Syllabus
Fall 2009
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: www.fiu.edu/~oberbaue/plantphysiology2009.htm.
Instructor: Steve Oberbauer HLS 218A PH:x2580 oberbaue@fiu.edu. Office Hours W 9-12 AM.
Text: Plant
Physiology, Taiz and Zeigler, 4th Edition 2006
Time: MW 5-6:15 PC (Charles Perry) 447.
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Date |
Topic |
Readings |
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August |
24 |
Course overview |
Ch 1 |
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| 26 | Enzymes and energetics | Ch 2 | |||
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31 |
Ch 3 |
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2 |
Ch 4 |
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| 7 | Labor day holiday, no classes | ||||
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9 |
Ch 4 |
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14 |
Ch 5 |
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16 |
Solute transport, assimilation of minerals (see outlines at end) |
Ch 6, 12 |
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21 |
Respiration (see outlines at end of this web page) |
Ch 11 |
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23 |
Respiration continued (see outlines at end of this web page) |
Ch 11 |
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28 |
Photosynthesis (EXAM One has been delayed until Wednesday) |
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30 |
Exam I |
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5 |
Photosynthesis |
Ch 7, 8 |
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7 |
Photosynthesis |
Ch 8 |
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12 |
Whole plant aspects of Ps |
Ch 9 |
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14 |
Phloem transport |
Ch 10 |
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19 |
Gene expression
(http://4e.plantphys.net/) |
Ch 14 (on web) |
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21 |
Growth and development |
Ch 16 |
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26 |
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28 |
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Ch 18 |
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November |
2 |
Exam II |
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4 |
Growth regulators (auxins) |
Ch 19, 15 |
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9 |
Growth regulators (gibberellins) |
Ch 20 |
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| 11 | Veteran's day holiday, no classes | ||||
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Growth regulators (cytokinins) |
Ch 21 |
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18 |
Growth regulators (ethylene) |
Ch 22 |
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23 |
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25 |
Written report work day |
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30 |
Control of Flowering (critiq |
Ch 25 |
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December |
2 |
Seed germination |
Ch 23 |
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13 |
Final exam (time slot not yet assigned) |
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Course Structure
- Grading is based on two midterm exams and a final (short answer,
brief essay, matching), and writing assignments (see below). The exams
and final count for the majority of your grade (100 pts each) with 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.
Leaning 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:
August 29th Last day to drop courses or withdraw from the University without incurring a financial liability.
Aug 31. Last day to add a course, last day to change grading option,
Sept 18. Last day to withdraw with a 25% refund of tuition.
October 16th Last day to drop with a DR grade, last day to withdraw with a WI grade.
Course Policies - You are expected to be on time to class, and to stay the full period. 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 Section 2.44 of the Academic Affairs Policies and Procedures Manual (http://academic.fiu.edu/docs/aapolicies.htm), it is expected that students in Bot-4503 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
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 2004,
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.
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 14th – your topic should be chosen
2) Oct 21st Critique 1 due
3) Oct 28th Critique 2 due
4) Nov 4th Critique 3 due
2) Final report due Nov 30th, 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?
the z scheme, is it dead?
Journals
Plant Physiology
International Journal of Plant Science
Journal of Experimental Botany
Physiologia Plantarum (electronic)
Planta
Tree Physiology
Functional Plant Biology (formerly Australian Journal of Plant Physiology)
American Journal of Botany
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).
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
Isozymes
regulation of enzyme activity
external factors that affect
enzyme activity
enyzme kinetics
Michaelis Menton
Lineweaver burke
Vmax, km
Inhibitors
Allosteric interactions - feedback and activating
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
diffusion
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 to measure water potential
How does water move in plants
The tension cohesion theory
driving force
adhesion
cohesion
plants are just a resistor in between soil
and atmosphere
Cavitation
diurnal patterns of Psi and transpiration
Water uptake from roots
Root pressure
guttation
soil properties
texture
structure
soil water holding capacity
soil water potential
Transpiration
adaptations to minimize water loss
stomata as ultimate regulators of
transpiration
Mechanism of stomatal opening
Foliar
absorption
mycorrhizae
sources of nutrient inputs
Hoaglands macro and micronutrients
roles
that nutrients fulfill
Fertilizers
how
to test for nutrient requirements
Chelating agents to insure availability
Mineral
content of the soil
cations
anions
pH
effects on ion availability
accumulators
Ion
uptake
Mineral nutrition
Solute transport (ion
transport in roots)
Nitrogen
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
cyanobacteria
Analyzing nitrogen fixation
Elements and their major
uses, mobility
Phosphorus
Potassium
Sulfur
Magnesium
Calcium
Iron
Copper
Manganese
Zinc
Molybdenum
Chlorine
Sodium
Respiration
RESPIRATION
Growth and maintenance
respiration
Three main pathways of
respiration
Localization of the pathways
Glycolysis
What you need to know about
respiration
Fermentation
Energy yield of glycolysis
Oxidation of pyruvate
KREBS CYCLE
High energy compounds
produced NADH, ATP, FADH2
Electron transport system
Membranes and pathways
Membrane fluidity
Four main complexes of
Electron transport
Oxidation of NADH
Chemiosmosis
Coupling factors and ATP ase
Uncouplers
Energy yield
Cyanide resistant respiration
Function of cyanide resistant
respiration
Hexose monophosphate shunt
(Pentose shunt)
Photosynthesis
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
Deexcitation
Photosynthetic pigments
Light reactions
Two photosystems
Light harvesting complexes
Z scheme
Water splitting
Photophosphorylation
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
Photorespiration
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
light
nutrients
CO2
concentration
plant
water status
temperature
sink
strength
Phloem Translocation
Sources and sinks
Phloem
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:
luciferase
herbicides
antisense RNA
#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
differentiation
Totipotency
plant
growth and development is controlled by 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
Approaches
to analyze the mechanism of action of a plant growth substances
#LIGHT
EFFECTS ON PLANTS-PHOTOMORPHOGENESIS
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
inhibition of stem elongation
phototropism
stimulation
of stomatal opening
blue
light receptors (cryptochrome)
flavin?
carotenoid?
zeaxanthin?
signal
transduction
Auxins
modes
of auxin action
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
Gibberellins
discovery
isolation
physiological
effects of gibberellins
elongation
juvenility
flowering
in rosette plants
fruit
set
seed
dormancy
barley
aleurone system
synthesis
transport
Cytokinins
division
factor
bioassays
physiological
effects
cell
division
senescence
bud
development
cell
expansion
chloroplast
development
auxin
to cytokinin ratio
synthesis
–
transport
Abscisic acid
abscisin
and dormin
physiological
effects
senescence
chlorophyll
loss
dormancy
gibberellin
interaction
desiccation
tolerance
seed
storage proteins
stomatal
closure
inhibition
of cell wall growth
hydraulic
conductivity
synthesis
transport
mechanism
of action
Ethylene
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
Brassinosteroids
Identified
in 1970’s only recently widely accepted as a broad class of hormones
bioassays-
bean stem, rice leaf bending
multiple
active forms in plants
synthesized
throughout plants
moves
in xylem when externally applied
effects
tissue
differentiation
cell
expansion
lateral
root production
xylem
differentiation
pollen
tube growth
seed
germination
Control of Flowering
photoperiodism
Garner
and Allard using Maryland Mammoth identified photoperiod control of flowering
photoperiod
is phytochrome effect
short
day plants
long day plants
day neutral plants
intermediates
longday-short day
short day long day
ecotypic
variation in photoperiod
Time
required to trigger response
Nature
of the daylength response- the period of uninterrupted darkness is what counts.
Detecting
the signal
signal
transport
Florigen
concept
Other
factors important for flowering
1)
age of plant
2)
temperature
3)
vernalization
4)
water, carbon nutrient status
Seed germination
Seed
properties
How
long seeds retain viability
seed
germination process
Conditions
required for seed germination
1)
temperature- heat and cold treatment
2)
scarification
3)
removal of inhibitors
4)
light