Biological cycles of the elements and microbial groups involved (0.6 CFU). 8) Laboratory (1 CFU): bacterial cultures, microscopy, and microbiological analysis.

General microbiology
Microbiology fields of application. Prokaryotic and eukaryotic microorganisms: comparison.
Morphology of prokaryotes.
Cytology of prokaryotes: capsule, cell wall, cytoplasmic membrane, flagella and pili, ribosomes, bacterial genome. Endospore.
Microbial growth, its evaluation and expression. Influence of environmental factors on growth (O2, temperature, pH, available water, radiation). Bacterial growth control: antimicrobial (physical and chemical) treatments and factors influencing their effectiveness. Antibiotic resistance.
Nutritional needs of microorganisms. Microbial metabolism and physiological groups. Bacterial photosynthesis, aerobic and anaerobic respiration, fermentations. CO2 assimilation, N fixation. Regulation of metabolism in prokaryotes.
Bacteriophages: lytic and lysogenic cycle.
Genetics of prokaryotes: mutations and gene recombination.

Agro-environmental microbiology
Interactions between micro-organisms in microbial ecosystems (neutralism, competition, amensalism, predation, commensalism, parasitism, mutualism).
Interaction between micro-organisms and animals (digestive system).
Interactions between micro-organisms and plants (mutualistic symbiosis)
Biological cycles of elements and microbial groups involved. Biodegradation of natural organic matter and xenobiotics. Problems related to reintegration of organic matter into agricultural soil.

Laboratory activities
Work in sterility, sterilization techniques. Bacterial growth and culture media. Transplantation, isolation in pure culture, research of specific microbial groups in environmental and food samples.
Prerequisites for admission
Full understanding of the Course contents strictly depends on the knowledge, from previous Courses, of fundamentals of Plant Biology, Physics, Inorganic Chemistry and Organic Chemistry. Such prerequisites apply to all students, both attending the Course or not.
Teaching methods
The Course uses e-learning teaching tools present in the Ariel 2.0 platform (Power Point slides, video recordings of the lectures).
Teachers will use: a) frontal lessons; b) classroom exercise; c) laboratory practices (Microbiology). All the activities will contribute to gaining the Expected Learning Outcomes (see dedicated paragraph).
Attending the lectures is strongly recommended.
Teaching Resources
U.D. 1
Nelson D., Cox M. "Introduzione alla biochimica di Lehninger", ed. Zanichelli (T.U. 1, Biochemistry).
Pinton et al., Fondamenti di Biochimica Agraria, Patron Editore, Bologna (T.U. 1, Biochemistry).
D'Andrea G. Biochimica Essenziale EdiSES (T.U. 1, Biochemistry).
N. Rascio, "Elementi di Fisiologia Vegetale", Edises (T.U. 1, Plant Physiology).
R.F Evert, S.E Eichhorn, Biologia delle piante di Raven, Zanichelli (T.U. 1, Biochemistry and Plant Physiology).
Notes from the course lectures. Copy of the slides shown during the lectures will be made available to the students of the Degree Course in the dedicated UniMi Ariel 2.0 website.

U.D. 2
B. Biavati e C. Sorlini, 2012: Microbiologia generale e Agraria. Vol. 1, Casa Editrice Ambrosiana, Milano.
On (Prof. R. Zanchi) a handbook of Gneral Microbiology, with a photo-gallery, and material for the laboratory practices, with some videos, are available. Moreover, you can find files with all the slides showed during the lessons and handbooks of Microbial Ecology and Food Microbiology.
Assessment methods and Criteria
The student should demonstrate the ability to elaborate the Course contents by integrating them with those of the prior Courses. There is no mandatory prerequisite concerning other Courses of the Study Course. Nevertheless, successful getting through the First Year Courses (Plant and Animal Biology, Physics, General and Inorganic Chemistry and Organic Chemistry) is strongly recommended prior to start the study of the topics inherent to the exam.
PREMISE: knowledge and understanding of the topics of the first 3.25 CFUs (T.U. 1) of the Course are imperative in order to understand the topics that will be considered subsequently, concerning both the Plant Physiology (last 2.75 CFUs of T.U. 1) and Agricultural Microbiology (4 credits, T.U. 2).
In this framework, and with the aim of facilitating the exam preparation, assessment of the student's knowledge will take place by means of three distinct tests, which will be scheduled as follows. In general, the answers will be evaluated on the basis of the student's capability to organize his/her knowledge of the topics, speech quality use of proper terms.
1st test (Principles of Thermodynamics and Biochemistry): oral examination, which typically includes two questions concerning bioenergetic and biochemical principles.
2nd test (Agricultural Microbiology): oral examination, which typically includes four questions: two concerning General Microbiology (also dealing with microbiological analysis techniques) and two concerning agricultural-ecological microbiology, in which the student will demonstrate the ability to use the knowledge gained in the Course to solve agro-environmental problems in an interdisciplinary way.
3rd test (Principles of Plant Physiology): oral examination, which typically includes two questions concerning plant physiology topics.
Assessment methods and criteria will be identical for attending and non-attending students.
The final score will result from the weighted average, with respect to the relative CFUs, of the two Teaching Units.
Examinations will take place at Edolo with a minimum number of students equal to 5; otherwise, they will take place at the Facoltà di Scienze Agrarie ed Alimentari, via Celoria 2, Milano. The location will be therefore communicated to the students (on-line registration) by e-mail after the deadline of the registration time, i.e., 2 d before the test date. Students are therefore prompted to check regularly their institutional e-mail boxes ( and the Ariel 2.0 notice boards.
Students enrolled to an exam session who no longer wish to take the exam are therefore required, if access to the on-line system is already closed, to promptly notify their decision to the teachers. If not, the student will not be allowed to take the next exam session.
Students with Specific Learning Disorders (DSA): in order to take advantage of the foreseen dispensatory and compensatory tools, it is mandatory to have delivered the appropriate certification to the UniMI DSA Service ( The DSA contact for the Study Course is Prof. Raffaella Zanchi ( Furthermore, DSA students are required to agree with the Teacher(s), in due advance, the methods of examination and the eligible supporting material (logical schemes, tables, etc.), provided their specific situation has been certified.
In one solar year, six examination dates for each of the three parts of the whole exam are foreseen, scheduled according to the teaching calendar and to the week of teaching interruption. During the periods of teaching activity, examinations are NOT foreseen. Only for Off-Course students, on the basis of specific and documented requirements and upon agreement with the Teacher(s) additional exam sessions may be planned at the Faculty of Agriculture in Milan.
Any additional information about the examination procedures will be illustrated by the Teachers during the course.
Biochimica e fisiologia vegetale
AGR/13 - AGRICULTURAL CHEMISTRY - University credits: 0
AGR/16 - AGRICULTURAL MICROBIOLOGY - University credits: 0
Lessons: 48 hours
Microbiologia agraria
AGR/13 - AGRICULTURAL CHEMISTRY - University credits: 0
AGR/16 - AGRICULTURAL MICROBIOLOGY - University credits: 0
Laboratories: 16 hours
Lessons: 24 hours
Professor: Zanchi Raffaella
Every day (phone or e-mail appointment)
Office at Department of Agricultural and Environmental Sciences