Syllabus Fall 2013

Plant Physiology BOT 4503 (3 cr).  Fulfills the Upper Division Section C requirement (Physiology/Biochemistry). Prerequisites: Organic Chemistry (2210) and General Biology I and II.  Web site:  Instructor: Steve Oberbauer AHCI 218A phone 305-348-2580, email: 

Text: Plant Physiology, Taiz and Zeiger, 5th Edition 2010 ( for online supplemental materials)

Time: MW 5:00-6:15 OE 105







Course overview




Plant Cells

Ch 1



Labor day holiday, no classes




Enzymes and energetics

Appendix I



Water and cells

Ch 3



Plant water relations

Ch 4



Water uptake and transport

Ch 4



Mineral nutrition

Ch 5



Solute transport, assimilation of minerals

Ch 6,12




Ch 11



Respiration continued

Ch 11



Exam I





Ch 7



Photosynthesis carbon fixation

Ch 7, 8



Whole plant aspects of Photosynthesis

Ch 9



Phloem transport

Ch 10



Gene expression

Ch 2



Growth and development

Ch 14,16




Ch 17



Blue light responses

Ch 18



Exam II




Growth regulators (auxins)

 Ch 19, 15



Veteran's Day (University Holiday)



Growth regulators (gibberellins)

Ch 20



Growth regulators (cytokinins)

Ch 21



Growth regulators (ethylene)

Ch 22



Growth regulators (abscisic acid, brassinosteroids)

Ch 23,24



Written report work day




Control of Flowering

Ch 25



Seed germination

Ch 23



Exam III  5-7:00 PM


Course Structure - Grading is based on two midterm exams and a final (short answer, brief essay, matching), occasional quizzes, and writing assignments (see below). The exams and final count for the majority of your grade (50 pts each), quizzes worth 5 pts each, each critique worth 15 pts (3 x 15 = 45) and proposed experiment worth 50 pts. This syllabus is subject to change without notice. Grading will generally be based on traditional 90, 80, 70, 60 percentage scale of total points. The course policy is that NO MAKE UP EXAMS WILL BE GIVEN. You are expected to be on time to exams. No student will be allowed to start taking the exam after any students have finished and left the room.

Emailing Dr. Oberbauer:  Use the subject line “BOT4503” 

Learning outcomes Students finishing this course will have fundamental understanding of plant photosynthesis, respiration, plant hormone control of growth and physiology, plant mineral nutrition, control of flowering and secondary compounds.

Important Academic Calendar dates: (

September 3rd Last day to add courses; last day to drop courses or withdraw from the University without incurring financial liability for tuition and fees

September 5th   $100 late payment fee assessed for outstanding balances

September 20th  Last day to apply for graduation at the end of Fall 2013 term; Last day to withdraw from the University with a 25% refund of Tuition

November 4th Deadline to drop a course with a DR grade; Deadline to withdraw from the University with a WI grade.

Course Policies ­ You are expected to be on time to class, and to stay until the experiment and data review is done. You are expected to maintain high standards of academic honesty. Any student found in violation of these standards will earn an automatic F and be reported to the Deans Office, no exceptions made. In accordance with FIU's policy on academic honesty, as set forth in the Academic Affairs Policies and Procedures Manual, it is expected that students in Bot-4503L will not submit the academic work of another as their own. Additional discussion of academic honesty and integrity may be found in the Manual.

Writing assignments  '

Some variation of the following will be used (depending on final enrollment of the class)

Objectives. The objectives of the writing assignments are to: 1) give you an opportunity to improve your grade if you do not do well on the exams, and 2) give you some writing practice and 3) get you into the primary plant physiological literature.

What you need to do.


1)  Choose a topic from the list provided or any other plant physiological topic.  Email your chosen topic to me.   I will provide you feedback as to the suitability of the topic.  It definitely needs to be plant physiological.  For example, if you wonder why certain bromeliads grow only on certain tree species, you would need to consider the physiological basis for germination on various substrates or inhibition of root growth etc.


2)  Find THREE recent research papers on the SAME topic (recent meaning in the last 5 years, nothing from before 2008, and from the research literature, not the newspaper or some other popular article).  On the next page I have provided a list of journals that typically carry plant physiological articles. 


3) Write a 1-page critique of each article (we will do this once for an article as a class to provide guidance and I will provide a series of questions that you will answer about the article to guide your critique).  Include the article with your critique.  Critique questions to answer:

1)    Full citation of the paper:

2)    What was the hypothesis or question(s) (1-2 sentences)

3)    What was the methodological approach (1-2 sentences)

4)    What did they find? (3-4 sentences)

5)    Do the results support their conclusions.

a)    statistically valid?
b)    Is what is in the figures/tables in agreement with what they say they found?
c)    Did they really test what they say they were testing?



4)  In a 3 page document of your own original writing, design an experiment to further advance the science of your chosen topic.  You may think that you do not know enough or are not creative enough to design a cutting edge experiment, but you WILL know enough after reading these papers and you are definitely creative enough.  Many undergraduates are designing, conducting, and publishing research throughout the U.S.  It sounds hard, but many papers often propose the direction for future research in their Discussion.  The 3 page experimental description should include: the background context, what your hypothesis is, what methods you will use, and what you expect to find.  You will need to cite research references for your chosen methods and the general context that will go on a separate page after the three pages of your description of what you are proposing to do.


Critique documents should be single-spaced typed (12 point Times Roman font) plus a cover sheet with your name and the full citation of the paper.


The experiment document should be a total of 5 pages, a cover sheet with your name and title of what you propose, 3 pages of the experiment as described above (single-spaced typed 12 point Times Roman font) and 1 of references (more if necessary).


In total, I am looking at 3 one-page critiques, and one 3 page experiment description with their cover sheets.  (More is ok, less would require seriously clear and concise writing on your part).  I will need the documents in both paper and electronic format


Important dates:

1) October 2nd – your topic should be chosen

2) Oct 21 Critique 1 due

3) Oct 30 Critique 2 due

4) Nov 6  Critique 3 due

5) Final report due Dec 2nd, 5 PM.

If you need help /guidance I will be happy to help with the design and look over drafts of your materials, but only if I see them at least one week before the due date.


** I have to put this in**.

Finally, all students have agreed to abide by the University Honor code, which prohibits copying text from other sources including the Web and claiming it as their own.  Also know that software specifically exists that is designed to find such plagiarized text for teachers.  Students caught plagiarizing will be subject to strong measures that may result in failure of the class or more serious consequences.


Example topics for experiments

control of fermentation pathways.

effects of low temperature on stomatal conductance

effects of severe water stress on CAM plants

effects of water stress on photosynthesis- direct or indirect?

Functional role(s) of the alternate oxidase

importance of hydraulic conductivity (stem resistance) on water transport

mechanism of water splitting in photosynthesis

mechanism of water uptake in plants ?

Mitochondrial activity during the daytime

photorespiration in C4 plants- how much if any?

physiology of C3-C4 intermediates

physiology of guard cells- do they carry out all of photosynthetic pathways?




Plant Physiology

International Journal of Plant Science

Journal of Experimental Botany

Physiologia Plantarum (electronic)


Tree Physiology

Functional Plant Biology (formerly Australian Journal of Plant Physiology)

American Journal of Botany

Annals of Botany

New Phytologist

There are quite a few more and many journals publish a few articles each issue but only in special sections (such as does American Journal of Botany).

Lecture outlines
Enzymes and energetics

Enzymes - biological catalysts

Gibbs Free energy

Activation energies of reactions

Factors affecting rates of reactions

How to make endergonic reactions proceed

names of enzymes

Reversible reactions

Enzyme function

Cofactors, prosthetic groups and metal ion activators


regulation of enzyme activity

external factors that affect enzyme activity

enyzme kinetics

Michaelis Menton

Lineweaver burke

Vmax, km


Allosteric interactions - feedback and activating

Water and plant cells
Importance of water for plant cells and water's roles in plant function

properties of water

water availability and plant and ecosystem production

the big picture

Water potential and free energy

Components of water potential

water movement

bulk flow


osmotic potential

turgor or pressure potential

gravitational potential

Plant water relations
water movement in model systems

Hofler diagrams. how plants adjust turgor in response to changes in water content

Matrix potential - a mythical component

How does water move in plants

Water uptake and transport

The tension cohesion theory
    driving force

plants are just a resistor in between soil and atmosphere


diurnal patterns of Psi and transpiration

Water uptake from roots

Root pressure


soil properties

soil water holding capacity

soil water potential


adaptations to minimize water loss

stomata as ultimate regulators of transpiration

factors affecting stomata opening:

leaf water potential (soil moisture)
internal cycles
abscisic acid
CO2 concentration in the leaf
Mechanism of stomatal opening

Mineral nutrition
Foliar absorption

mycorrhizae sources of nutrient inputs

Hoaglands macro and micronutrients

roles that nutrients fulfill


how to test for nutrient requirements

Chelating agents to insure availability

Mineral content of the soil



pH effects on ion availability


                                                                                                            Mineral nutrition II

Solute transport (ion transport in roots)


forms of nitrogen for plant use

nitrate reductase

sources of nitrogen

the nitrogen cycle

nitrogen fixation

sources of biologically fixed N

The legume Rhizobium symbiosis


Analyzing nitrogen fixation

Elements and their major uses, mobility














Growth and maintenance respiration

Three main pathways of respiration

Localization of the pathways


What you need to know about respiration


Energy yield of glycolysis

Oxidation of pyruvate

Krebs cycle and electron transport

High energy compounds produced NADH, ATP, FADH2

Electron transport system

Membranes and pathways

Membrane fluidity

Four main complexes of Electron transport

Oxidation of NADH


Coupling factors and ATP ase


Energy yield

Cyanide resistant respiration

Function of cyanide resistant respiration

Hexose monophosphate shunt (Pentose shunt)

Overall reaction

water splitting versus splitting CO2

Light reactions and light independent reactions

Hill Reaction - photosynthetic reducing power of chloroplasts

Chloroplast structure and localization of reactions

Properties of light

Electron excitation


Photosynthetic pigments

Light reactions

Two photosystems

Light harvesting complexes

Z scheme

Water splitting


Quantum yield

Cyclic phosphorylation

Inhibitors of photosynthetic light harvesting

Localization of photosystems

Carbon fixation

Calvin Benson cycle

Regulation of Calvin cycle

Thioredoxin activation

Warburg effect


Function of photorespiration

Bicarbonate pumps

C4 pathway

Whole plant aspects of photosynthesis

guiding principles

Plants have high photosynthesis in high resource environments

Plants can acclimate

Factors affecting photosynthesis

CO2 concentration
plant water status
sink strength

                                                        Phloem Transport
Sources and sinks


Components of xylem and phloem sap

Mechanism of movement in phloem

Munch mass flow

Problems with mass flow

Multidirectional flow
differential rates of transport

P proteins

                                                     Gene Expression and Signal Transduction

Central dogma of molecular biology
DNA ---> mRNA ------> protein

plants have post-translational modification of mRNA

How to approach study of particular gene or genes activated in response to some treatment or condition

Example auxin stimulation of new protein synthesis

Making cDNA

Inserting DNA into bacteria & cloning it

Selecting the genes in clones
1) antibodies - Western blot
2) DNA hydridization - using probe if sequence is known
3) probes based on similar genes from other species
4) transposons

What can you do with gene once identified
a) transfer to another species
b) analyze when and where genes are expressed

How to transfer to other species
1) Agrobacterium tumefaciens
2) virus
3) naked DNA
4) microprojectile

How do you know your plant has the gene
1) add selectable gene
2) reporter genes

Expression of insert gene
inserted promoters
examples in plants:
antisense RNA

Plant growth and development

Growth can mean different things

cell expansion, cell division, cell differentiation

How do plants grow - at meristematic tissues

types of plant growth - determinant, indeterminant

phases of growth - vegetative and reproductive

juvenility - heteroblastic development



plant growth and development is controlled by environmental factors
signals from environment are translated into growth changes via plant growth substances (hormones)

plant growth regulators

5 classes of widely recognized plant growth substances

1) auxins

2) gibberelins

3) cytokinins

4) abscisic acid

5) ethylene

6) others - brassinosteroids


promotion of leaf expansion and leaf rolling

inhibits stem elongation

promotes root development

promotes branching and tillering

sets timing of sleep movements

promotes chlorophyll synthesis and accessory pigments

promotes seed germination -Light response is red/farred response

controlled by phytochrome - a tetrapyrole chromophore

phytochrome effect may have temperature and moisture interactions

Why a red light requirement
1) photosynthesis
2) spread out timing of germination
3) canopy sensing mechanism

phytochrome responses
very low fluence responses
low fluence responses
High irradiance responses

phytochrome forms and genetics

Blue light responses

action spectrum has characteristic 3 finger structure

blue light inhibition of stem elongation


stimulation of stomatal opening

blue light receptors (cryptochrome)

3 primary classes

zeaxanthin in stomata

signal transduction

Darwin coleoptile experiments

isolation of auxin

chemistry of auxin

auxin induced cell elongation

Acid growth hypothesis

Auxin and root production

Auxin and apical dominance

auxin sensitivities of different tissues

Auxin transport

Auxin balance within the plant

mechanism of action




physiological effects of gibberellins



flowering in rosette plants

fruit set

seed dormancy

barley aleurone system




division factor


physiological effects

cell division


bud development

cell expansion

chloroplast development

auxin to cytokinin ratio

synthesis –



it’s a gas

fruit ripening and respiration rate

commercial uses

effects on seedling development

effect on cell expansion

interaction with auxin

ethylene transport

site of synthesis

ethylene synthesis