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Plants, Cells, and Water

Chapter 1
Learning objectives
• Know the unique properties of water and
their biological importance.

• Understand the meaning of the terms

adhesion, cohesion, and tension.

• Understand the processes of diffusion and

bulk flow as mechanisms of water
Learning objectives
• Understand the process of osmosis as a
process of water movement across a
selectively permeable membrane.

• Understand the concept of water potential

and its component potentials.

• Know the role of aquaporins in the

transport of water.
Plants, cells, and water
• The properties of water allow this molecule to
fulfill specific roles in plants.
– The thermal properties of water provide temperature
regulation and maintain water in a liquid state.
– Water serves as the universal solvent.
– The hydrolysis or condensation of water can
contribute to biochemical reactions.
– The transparency of water does not hinder
– Water creates turgor pressure.
Physical and chemical properties of water

• The electronegativity of the oxygen atom in

water makes the molecule polar.

• The partial negative charge on the oxygen atom

and the partial positive charge on the hydrogen
atoms allows water to form hydrogen bonds.

• This polarity also allows water to interact with

other molecules and surfaces, creating layers of
water molecules called bound water.
Physical and chemical properties of water

• Figure 1.1
Physical and chemical properties of water

• The thermal properties of water are key to

its role in biological systems.
– Water has a high specific heat, which means
it has a high capacity to absorb heat.
– Water has high thermal conductivity, which
allows it to conduct heat away from the site
where the heat is generated.
– The heat of fusion for the conversion of ice
to water is high.
Physical and chemical properties of water

• Table 1.1
Physical and chemical properties of water

• The thermal properties of water are key to

its role in biological systems.
– The density of water is highest at 4º C rather
than at the freezing point (0º C).
– The heat of vaporization of water, which is
the energy required to covert liquid water to
water vapor, is also high.
– The high dielectric constant contributes to
water’s ability to form hydration shells
around molecules.
Physical and chemical properties of water

• Figure 1.2
Physical and chemical properties of water

• Table 1.2
Physical and chemical properties of water

• The polarity of water molecules creates a

strong attraction between water molecules
called cohesion.

• The cohesive properties of water directly

contribute to water’s tensile strength and
surface tension.

• The polarity of water also creates a strong

attraction to surfaces called adhesion.
Physical and chemical properties of water

• Figure 1.3
The movement of water
• The transport of water occurs by the
energetically passive processes of
diffusion and bulk flow.
– Bulk flow (or mass flow) is driven by
differences in pressure.
– Diffusion is driven by difference in the
concentration of water.
The movement of water
• Diffusion is governed by Fick’s first law.
J = -D A C l
– J is the flux (amount of material crossing per unit area
per unit time.
– D is the diffusion coefficient of the media.
– A is the cross-sectional area.
– L is the length of the diffusion path.
– C represents the concentration gradient.
– The negative sign indicates that diffusion only occurs
from a higher concentration to a lower concentration.
The movement of water
• Figure 1.4
The movement of water
• Osmosis is a special case of diffusion
involving the movement of water across a
selectively-permeable membrane.

• A selectively permeable membrane allows

for the movement of water, but restricts the
movement of other solutes.
The movement of water
• Figure 1.5
Selectively permeable membranes
in plant cells
• Plant cells have a variety of selectively
permeable membranes that create various
subcellular compartments.
– The outer plasma membrane encloses the
cell’s liquid protoplasm.
– The internal cellular structures, called the
organelles, are either composed of, or
surrounded by, membranes.
– In addition to the various membranes, the cell
is encased with a cell wall.
Selectively permeable membranes
in plant cells
• Figure 1.6
Thermodynamics of water movement

• The passive movement of water or other

substances across a membrane is dictated
by the chemical potential ( ) of that
substance on each side of the membrane.
– The chemical potential is the free energy per
mole of a substance.
– The chemical potential also is a measure of
the capacity of a substance to move.
Thermodynamics of water movement
• Pure water has a chemical potential of zero.

• The addition of solutes decreases the mole

fraction of water, calculated by:

– Xw is the mole fraction of water

– W is the moles of water
– S is the moles of solute
Thermodynamics of water movement
• Using the mole fraction of water, the
chemical potential for water on each side
of the membrane can be calculated by:
w w
R T ln X w

– w is the chemical potential of water on a

given side of the membrane
– w* is the chemical potential of water under
standard temperature and pressure
– Xw is the mole fraction of water
Thermodynamics of water movement

• For two sides of a membrane with different

chemical potentials, water will move
passively from the higher chemical
potential to the lower chemical potential.

• Since water only moves passively, plants

control the movement of water indirectly
by moving ions to alter the w.
Thermodynamics of water movement

• The movement of ions to control the

movement of water may require that the
ions be moved against their gradient,
which is an example of active transport.

• The manipulation of ion transport to

control water transport is an example of
osmotic adjustment.
Thermodynamics of water movement

• Figure 1.7
Thermodynamics of water movement
• The effect of ions on the osmotic component of
the chemical potential of water can be
demonstrated with an osmometer.

• When water moves down its chemical potential

gradient across a membrane, it will continue to
do so until an equilibrium is reached.

• If a piston applies positive pressure to exactly

balance (and prevent) the flow of water, this
pressure is called the osmotic pressure
Thermodynamics of water movement

• The magnitude of osmotic pressure

needed to prevent the osmosis of water is
directly related to the solute concentration.

• Since the osmotic pressure offsets the

potential for water movement, the solute
potential ( S) of the solution is the
opposite sign of the osmotic pressure.
Thermodynamics of water movement

• Figure 1.8
Thermodynamics of water movement

• As the osmometer illustrates, the chemical

potential also has a pressure potential
(VP) such that:
w w
R T ln X w + V W P

• There are also electrical and gravitational

components to the chemical potential, but
for water these are generally negligible, so
they are omitted from the equation.
Thermodynamics of water movement

• By substituting values in the equation, and

including both the osmotic and hydrostatic
pressure, the chemical potential of water
can be described as:
w w
V W (P- )

• And with some final substitutions the

water potential of a solution is illustrated
as: P-
Thermodynamics of water movement

• Water potential is a useful measurement

for plant physiologists because:
– P and can be measured experimentally.
– The units for water potential (pascals) are
relevant to the soil-plant-atmosphere system.
– Gradients in water potential also describe the
passive flow of water, specifically from more
positive to more negative values.
– Water potential can be used as a measure of
physiological status.
Thermodynamics of water movement
• The water potential can also be expressed as
the sum of the component potentials.

+ S

– P is the pressure potential (same as P)

– S is the solute (or osmotic) potential

• The matric potential is sometimes also included,

which accounts for the adsorption of water to
solid surfaces, such as in seed imbibition.
Thermodynamics of water movement

• In plant cells, the vacuole makes the

greatest contribution to the water potential
because the vaciole contains dissolved
solutes and 50-80% of the cellular water.

• When plant cells gain water, they exert an

outward pressure called turgor pressure.

• A plant cell full with water is turgid.

Thermodynamics of water movement
• When turgid plant cells exert turgor
pressure against the wall, there is an
equal, opposite wall pressure.

• If the cell loses water to the point that the

turgor pressure is zero, the cell is flaccid.

• Incipient plasmolysis refers to the

condition where the protoplast is filled with
water and turgor pressure is zero.
Thermodynamics of water movement

• In a hypotonic solution the cell would

gain water because cell is more negative
than the solution.

• In a hypertonic solution the cell would

lose water and undergo plasmolysis
because cell is more positive than the
Thermodynamics of water movement

• Water potential gradients also determine

the flow of water from one cell to another.

• In nature, an excessive loss of water from

plant cells leads to wilting.

• Under conditions of wilting, the water

potential of the cell becomes highly
Thermodynamics of water movement

• Figure 1.9
• Porins are major intrinsic proteins
(MIPS), a class of membrane proteins.

• Porins are non-selective cation channels.

• Aquaporins are found in the plasma

membrane and tonoplast and mediate the
transport of water and neutral solutes like
• Figure 1.10a
• The structure of aquaporins is very similar
across different organisms.

• Aquaporins are formed from four protein


• Aquaporins are gated channels, which

means that they can be selectively opened
and closed.
• Figure 1.10b
• Aquaporins are not the only mean by
which water can enter cells.

• Water can diffuse directly through the cell

membrane between the phospholipid

• Aquaporins provide a more rapid rate of

water movement, and therefore make a
greater contribution to osmoregulation.
• Figure 1.10c
• Osmoregulation allows cells to respond to
the external environment.

• An osmoregulatory system involves a two-

component system:
– A sensing mechanism (sensor protein or
– A transducing mechanism (response
regulators such as transcription factors)
• Figure 1.11
• In E. coli, the two-component system
consists of:
– The EnvZ sensor protein
– The OmpR response protein

• The system regulates the expression of

the pore proteins OmpF and OmpC.
• In yeast, the two-component system has
SLN1, a histidine kinase, as the

• A similar system is present in Arabidopsis

thaliana with ATHK1 as the osmosensor.
Whole Plant Water Relations

Chapter 2
Learning objectives
• Understand the driving force behind

• Know how environmental factors influence

the rate of transpiration water loss.

• Know the structure of water-conducting

tissues in plants.
Learning objectives
• Understand why a continuity of the water
column is essential to water transport and
plant water relations.

• Understand how soil water is transported

into roots.
• Plants lose ~95% of the water to the
atmosphere through transpiration.

• Transpiration is the loss of water from

plants as water vapor.

• Water loss from other surfaces is reduced

by the presence of a waxes and the
• Water escapes primarily through the
stomata, but also through lenticels in the

• Water loss through the stomata is

regulated by the guard cells.

• The water transpired is principally water

vapor in the intercellular spaces
surrounding the leaf mesophyll cells.
• Figure 2.1
• Transpiration is a two-stage process.
– Water evaporates from the mesophyll cell
walls into the substomatal air.
– The water vapor diffuses through the
stomates into the atmosphere.

• Other researchers have suggested that

transpiration involves peristomal
evaporation instead.
• Transpiration from leaves occurs via:
– Stomatal transpiration, which is passage of
water through the stomates.
– Cuticular transpiration, which is water loss
directly through the cuticular layer.

• Cuticular transpiration is thought to be only

5-10% of the total transpiration.
• The driving force for transpiration is a
difference in vapor pressure between the
substomatal and atmospheric water.

• The concentration of water in the vapor

phase is the vapor density (g m-3).

• The water concentration can be expressed

as the vapor pressure (e or kPA).
• When the gas phase is saturated with water, it
has reached the saturation vapor pressure.

• The vapor pressure an be quantified with

Raoult’s law.
e = X ie
– e is the vapor pressure
– Xi is the mole fraction of water
– eo is the saturation vapor pressure of the solvent
• Figure 2.2
• The rate of transpiration is affected by:
– Humidity
– Temperature
– Wind speed

• Transpiration (T) is governed by the

magnitude of the difference in vapor
pressure between the leaf and air.
T e leaf - e air
• Transpired water encounters resistance to
– The movement through the intercellular
spaces is tortuous.
– Movement through the stomata represents a
– The unstirred boundary layer impedes water
movement to the bulk air.
• The resistances (r) to movement can be
incorporated into the mathematical
expression for transpiration.
e leaf - e air
rleaf - rair
• Figure 2.3
• Relative humidty (RH) is the ratio of
actual water content to maximum water

• Precent relative humidity is the actual

vapor pressure relative to the saturation
vapor pressure.

• Temperature increases the capacity of air

to hold water.
• Table 2.1
• The relative humidity of the air contributes to the
air’s water potential ( ).

• As humidity decreases, water potential becomes

more negative.

• Since substomatal air is more humid, it has a

more positive water potential that bulk air, so
transpiration is the movement of water down its
water potential gradient.
• Table 2.2
• Temperature also affects the vapor
pressure gradient, increasing it as
temperature increases through the day.

• This insures that transpiration occurs,

even as the relative humidity of the air
approaches 100%.
• Table 2.3
• Wind influences transpiration by affecting the
distance over which water must move.

• Increasing wind velocity disrupts the

boundary layer and enhances transpiration
because the distance of water movement

• Wind movement also cools and dries the leaf,

which may further increase transpiration.
• Figure 2.4
Water conducting tissues
• The plant vascular tissues consist of the:
– Xylem
– Phloem

• Xylem consists of three cell types.

– Fibers are elongated cell with thickened cell
walls for structural support.
– Parenchyma cells provide storage.
– Tracheary elements, which consist of
tracheids and vessel elements, are the
conducting cells.
Water conducting tissues
• Figure 2.5
Water conducting tissues
• Tracheid and vessel element structure
provides for the efficient movement of
water through the xylem.

• The tracheids have bordered pit pairs

with a central torus that provides a way of
sealing the tracheids if necessary.
Water conducting tissues
• Figure 2.6
Water conducting tissues
• Vessel elements are made up of vessel
members that have a perforation plate at
each end.

• The perforation plate may have a

scalariform or reticulate structure.

• Vessels are more evolutionarily derived

than tracheids.
Water conducting tissues
• Figure 2.7
Water conducting tissues
• The movement of water through the xylem
is governed by Poiseuille’s equation.
P r
Jv =

– Jv is the flux rate.

– The pressure gradient is P.
– The solution viscosity is
Sap ascent in the xylem
• Atmospheric pressure can raise a column
of water only about 10 m, but xylem
transport must reach greater heights.

• The mechanism of xylem transport

– Root pressure
– Capillarity
– Cohesion theory
Sap ascent in the xylem
• Figure 2.8
Sap ascent in the xylem
• Root pressure is a positive pressure at the
root level that pushes water up the xylem.

• Root pressure is a function of:

– Root structure
– Water uptake
– Mineral uptake
Sap ascent in the xylem
• Root pressure is generated as follows:
– Roots take up mineral ions from the soil.
– The change in solute potential decreases
water potential and induces water uptake.
– Water moves radially to the endodermis
surrounding the stele.
– The endodermis has a Casparian band
made of suberin.
Sap ascent in the xylem
• Root pressure is generated as follows:
– The Casparian band prevents the movement
of water back to the cortex
– Therefore the continual influx of water causes
a positive pressure to develop which forces
water up the stem in the xylem.

• Root pressure can be measured with a

Sap ascent in the xylem
• Figure 2.10
Sap ascent in the xylem
• Figure 2.9
Sap ascent in the xylem
• Root pressure can only raise a column of
water a short distance so it is insufficient
to raise water to the necessary height.

• Measurements have also shown that the

xylem sap is under negative pressure, or
tension, so root pressure cannot be the
driving force.
Sap ascent in the xylem
• Capillarity contributes to the rise of sap in
the xylem.

• Capillarity occurs because water shows

adhesion, an attraction to solid surfaces.

• The surface tension of water also

contributes to capillary rise.
Sap ascent in the xylem
• The capillary rise in the xylem can be calculated
using this equation:
-5 2
1.49x10 m
– h is the capillary rise
– r is the radius (in meters)

• For the radius of a typical xylem element,

capillarity would raise the water column <1 m.
Sap ascent in the xylem
• The current hypothesis describing sap
ascent is the cohesion theory.
– Water evaporation from cell walls of
mesophyll cells in leaf is the driving force.
– As the water evaporates, it creates a tension
in the minute contours of the wall.
– Because water is cohesive, the tensile
strength that develops pulls the continuous
network of water up from the soil to leaves.
Sap ascent in the xylem
• Figure 2.11
Sap ascent in the xylem
• When water is under tension in the xylem,
it is in a metastable state and dissolved
gases are released as bubbles.

• This formation of bubbles is called


• These bubbles can cause an embolism, a

blockage of xylem vessels.
Sap ascent in the xylem
• Figure 2.12
Sap ascent in the xylem
• The structural nature of xylem elements
allows embolisms to be overcome.

• The bordered pits in xylem elements

allows water to bypass emoblized vessels
to keep xylem flow moving.

• As the xylem tension decreases during the

night, some embolisms will disappear.
Sap ascent in the xylem
• Embolisms may actually serve beneficial roles in
terms of preventing excess water loss during

• The designed leakage hypothesis proposes

that plants evolved to use cavitation to protect
themselves when water potentials become too

• Root are also prone to cavitation, particularly

when first transplanted into new soil.
The soil-plant-atmosphere continuum
• Water movement through plants relies on an
integrated connection of water from the soil,
through the roots, stem, and leaves, and into the

• This continuum must be maintained.

• This means that plants are highly dependent

upon the environment and soil water.
The soil-plant-atmosphere continuum
• Water is obtained principally from the soil.

• Soil has three phases.

– The solid surfaces
– The soil solution phase
– A gaseous phase

• Soil also contains various organic

components and living organisms.
The soil-plant-atmosphere continuum

• The size of the soil particles determines

the characteristics of the soil, including the
retention of water.
– Soils have a porosity composed of large
pores and capillary pores, which together
account for 40-60% of the soil volume.
– When the pore space is filled with water, the
soils is at field capacity.
The soil-plant-atmosphere continuum

• Water in soils is subject to the same forces

as water in plants.
– The curvature of soil particles create the
same adhesive force as cell wall water.
– Water in the pore space shows cohesion and
tension, and can be drawn to roots.
– Water moves in the soil primarily by pressure-
driven mass flow.
The soil-plant-atmosphere continuum
• The water potential of the soil and the
roots determines water movement.
– Root uptake of water can only occur if the
water potential of root cells is more negative
that the soil water potential.
– The soil water percentage at which the root is
unable to obtain water corresponds to the
permanent wilting percentage.
– The water content between field capacity and
permanent wilting percentage is available
Uptake of water by roots
• The functions of roots include:
– Anchoring the plant in the soil.
– Storing carbohydrates and other molecules.
– Synthesis of some hormones and secondary
– Uptake and transport of water and minerals.

• In order to provide the uptake and transport

needed, root systems need to be extensive in
length and surface area.
Uptake of water by roots
• Roots take up water primarily at the tips.

• The uptake of water occurs along other

root sections as a function of age,
physiological condition, and water status.

• Water is also taken up by the root along

the zone of maturation.
Uptake of water by roots
• Figure 2.13
Uptake of water by roots
• Root hairs are also primary sites for water

• Root hairs are outgrowths of the

membrane of individual epidermal cells.

• The small diameter allows root hairs to

explore smaller pore spaces in the soil to
obtain water.
Uptake of water by roots
• Figure 2.14
Radial movement of water in roots
• Water moves across the diameter of the root to
the stele by two pathways.
– The apoplast represents the continuity of the cell wall
space outside of the cells.
– The symplast represents the connection of cellular
cytoplasm between cells provided by the

• Water movement radially also varies depending

upon whether the suberization of the
endodermis in that area of the root has fully
Radial movement of water in roots
• This radial movement of water creates a lag
between uptake and transpiration.

• If transpiration exceeds root uptake of water,

there may be a midday closure of the stomates
while the balance is restored.

• Water uptake is dependent upon physiological

processes in the root, such as respiration
Radial movement of water in roots
• Figure 2.15
Roots, Soils, and Nutrient
Chapter 3
Learning objectives
• Understand the properties of soils and
how these properties dictate the
availability of nutrients to plants

• Understand the mechanisms by which

solutes are transported across
membranes, including the role of
membrane transport proteins
Learning objectives
• Understand how solute ions move through
root tissues and cell walls

• Understand how soil microorganisms

assist plants in acquiring nutrients for
Nutrients in the soil
• Soil colloids, clay particles suspended in
but not dissolved in the soil solution, are
the main reservoir of soil nutrients.

• Soil colloids are distinguished from other

soil constituents (e.g., silt and sand), by
the Tyndall effect.

• Colloidal suspensions form micelles.

Nutrients in the soil
• Some soils also contain colloidal organic
material called humus.

• The role of the colloidal fraction as a

nutrient reservoir depends upon:
– Specific surface area.
– The density of fixed negative charges.
Nutrients in the soil
• Figure 3.1
Nutrients in the soil
• The ability of colloidal surfaces to bind soil
cations follows the lyotropic series.

Al3+ > H+ > Ca2+ > Mg2+ > K+ = NH4+ > Na+

• Cation binding to colloidal surfaces is

reversible, so nutrient ions in the soil show
ion exchange, or exchangability.
Nutrients in the soil
• Colloidal binding contributes to the
dynamic equilibrium of cationic nutrients in
the soil.

• Soils do not generally bind anionic


• Anionic nutrients may have to be supplied

in order to meet plant growth
Nutrients in the soil
• Figure 3.2
Nutrient uptake
• In order for nutrients to enter plants, they
must cross cell membranes.

• The mechanisms by which nutrients cross

membranes include:
– Simple diffusion
– Facilitated diffusion
– Active transport
Nutrient uptake
• Figure 3.3
Simple diffusion
• Simple diffusion is governed by Fick’s law.
o i
J = PA(C -C )

– J is the flux.
– P is the permeability coefficient of the
– A is the cross-sectional area.
– (Co-Ci) represents the concentration
Simple diffusion
• Since membranes are made of lipids,
nonpolar substances can diffuse more
readily into cells than nutrient ions.

• The permeability coefficient is a measure

of how readily a given solute can diffuse
through a membrane.

• Diffusion is a passive process in response

to a concentration gradient.
Membrane transport proteins
• Facilitated diffusion describes the rapid,
passive, protein-assisted diffusion of
solutes across membranes.

• Facilitated diffusion can be mediated by:

– Carrier proteins
– Channel proteins
Membrane transport proteins
• Pumps are membrane transport proteins
that move solutes against their gradient.

• Pumps require the input of energy to

achieve transport, so this is referred to as
active transport.
Selective accumulation of ions
• Active transport allows for the
accumulation of ions inside cells to
concentrations higher than those outside
the cells.

• This corresponds to an accumulation

ratio (ratio of plant concentration to soil
concentration) >1.0.
Electrochemical gradients dictate
ion movement
• For uncharged solutes, the concentration
gradient can be expressed in terms of a
gradient of chemical potential (m).
[U i ] [U i ]
 m u = R T ln = 59 log
[U o ] [U o ]

• The charge of ions creates an electrical

potential that must also be considered.
Electrochemical gradients dictate
ion movement
• Hence, ion transport is dictated by the
electrochemical gradient across the cell

• Because the electrochemical gradient

influences charge as well as concentration
gradients of ions, cells have a
transmembrane potential (a net negative
charge) across their membranes.
Electrochemical gradients dictate
ion movement
• Figure 3.8
The Nernst equation
• When the charge and concentration
gradients are taken into account, it is
possible to estimate whether an ion moves
by passive or active transport.

• The equation used is the Nernst equation.

[C i ]
- z  E c = 59 log
[C o ]
The Nernst equation
• The equation predicts the Nernst
potential (Ec) that would be established if
an ion with charge “z” came to equilibrium
due to simple diffusion.

• If the observed values deviate from those

predicted by the model, this suggests that
there is a protein-mediated active uptake
or efflux of the ion of interest.
Electrogenic pumps
• The energy for active transport comes
from two sources.
– The direct use of ATP to transport a solute
across the membrane.
– The use of an ATPase proton pump to
establish a proton motive force.

• The ATPase is a uniport that is

electrogenic, in that it maintains a charge
gradient across the membrane.
Electrogenic pumps
• Figure 3.9
Electrogenic pumps
• Figure 3.10
Electrogenic pumps
• Solutes coupled to the proton motive force
(cotransport) can be moved against their
concentration gradient.
– Symports move the proton and the ion of
interest in the same direction across the
– Antiports move the proton and the ion of
interest in opposite directions across the
Electrogenic pumps
• There are electrogenic ATPases in both
the plasma membrane and the tonoplast.

• The tonoplast ATPases (V-type) differ

from those in the plasma membrane.
– This ATPase is not inhibited by vanadate as
the plasma membrane ATPase is.
– This ATPase is inhibited by oligomycin.
– The V-type ATPase is more similar to the
mitochondrial F-type ATPase.
Electrogenic pumps
• In addition to facilitating ion transport, the
V-type ATPase helps to maintain pH
balance between the vacuole and cytosol.

• There are also Ca2+-ATPases that use

ATP to pump calcium against its
concentration gradient to store this ion in
specific subcellular compartments.
K+ transport
• Like other ions, K+ transport is mediated
by two classes of transport proteins.
– Low affinity transporters, such as membrane
channels, are used when K+ concentrations
outside the cell are high.
– High affinity transporters, such as carriers
energized by the proton motive force, are
used when K+ concentration outside the cell
are low.
Ion transport interactions
• The transport of various ions interact with
one another.
– Deficiencies of one nutrient can increase the
uptake of other elements.
– Some nutrients compete with one another for

• Ion transport interactions such as these

are examples of cross talk.
Transport across the cell wall
• Before ions can be transported across the
cell membrane, they must cross the cell

• The cell wall has an apparent free space

(APS) that retains soil solution and ions.

• The APS is an apoplastic compartment.

Transport across the cell wall
• Ions in the APS can move through the
APS to the cell membranes, where they
can then be taken up.

• Ions in the APS can also diffuse back out

of the APS because they may be unbound
or on exchangeable sites in the cell wall.
Transport across the cell wall
• Figure 3.11
Radial transport
• Movement through the APS begins at the
rhizodermis (root epidermis).

• Ions move radially through the cortex via:

– The apoplastic pathway through the APS.
– A transmembrane pathway across cortex cell

• Ion are transported in an energy-dependent

manner across the endodermis into the stele.
Radial transport
• Figure 3.12
Radial transport
• Passage cells in the endodermis also
allow for the transport of ions.

• Lateral roots, emerging from the

meristematic pericycle layer inside the
endodermis, give rise to lateral roots which
also transport ions.
Root-microbe interactions
• The rhizosphere is the zone of soil
influenced by root biological processes.

• The various exudates released by roots

provided a habitat for soil microorganisms.

• The mixture of root exudates, living and

dead microorganisms, and soil colloids
forms the mucigel.
Root-microbe interactions
• These microorganisms aid the root in
obtaining nutrient ions.
– Some bacteria convert nitrogen in the soil to
ammonium and nitrate.
– Other bacteria can stimulate the formation of
proteoid roots specialized for the uptake of
nutrients such as phosphorus.
Root-microbe interactions
• Mycorrhizal fungi form mutualistic
interactions with the roots of most plants.

• There are two types of mycorrhizae.

– Ectotrophic or ectomycorrhizal
– Endotropic or endomycorrhizal

• The ecotmycorrhizae form a Hartig net

that penetrates into the apoplastic space.
Root-microbe interactions
• Endomycorrhizae such as the vesicular-
arbuscular mycorrhiza form branched
arbuscles inside cells of the root cortex.

• Both types of mycorrhizae increase the

surface area of roots and create a larger
nutrient depletion zone to provide the
plant with nutrients.
Root-microbe interactions
• Figure 3.13
Plants and Inorganic Nutrients

Chapter 4
Learning objectives
• Understand the methods used to study
plant mineral nutrition

• Understand the distinction between

essential and beneficial nutrients and
between macronutrients and
Learning objectives
• Understand the biological roles for the 14
essential mineral elements

• Understand the critical and deficient

concentrations for essential elements

• Understand the symptoms associated with

nutrient deficiency and toxicity
Plant and inorganic nutrients
• Unlike heterotrophs, plants are autotrophic,
which makes them capable of surviving in an
inorganic environment.

• Plant nutrition is treated in two aspects.

– Organic nutrition (e.g., photosynthesis)
– Inorganic nutrition

• The study of the inorganic nutritional

requirements of plants is called mineral
Methods in mineral nutrition
• The impetus to study plant mineral nutrition was
a need to increase crop productivity to feed
growing populations.

• Some of the early researchers were:

– N. T. de Saussure
– C. S. Sprengel
– J-B Boussingault
– J. Sachs
– J. B. Lawes and J. H. Gilbert
Methods in mineral nutrition
• An important milestone was the
development of superphosphate as a

• This development, and others, expanded

the use of fertilizers to increase crop
Methods in mineral nutrition
• A significant development in the study and
understanding of mineral nutrition was the
development of hydroponic solutions to
simulate the nutrient environment.

• The first nutrient solution was developed

by Sachs and included many, but not all,
of the necessary plant nutrients.
Methods in mineral nutrition
• Table 4.1
Methods in mineral nutrition
• More balanced nutrient solutions were
developed by Hoaglund and included nearly all
of the necessary nutrients.

• The base solution has been modified by many

researchers and is thus referred to as a
modified Hoaglund’s solution.

• These nutrients solutions provided nutrients in

higher concentrations that typical in the soil.
Methods in mineral nutrition
• Table 4.2
Methods in mineral nutrition
• Hydroponic solutions must be aerated to
prevent anoxia.

• Light needs to be excluded from the

solution to prevent the growth of algae.

• The plant must be supported in the

solution so it will grow.
Methods in mineral nutrition
• Figure 4.1
Methods in mineral nutrition
• There are some drawbacks to the use of
hydroponic solutions.
– Depletions zones can develop unless the
solution is mixed.
– In order to maintain nutrient levels, the
hydroponic solution has to be replenished via:
• Slop culture.
• Drip culture.
• Subirrigation.
• A nutrient film technique.
Methods in mineral nutrition
• Figure 4.2
Essential nutrients
• Essential nutrients are those that:
– Must be provided to plants in order for it to
complete its life cycle.
– Are part of some essential plant constituent or
– The nutrient must be involved in an essential
biological process.

• There are 17 mineral nutrients that meets

these requirements.
Essential nutrients
• Essential nutrients are placed into two
categories based upon the concentration
in plant tissues.
– Macronutrients are found in concentrations
in >10 mmole kg-1 DW.
– Micronutrients, or trace elements, are found
in concentrations in <10 mmole kg-1 DW.
Essential nutrients
• The essential macronutrients are:
– Hydrogen
– Carbon
– Oxygen
– Nitrogen
– Potassium
– Calcium
– Magnesium
– Phosphorus
– Sulfur
Essential nutrients
• The essential micronutrients are:
– Chlorine
– Boron
– Iron
– Manganese
– Zinc
– Copper
– Nickel
– Molybdenum
Essential nutrients
• Determining essentiality of a mineral
nutrients is a difficult process.

• Studies must use high purity reagents and

extremely clean materials to prevent small
amounts of nutrients from contaminating
the experiment.
Beneficial nutrients
• Beneficial nutrients may not be
universally required by plants, but may
promote plant growth and development if

• Beneficial elements include:

– Sodium
– Silicon
– Cobalt
– Selenium
Beneficial nutrients
• Sodium for example is required by C4 plants but
less so by C3 plants.

• Silicon increases the rigidity and elasticity of cell

walls and the resistance to lodging.

• Cobalt is required by legumes.

• Some plants accumulate high concentrations of

Nutrient functions and deficiency
• A plant species’ requirement for a
particular nutrient is defined as the critical

• The critical concentration is the

concentration of a nutrient in the plant
tissue just below that which provides for
maximum growth.
Nutrient functions and deficiency
• At tissue concentrations above the critical
concentration, the nutrient is present in
adequate amounts.

• At concentrations in excess of the critical

concentration, nutrients can be toxic.

• At tissue concentrations below the critical

concentration, the nutrient is deficient.
Nutrient functions and deficiency
• Figure 4.3
Nutrient functions and deficiency
• Plants that are deficient in a nutrient may
display visual symptoms such as:
– Chlorosis, the loss of chlorophyll pigment.
– Necrosis, the death of cells and tissues.

• The location of deficiency symptoms in a

plant depend upon the mobility of the
nutrient in the phloem.
• Plants generally acquire nitrogen as
ammonium or nitrate.

• Nitrogen is required for the synthesis of

macromolecules such as amino acids,
proteins, and nucleic acids.

• Nitrogen stimulates shoot growth more so

than root growth.
• Symptoms of nitrogen deficiency include:
– Chlorosis of the older leaves first, and then
the younger leaves.
– An accumulation of anthocyanin pigments.
• Phosphorus is acquired as phosphate and
the plant may have to convert organic
forms to inorganic forms to get phosphate.

• Phosphates are found in the sugar-

phosphates involved in metabolism.

• Phosphates are also a structural

component of nucleic acids.
• Phosphate is also found as a component
of ATP.

• Phosphorus deficiency symptoms include:

– Over-greening of the leaves.
– Accumulation of anthocyanins.
– Malformation of leaves and necrosis.
– Symptoms in the older leaves initially.
• Potassium is the primary osmolyte in plants
used for water relations.

• Potassium activates or is a cofactor for a wide

range of enzymes, including those in
photosynthesis and respiration.

• Potassium deficiency symptoms include:

– Chlorosis and mottling in older leaves
– Necrosis, especially in grasses.
• Sulfate is the only form of sulfur plants
take up.

• Sulfur deficiencies are rare.

• Sulfur deficiency symptoms include:

– Generalized chlorosis.
– Symptoms primarily in the young leaves.
• Sulfur has biological roles in:
– Disulfide bonds in proteins.
– Vitamins and coenzymes.
– Iron-sulfur proteins in electron transport.
– Secondary compounds, such as the
thiocyanates and isothiocyanates.
• Calcium is taken up as Ca2+.

• Calcium is important:
– As a second messenger.
– For mitosis and the spindle fibers.
– The structure of the cell wall.
– The integrity of the cell membrane.
• Calcium deficiency symptoms appear in
the young leaves.
– The meristematic region is affected because
of the importance of Ca2+ to mitosis.
– Young leaves are deformed and necrotic.

• In hydroponic solution, Ca2+ deficiency

affects the roots.
• Magnesium is taken up as Mg2+.

• Biological roles for magnesium include:

– Serving as the cofactor for chlorophyll.
– Stabilizing ribosome structure.
– Activation of several enzymes, including those
in photosynthesis.
– Serving as a cofactor in ATP-mediated
• Magnesium deficiency symptoms include:
– Chlorosis, particularly in the leaf veins.
– Symptoms in the older leaves.
• Iron can be taken up as Fe2+ or Fe3+,
depending upon the plant species.

• Iron is required for:

– Chlorophyll synthesis.
– Iron-sulfur proteins in electron transport.
– Nitrogen fixation in legumes.
– Redox enzymes.
• One reason that plants experience iron
deficiency is because iron can have a
limited solubility in soil.

• The deficiency can be minimized is iron is

provided in a chelated form, such as with
ethylenediaminetetraacetic acid
• Because of the problems with iron
solubility, plants have specific
mechanisms to acquire this nutrient.
– Protons are released to acidify the soil.
– Ligands like caffeic acid are released.
– In non-grasses, a ferric reductase is used to
reduce solubilized Fe3+ to Fe2+ for uptake.
– Grasses secrete phytosiderophores to
solubilize and take up Fe3+.
• Figure 4.4
• Figure 4.5
• Figure 4.6
• Boron can be present primarily as the
neutral chemical species H3BO3.

• Roles for boron are unclear but include:

– A contribution to cell wall structure.
– Potential roles in carbohydrate metabolism.
– Potential roles in cell division and elongation.
• Deficiency symptoms include:
– Decreased root elongation.
– Decreased cell division.
– Distorted roots, including a stubby, bushy
appearance or cork-screw roots.
– Shortened internodes.
• Copper is present in soils as Cu2+ and
Cu+, depending upon the redox conditions.

• Copper is primarily a cofactor for various

oxidative enzymes, such as superoxide

• Copper is also a component of electron

carriers in the chloroplast and
• Symptoms of copper deficiency are more
prominent in soils with high organic matter
because Cu2+ binds strongly to organic

• Symptoms of copper deficiency include:

– Stunted growth.
– Distortion of young leaves.
• Roots take up Zn2+.

• Zinc is an activator of enzymes, including:

– Alcohol dehydrogenase.
– Carbonic anhydrase.

• Zinc is also involved in auxin metabolism,

perhaps with respect to tryptophan
• Symptoms of zinc deficiency include:
– Chlorosis.
– Shortened internodes.
– Smaller leaves.
• Manganese occurs in several chemical species
in soil, but is taken up as Mn2+.

• Manganese is a cofactor for several enzymes,

including decarboxylase and dehydrogenase
enzymes involved in the respiratory carbon

• Manganese can substitute for magnesium in

ATP-mediated reactions.
• Manganese is critical for the
magnoprotein involved in oxygen
evolution during photosynthesis.

• Manganese deficiency symptoms include:

– Gray speck in cereal grains.
– Chlorosis.
– Discoloration and deformities in legume
• Molybdenum is taken up primarily as
molybdate (MoO42-).

• Molybdenum is required for dinitrogenase

and nitrate reductase.

• Deficiency symptoms include:

– Chlorosis and necrosis.
– Whiptail, the deformation of young leaves.
• Chlorine is rarely deficient in plants and
then only in laboratory experiments.

• Chloride is a counterion for water relations

and charge balance.

• Chloride is also required for cell division

and photosynthesis.
• Although considered an essential nutrient,
the essentiality of nickel has been difficult
to establish.

• Nickel is required for the function of

enzymes in nitrogen metabolism,
particularly in legumes.
– Urease, which is involved in the metabolism
of the ureides formed by legumes after
nitrogen fixation.
– Hydrogenase
Micronutrient toxicity
• There is a critical toxicity level for each
micronutrient, above which the essential
nutrients can become toxic.

• Toxicity symptoms are often similar to

those of nutrient deficiency.
– Chlorosis
– Inhibition of root growth
Bioenergetics and ATP
Chapter 5
Learning objectives
• Understand the physical and biological
aspects of bioenergetics, including the
laws of thermodynamics, and the concepts
of entropy, enthalpy, and free energy.

• Recognize how living organisms use

various coupled reactions to overcome the
limitations of free energy and entropy.
Learning objectives
• Understand the role of oxidation-reduction
reactions in biological energy transformations.

• Know the structural features of two energy-

transducing organelles – the chloroplast and the

• Know the chemiosmotic model for the synthesis

of ATP in chloroplasts and mitochondria.
• Living organisms must constantly derive,
transform, and utilize energy to counter natural
processes of disorder and decay.

• Bioenergetics is the study of the energy

transformations in living organisms.

• There are two broad strategies by which

organisms derive the necessary energy.
– Photoautotrophs derive energy from the sun.
– Chemoheterotrophs derive their energy from
organic substances obtained from the environment.
• There are chemical and physical principles
that influence living organisms.

• In the biological context, there are

principles of thermodynamics that govern
energy transformation and work.

• Bioenergetics is the application of

thermodynamic laws to study energy
transformation in living organisms.
• The first thermodynamic law, the law of
conservation of energy.
– The basic tenet is that the amount energy in
the universe is constant.
– Energy is neither lost or gained, but can
change form.
– Not all energy is translated into work, some
energy can be lost as heat.
• The second thermodynamic law involves
the concept of entropy.
– Entropy is an expression of the randomness
or disorder in a system.
– In thermodynamic terms, this means that
systems are continually moving towards a
state of lower energy and more disorder.
– In essence, the growth and organization
associated with life is moving towards less
– The opposition of entropy requires energy.
• The energy available to do work and
oppose entropy is the Gibbs free energy.
H = G + TS

– H is the total heat energy (enthalpy)

– G is the free energy available to do work.
– T is the temperature
– S represents entropy, or the energy not
available to do work.
• Changes in energy during the course of a
reaction provide important information about the
nature of that reaction.
H= G+T S
– If a reaction is spontaneous, then G<0 and it is
termed an exergonic reaction.
– If a reaction is endergonic, then G>0 and a reaction
needs an input of energy to proceed.
– The standard free energy of change ( Gº)
represents the free energy change at pH 7 and when
concentrations of reactants and products are 1 M.
• The equilibrium of a chemical reaction can
be related to the concept of free energy.
– At equilibrium, the concentrations of reactants
and products are at zero, so G=0.
– The farther away from the reactants are from
equilibrium, the more free energy will be
available ( G<0).
– Beyond equilibrium, where the product to
reactant ratio is >1, G>0.
• Figure 5.1
• The relationship between G and the
equilibrium constant (Keq) of a reaction can
be expressed as:
G = G º' + R T ln K eq

• Or in a form showing the displacement of

a reaction from equilibrium:
K eq
G = 2.3 R T log ( )
Energy transformation and
coupled reactions
• Living organisms can accomplish energetically
unfavorably reactions by coupling them to an
exergonic reaction.

• Coupled reactions are spontaneous if the net

change in free energy is negative, such as in this

ATP  ADP + Pi Gº’=-32.2 kJ mol-1

Glucose + Pi  Glucose-6-P Gº’=13.8 kJ mol-1
ATP+Glucose  Glucose-6-P + ADP Gº’=-18.4 kJ mol-1
Energy transformation and
coupled reactions
• ATP is recognized as a high-energy
molecule whose hydrolysis is coupled to a
wide variety of biochemical reactions.
– The hydrolysis of ATP generates a significant
amount of free energy ( G=-56 kJ mol-1).
– Since cells maintain pools of ATP, and this
concentration is maintained far from equilibrium,
ATP has a perpetual capacity to provide energy.
– The constant maintenance of ATP concentrations
in a non-equilibrium state is an example of
Energy transformation and
coupled reactions
• Figure 5.2
Oxidation-reduction reactions
• Oxidation-reduction reactions are another
example of a coupled reaction.
– The molecule that donates the electron is the
reductant while the molecule that receives
the electron is the oxidant.
– The tendency of a molecule to accept or
donate electrons is its redox potential.
– There are a wide variety of biological redox
agents that reagents can be coupled to.
Oxidation-reduction reactions
• Figure 5.3
Oxidation-reduction reactions
• Oxidation-reduction reactions are another
example of a coupled reaction.
– The half-reactions for a reductant and an
oxidant’s reaction form a redox couple.
– Since it is possible to predict the redox
potential of redox couples, it is possible to
predict the direction of electron transfers.
– Electron transfer proceeds from couples with
a more negative redox potential to a less
negative redox potential.
Oxidation-reduction reactions
• The free energy of a redox reaction can be
determined from the redox potentials.
G º' = -n F Em

– Em = EM(acceptor) – Em(donor)
Chemiosmosis and energy-
transducing organelles
• One of the principal energy-transducing
membrane systems in cells accomplishes the
synthesis of ATP.

• This mechanism by which this occurs is called

the chemiosmotic hypothesis.
– One tenet of this hypothesis requires that membranes
are impermeable to protons.
– The second tenet is that there need to be carriers that
move the protons against their concentration gradient.
Chemiosmosis and energy-
transducing organelles
• In plants, the chloroplast and the
mitochondria are sites of the chemiosmotic
synthesis of ATP.

• These double-membrane structure of

these organelles allow these structures to
synthesize ATP via chemiosmosis.
Chemiosmosis and energy-
transducing organelles
• Figure 5.4
Chemiosmosis and energy-
transducing organelles
• The chloroplast has four major regions:
– Two outer membranes, the envelope and the
intermembrane space between them.
– The internal matrix, or stroma.
– A system of interconnected system of disk-
shaped membranes, the thylakoids, which
can be stacked into grana.
– The space inside the thylakoids, the lumen.
Chemiosmosis and energy-
transducing organelles
• The stroma of the chloroplast is largely protein,
most of which is the photosynthetic enzyme

• The network of grana and stroma thylakoids

comprise the lamellae.

• The lumen of the thylakoids play a key role in

the oxidation of water during photosynthesis.
Chemiosmosis and energy-
transducing organelles
• Figure 5.7A
Chemiosmosis and energy-
transducing organelles
• The mitochondria has four major features:
– An outer membrane
– An inner membrane, which is extensively folded to
form invaginations called cristae.
– An intermembrane space between the two
– The matrix inside the inner membrane

• Plant mitochondria have inner membrane

formed into a system of tubes and sacs instead
of cristae.
Chemiosmosis and energy-
transducing organelles
• Figure 5.7b
Chemiosmosis and energy-
transducing organelles
• Figure 5.8
Chemiosmotic synthesis of ATP
• The chemiosmotic synthesis of ATP utilizes a
proton motive force (pmf).
– Redox carriers in the inner membrane of the
mitochondria or the thylakoid membrane pump
protons against their gradient, forming a proton
– When these protons are released through an ATP
synthase, the process is exergonic and the energy
released can be coupled to the synthesis of ATP.
– The redox carrier that pumps the protons and the ATP
synthase form a proton circuit in each organelle.
Chemiosmotic synthesis of ATP
• Figure 5.9
Chemiosmotic synthesis of ATP
• Figure 5.7c
Chemiosmotic synthesis of ATP
• The proton circuit which synthesizes ATP in the
chloroplast is a light-dependent process called

• The chemiosmotic synthesis of ATP in the

mitochondrial, drive by aerobic respiration, is
called oxidative phoshporylation.

• ATPase proton pumps are proteins related to

ATP synthases, but create proton gradients
across membranes.
The Dual Role of Sunlight

Chapter 6
Learning objectives
• Understand the nature of light and its interaction
with matter.

• Know ways to measure light.

• Know the light environment of plants.

• Understand the nature of plant pigments and

their role in the capture of light.
• Sunlight is a source of energy which drives

• Sunlight is a source of information for plants that

drives phenomena such as
photomorphogenesis and photoperiodism.

• The study of the role of light in plants is called

The nature of light
• Light is a form of radiant energy within the
electromagnetic spectrum.

• Visible light is the solar radiation between 400

and 700 nanometers and is traditionally defined
in terms of he range of human vision.

• Radiation is the term used to describe regions

of the spectrum outside the human visible range,
such as infrared and ultraviolet (UV) radiation.
The nature of light
• Figure 6.1
The nature of light
• Light has properties of both particles and waves.
– The wave properties can be characterized in terms of
the wavelength and frequency.

– The frequency ( ) is the number of wave crests per

– The wavelength ( ) is the distance between crests of
the wave.
– The speed of light is c.
The nature of light
• Figure 6.2
The nature of light
• The particle nature of light is described in terms
of photons.

• The energy (Eq) of a particular photon is called a

quantum and is related to the wavelength and
frequency by:
Eq = h
– where h is Planck’s constant
The interaction of light with matter
• Photons of light can interact with matter and
impart their energy to those atoms by influencing
the energy state of electrons.

• Absorbed light can induce photochemical

reactions according to the Gotthaus-Draper

• A molecule that absorbs light is a pigment.

The interaction of light with matter
• The absorption of light by a pigment molecule
causes a change in the energy state of an
electron, raising it from the ground level to a
higher excited level.

• The energy levels of electrons occur in discrete

levels with specific energy.

• A photon is absorbed only if the photon’s energy

matches the energy required to raise an electron
to a specific excitation level.
The interaction of light with matter
• Entropy dictates that an excited molecule
must release the excitation energy and
return to the ground state by:
– Thermal deactivation (heat loss)
– Fluorescence (release of a red photon)
– Inductive resonance or radiationless
transfer of the energy to another molecule
– Reverting to a metastable triplet state,
perhaps leading to the photooxidation of the
The interaction of light with matter
• Since pigments absorb only specific
wavelengths of light, an absorption spectrum
for a pigment can be produced.

• The absorption spectrum is characteristic for

each pigment.

• Similarly, the action spectrum for a pigment

illustrates the effectiveness of light in activating a
particular process.
The interaction of light with matter
• Figure 6.3
Measurement of light
• Three parameters are relevant to the
measurement of light.
– Light quantity
– Light quality, spectral composition, or
spectral energy distribution (SED)
– Timing and duration of light treatment
Measurement of light
• Light quantity is measured in terms of the
– Photon fluence is the total number of incident
– Energy fluence is the total amount of incident
– These fluence terms can also be expressed as the
photon fluence or energy fluence rate.
– The energy fluence rate is also referred to as
– Visible light relevant to photobiological processes is
broadly defined as photosynthetically active
radiation (PAR).
Measurement of light
• Light quality is defined by an emission or
incidence spectrum.
– The SED is commonly measured as either the
spectral photon fluence rate or the spectral
energy fluence rate.
– Spectral irradiance can also be measured.

• The SED of natural and artificial light

sources varies.
Measurement of light
• Figure 6.5
The natural radiation environment
• Not all of the solar radiation that strikes the
earth’s atmosphere reaches the surface.

• For example, infrared radiation is

absorbed by CO2 and other gases, giving
rise to the greenhouse effect.
The natural radiation environment
• Figure 6.6
The natural radiation environment
• Ultraviolet radiation absorbed by
molecules produces highly reactive

• If a living organism absorbs UV light, the

reactive molecules produced can be
The natural radiation environment
• The fluence rate and spectral quality of
visible light changes during the course of
the day.
– The fluence rate varies and is lowest at dawn
or twilight and highest at noon.
– Spectral quality shifts at the end of the day as
the atmosphere scatters different wavelengths
of light.
– Sunflecks are intermittent spots of direct
Absorption of light by plants
• Photoreceptors are pigment molecules
that absorb and process light into a form
that can be used by the plant.

• Photoreceptors can be chromoproteins,

consisting of a pigment (chromophore)
and a catalytic protein (apoprotein).
Absorption of light by plants
• Chlorophyll is the pigment primarily responsible
for harvesting light for photosynthesis.
– The molecule has two parts – a porphyrin ring and a
phytol tail.
– The porphyrin ring is composed of four nitrogenous
pyrrole rings.
– The phytol tail is derived from isoprene.
– When the Mg2+ cofactor is inserted, the cholorophyll
molecule is complete. If the Mg2+ is lost, the molecule
is called pheophytin.
Absorption of light by plants
• Figure 6.7
Absorption of light by plants
• Chlorophyll is the pigment primarily responsible
for harvesting light for photosynthesis.
– There are four forms of chlorophyll, designated a, b,
c, or d.
– Chlorophyll a is formed from protochlorophyll a by the
action of NADPH:protochlorophyll oxidoreductase.
– Chlorophyll b is synthesized from chlorophyll a.
– Chlorophyll c is found in diatoms, dinoflagellates, and
brown algae while chlorophyll d occurs in red algae.
– The different forms of chlorophyll have slightly
different properties in terms of light absorption.
Absorption of light by plants
• Figure 6.8
Absorption of light by plants
• Phycobilins also participate in the
harvesting of light for photosynthesis in
red algae and cyanobacteria.
– These molecules are straight- or open-chain
tetrapyrrole pigments.
– The tetrapyrrole group is covalently bound to
a protein, forming phycobilioproteins.
– While involved in light harvesting, these
pigments absorb different wavelengths of light
than chlorophyll in plants.
Absorption of light by plants
• Figure 6.9
Absorption of light by plants
• Figure 6.10
Absorption of light by plants
• An important phycobiliprotein in pants is
phytochrome, a receptor that mediates
several aspects of photomorphgenesis.
– Phytochromes have two chemical forms, one
which responds to red light at 660 nm and
one that responds to far red light at ~730 nm.
– The forms are interconverted between each
other by the absorption of light.
Absorption of light by plants
• The carotenoids are accessory pigments
for photosynthesis that provide the
characteristic color of autumn leaves.
– Carotenoids are terpenoids found in the
chloroplast membrane or in chromoplasts.
– The two primary examples in plants are
carotenes and xanthophylls.
– In addition to absorbing blue light for
photosynthesis, -carotene quenches triplet
excited chlorophyll, protecting in from
Absorption of light by plants
• Figure 6.11
Absorption of light by plants
• Figure 6.12
Absorption of light by plants
• Blue light and UV-A radiation is perceived
by cryptochrome and phtotropins.
– The chromophore for cryptochrome is a flavin,
such as riboflavin or its derivatives flavin
mononucleotide and flavin adenine
– While these flavins can form flavoproteins that
participate in light absorption, most flavins
acts as cofactors in cellular redox reactions.
Absorption of light by plants
• Figure 6.13
Absorption of light by plants
• Blue light and UV-A radiation is perceived
by cryptochrome and phototropins.
– Phototropins are also flavoproteins but with
two flavin mononucleotide molecules.
– The primary roles of phototropins in
photosynthesis are to optimize photosynthetic
efficiency through control of stomatal opening
and reduction of photoinhibition.
Absorption of light by plants
• Flavonoids are a colorful, functional group
of pigments.
– Flavonoids are best recognized as the
pigment that contributes to floral color.
• Purplish colors are provided by flavonoids called
• Yellows are provided chalcones and aurones.
• The color of some flavonoids is pH sensitive.
– Flavonoids are phenylpropane derivatives that
primarily absorb light between 475-560 nm as
well as in the UV-B region.
Absorption of light by plants
• Figure 6.14
Absorption of light by plants
• Figure 6.15
Absorption of light by plants
• Flavonoids are a colorful, functional group
of pigments.
– Because of the absorbance in the UV range,
flavonoids provide plants with a natural
– Other flavonoids serve as an attractant for
insect pollinators.
Absorption of light by plants
• Flavonoids are a colorful, functional group
of pigments.
– Another type of flavonoids, the isoflavonoids,
have antimicrobial properties.
– Isoflavonoids are also one example of a group
of compounds called phytoalexins, which
respond to elicitors released during bacterial
and fungal infection.
Energy Conservation in
Harvesting Sunlight
Chapter 7
Learning objectives
• Recognize the structural features of leaves that
optimize these plant organs for light harvesting.

• Understand the contribution of redox reactions

to photosynthesis.

• Understand the components of the

photosynthetic electron transport chain in the
thylakoid membrane.
Learning objectives
• Understand how the photosynthetic
electron transport facilitates the
chemiosmotic synthesis of ATP.

• Recognize how the mode of action of

some herbicides is targeted specifically to
elements of the photosynthetic machinery.
Harvesting sunlight
• Photosynthesis is the process by which plants,
green algae, and some prokaryotes:
– Convert sunlight to chemical energy.
– Expend that chemical energy to reduce inorganic
carbon dioxide to organic carbon for the synthesis of

• The conversion of sunlight to chemical energy

– The capture, or harvesting, of light.
– The conversion of that light energy to a stable
chemical form.
Harvesting sunlight
• The light-dependent reactions of
photosynthesis include the events
associated with both light harvesting and
the conversion of light to chemical energy.

• In plants and green algae, the organelle

where these events occur is the
Absorption of light by leaves
• The architecture of leaves is optimized for
light capture.
– The broad flat surface of leaves maximizes
intercept and allows capture of direct, incident
sunlight and diffuse sunlight.
– The internal arrangement of the palisade and
spongy mesophyll cells provides a sieve
effect that allows for greater absorption of
Absorption of light by leaves
• Figure 7.1
Absorption of light by leaves
• The mesophyll cells in leaves not only
absorb incoming light but also alter the
direction of the light path.
– Light can be reflected off the surfaces of leaf
– Since cells have an aqueous interior, light
passing through cells may be bent by
– The palisade mesophyll cells act as a light
guide, channeling light within the leaf.
Absorption of light by leaves
• Figure 7.2
Absorption of light by leaves
• In some plant species, leaf structure has
evolved to fit particular environmental
– In pine, the needles are circular, which
decreases the efficiency of light intercept but
reduces desiccation during the winter.
– In species found in arid environments, the
leaves may be thicker and more succulent.
– In cacti, the leaves have been greatly reduced
and photosynthesis occurs in the stem.
Photosynthesis is a redox process
• An overall equation for photosynthesis is:
6C O 2 + 12H 2 O C 6 H 12 O 6 + 6O 2 + 6H 2 O

– CO2 and O2 are involved in equimolar

– Glucose is not necessarily the specific
product of photosynthesis.
Photosynthesis is a redox process
• A simplified equation for photosynthesis is:
C O 2 + 2H 2 O (C H 2 O ) + O 2 + H 2 O

– The term (CH2O) represents the building

block of carbohydrates.
– The equation portrays photosynthesis as a
process for the reduction of CO2, or in another
sense, the hydration of carbon.
Photosynthesis is a redox process
• Photosynthesis in purple sulfur bacteria is
described by:
C O 2 + 2H 2 S (C H 2 O ) + 2S + H 2 O

– H2S serves as the reductant.

– Elemental sulfur is deposited.
– The equation portrays photosynthesis as a
clear example of a redox reaction.
Photosynthesis is a redox process
• Overall then, regardless of the
photosynthetic organism, the process of
photosynthesis can be generalized as:
C O 2 + 2H 2 A (C H 2 O ) + 2A + H 2 O

– A represents oxygen or sulfur.

– If A is oxygen, the reaction demonstrates that
oxygen evolved during photosynthesis comes
from water molecules.
Photosynthesis is a redox process
• Further evidence that water is the source of
evolved oxygen was obtained from experiments
with isolated chloroplasts.

• These experiments used an artificial electron

acceptor, ferricyanide:
3+ 2+ +
4Fe + 2H 2 O 4Fe + O 2 + 4H
• Additional evidence was obtained from studies
using a water labeled with a heavy isotope of
oxygen (18O).
Photosynthesis is a redox process
• In essence, photosynthesis involves the
photochemical reduction of CO2 by

• ATP is also required for CO2 reduction.

• The goal of the light dependent reactions

is to produce the NADPH and ATP
required for CO2 reduction.
Photosynthetic electron transport
• The central components of photosynthetic
electron transport are two multimolecular
chlorophyll-protein (CP) complexes.
– Photosystem I (PSI)
– Photosystem II (PSII)

• Between the two photosystems is the

multiprotein cytochrome complex (Cyt b6/f).

• This system raises low energy electrons

obtained from water to the higher energy level
needed to synthesize the reductant NADPH.
Photosynthetic electron transport
• Figure 7.3
Photosynthetic electron transport
• Figure 7.5
Photosynthetic electron transport
• Most of the chlorophyll present in a photosystem
functions as antenna chlorophyll.

• These chlorophyll molecules, along with

accessory pigments such as carotenoids, absorb
photons of light.

• The energy collected by the antenna complex is

transferred via resonance to the reaction center
Photosynthetic electron transport
• Figure 7.4
Photosynthetic electron transport
• The reaction center chlorophyll is a unique
chlorophyll a molecule with specific
absorbance maxima.
– The PSI reaction center chlorophyll has an
absorbance maxima of 700 nm, so it is
referred to as P700.
– The PSII reaction center chlorophyll has an
absorbance maxima of 680 nm, so it is
referred to as P680.
Photosynthetic electron transport
• Also associated with each photosystem is
an additional light-harvesting complex
(LHC) which maximizes light absorption.
– PSI is associated with LHCI.
– PSII is associated with LHCII.

• The LHC’s contain ~70% of the total

chlorophyll, as well as almost all of the
chlorophyll b.
Photosynthetic electron transport
• Also associated with PSII is the oxygen-
evolving complex (OEC), which supplies
electrons to PSII and produces oxygen.

• Present in the membrane between PS II

and Cyt b6/f is plastoquinone (PQ), a pool
of redox-sensitive molecules that
participate in electron transport.
Photosynthetic electron transport
• The fourth component of the
photosynthetic electron transport chain is
the CF0-CF1 coupling factor, or ATP

• These components of the electron

transport chain have a vectorial
arrangement which provides the directed
movement of protons across the thylakoid
Photosynthetic electron transport
• Figure 7.6
Photosynthetic electron transport
• The light-dependent reactions of
photosynthesis begin with photosystem II.
– The absorption of light by PSII leads to the
excitation of P680, raising it to its excited state
– There is a near-simultaneous transfer of
electrons P680* to pheophytin (Pheo), which
is a photo-oxidation step that produces a
charge separation (P680+Pheo-).
– This charge separation stores light energy as
redox potential energy.
Photosynthetic electron transport
• The light-dependent reactions of
photosynthesis begin with photosystem II.
– Pheo- rapidly passes the electron to a
quinone acceptor called QA.
– This “closes” P680 (P680+QA-), meaning that
is temporarily unable to absorb more light.
– QA transfers electrons to PQ, converting it to
the reduced form plastiquinol (PQH2).
Photosynthetic electron transport
• Figure 7.8
Photosynthetic electron transport
• The light-dependent reactions of photosynthesis
begin with photosystem II.
– To return P680 to the “open” state, the OEC splits
water and the electrons are transferred to P680.
+ -
2H 2 O O 2 + 4H + 4e

– The splitting of water produces oxygen.

• Anoxygenic photosynthetic bacteria do not

produce oxygen because H2S is used as the
oxygen donor instead of water.
Photosynthetic electron transport
• Electrons from PQH2 are transferred to
Cyt b6/f and then to LSI.
– The electrons from PQH2 are transferred first
to the Rieske iron-sulfur (FeS) protein of
Cyt b6/f and then to Cyt f.
– Electrons then pass from Cyt f to the copper
binding protein plastocyanin (PC).
– PC transfers electrons to PSI, but only if PSI
has absorbed light.
Photosynthetic electron transport
• Electrons from PQH2 are transferred to
Cyt b6/f and then to LSI.
– A simultaneous absorption of light by PSI
forms an excited P700* reaction center.
– After P700* transfers electrons to ferredoxin,
electrons from PC return P700 to the open
– Ferredoxin mediates the synthesis of NADPH
via the enzyme ferredoxin-NADP+-
Photosynthetic electron transport
• The efficiency of the light-dependent
reactions are expressed in terms of light
absorption and oxygen production.
– The quantum requirement for oxygen
evolution is the number of photons required
to evolve one molecule of O2.
– The quantum yield of oxygen evolution, or
the photosynthetic efficiency, is the number
of O2 molecules evolved per photon
Photosynthetic electron transport
• Figure 7.7
Photosynthetic electron transport
• Overall, the light-dependent reactions
move electrons from water to NADP+.
– Water is a weak reductant (Em=0.82 V).
– The reduction of NADP+has Em=-0.42 V.
– This process, which required excitation of
both P680 and P700, requires 692 kJ of
energy to excite each mole pair of electrons.
– Formation of NADPH conserves 32% of that
energy (281 kJ mol-1).
Photosynthetic electron transport
• The remaining energy is coupled to the
transport of protons against their gradient,
from the stroma to the lumen.

• The movement of electrons from PQH2 to

Cyt b6/f results in the transport of two
protons across the thylakoid membrane to
the lumen.
Photosynthetic electron transport
• The splitting of water also contributes
protons to the lumen.

• The proton gradient formed across the

thylakoid membrane allows for the
chemiosmotic synthesis of ATP via
Photosynthetic electron transport
• Figure 7.10
Photosynthetic electron transport
• The flow of electrons from water, through
PSII, to PSI leads to synthesis of ATP via
noncyclic photophosphorylation.

• This ATP is formed by ATP synthase.

– The proton gradient in the lumen moves down
its energetic gradient, through the ATP
synthase, back to the stroma.
– This is an exergonic process that provides for
the synthesis of ATP.
Photosynthetic electron transport
• ATP can also be formed via cyclic
photophosphorylation, which only requires
– If P700 is excited by a photon but without the
simultaneous excitation of P680, the electrons from
P700 passed to ferredoxin are transferred to the
protein PGR5, and then to PQ.
– The passing of electrons to PQ allows for the
movement of protons into the lumen, the formation of
ATP via ATP synthase, and the resupply of protons to
Photosynthetic electron transport
• Figure 7.9
Photosynthetic electron transport
• The photosystems also show a lateral
heterogeneity in the thylakoids.

• PSII and PSI complexes are spatially

segregated in the membranes.
– PSI and the ATP synthases are primarily in
the non-appressed regions of the grana
– PSII is primarily in the appressed regions of
the grana thylakoids.
Photosynthetic electron transport
• The cyt b6/f complexes are more uniformly
distributed in the grana thylakoids.

• Although spatially separated, the

photosystems are connected by the
mobile carriers of electrons.
– PQ
– PC
– Ferredoxin
Photosynthetic electron transport
• Figure 7.11
Photosynthetic electron transport
• The cyanobacteria are also oxygenic, but
utilize a light-harvesting complex called
the phycobilisome (PBSs).
– The PBSs are large, extrinsic pigment-protein
– The PBSs are chromoproteins.
– Proteins associated with PBSs include
allophycocyanin, phycocyanin, and
Photosynthetic electron transport
• Figure 7.12 A & B
Photosynthetic electron transport
• Figure 7.12C
Some herbicides are inhibitors of
photosynthetic electron transport
• There are two main classes of herbicides that
inhibit photosynthetic electron flow.
– Derivatives of urea
– Triazine herbicides

• These herbicides block the transfer of electrons

to PQ.

• Biotechnology can be used to provide crops with

tolerance to these herbicides.
Some herbicides are inhibitors of
photosynthetic electron transport
• Figure 7.13
Energy Conservation in
CO2 Assimilation
Chapter 8
Learning objectives
• Understand how gas exchange through
stomata in the leaf provides for the
absorption of the CO2 required for

• Know the pathway, energetics, and

regulation of the carbon reduction cycle,
also known as the Calvin cycle or C3
Learning objectives
• Recognize how photorespiration imposes
limitations on C3 plants.

• Understand the contribution of the

oxidative pentose phosphate pathway to
The stomates control leaf gas
exchange and water loss
• The lower epidermis of leaves contains most of
the stoma which allow for gas exchange
between the atmosphere and leaf interior.

• The exchange of gases is regulated by a pair of

guard cells which regulate the opening and
closing of the stoma.

• A stomatal complex, or stomatal apparatus,

consists of the stoma, its guard cells, and the
surrounding subsidiary cells.
The stomates control leaf gas
exchange and water loss
• Figure 8.1
The stomates control leaf gas
exchange and water loss
• Guard cells are most often elliptical or kidney-
bean shaped and display a specific anatomy
that contributes to their function.
– Cross-sectional images of guard cells show a ventral
wall bordering the pit and a dorsal wall adjacent to
the epidermal cells.
– The throat of the stomata has thickened cell walls
along the ventral wall, forming ledges.

• Guard cells in grasses often have a dumbbell

The stomates control leaf gas
exchange and water loss
• Figure 8.2
CO2 enters the leaf by diffusion
• The only mechanism by which CO2 can
enter through the stomata is diffusion.

• Yet the leaves have mechanisms that

facilitate greater rates of CO2 movement
than would be predicted.
CO2 enters the leaf by diffusion
• Normally, diffusion is governed by the
concentration gradient and the cross-sectional
area over which diffuses occurs, as described by
Fick’s law.
R ate of diffusion (v) = D A
– D is the diffusion coefficient of the media
– A is the surface area
– The concentration gradient is represented as the
difference in concentration (c) over a distance (x)
CO2 enters the leaf by diffusion
• For leaves, the diffusion of gases is
dictated by the stomatal diameter.
– Gases do not move through the stomate
along a linear path.
– As gases pass through the stomate, they can
“spill-over” the edge.
– This edge effect increases stomatal
conductance as stomatal diameter decreases.
– The overall effect is to enhance gas exchange
even across small diameter stomates.
CO2 enters the leaf by diffusion
• Figure 8.3
Stomatal control
• The guard cells control the aperture of the
stoma through changes in water content.
– When guard cells take in water, the cells swell
as a result of internal hydrostatic pressure.
– The arrangement of cellulose microfibrils in
each guard cell, and their position relative to
one another, insures that the hydrostatic
pressure can only cause the guard cells to
arch along the ventral surface.
Stomatal control
• The guard cells control the aperture of the
stoma through changes in water content.
– The arching causes the stomate to open.
– When guard cell lose water, the cells become
flaccid, the arch diminishes, and the stoma
Stomatal control
• Figure 8.4
Stomatal control
• Changes in the osmotic potential of the
guard cells drive the opening and closing
of the stomates.
– H+-ATPases in the guard cell plasma
membrane extrudes protons from the cell.
– The decrease in cytosolic proton content
hyperpolarizes the membrane.
– The hyperpolarization triggers the opening of
potassium channels.
Stomatal control
• Changes in the osmotic potential of the
guard cells drive the opening and closing
of the stomates.
– Potassium rapidly diffuses through the
channels, down its electrochemical gradient.
– To maintain charge balance in the cytosol:
• Chloride channels open, allowing chloride to
diffuse into the cell with potassium
• Malate is synthesized in the cytosol.
Stomatal control
• Changes in the osmotic potential of the
guard cells drive the opening and closing
of the stomates.
– Potassium, chloride, and malate move
through channels into the vacuole.
– The increase in the concentration of
osmotically-active solutes in the vacuole
decreases the water potential of the guard
cell, causing an influx of water.
Stomatal control
• The efflux of protons, driven by the plasma
membrane ATPase, would cause the
cytosolic pH to increase.

• The deprotonation of malate prior to its

entry into the vacuole balances the
cytosolic pH.
Stomatal control
• Figure 8.5
Stomatal control
• The mechanism that causes guard cells to
lose water, become flaccid, and close the
stomate is unclear, but may involve:
– An influx of calcium to depolarize the plasma
– The opening of efflux channels for chloride
and malate.
– The subsequent opening of potassium efflux
Stomatal control
• The opening and closing of the stomates are
also controlled by external environmental
– Stomatal opening is stimulated by low intracellular
CO2 concentrations and low-fluence blue light.
– High intracellular CO2 closes stomates, even in the
presence of light.

• The opening and closing of stomates also

follows an endogenous circadian rhythm.
The photosynthetic carbon
reduction (PCR) cycle
• The fixation of carbon occurs via the PCR cycle,
also called C3 photosynthesis or the Calvin

• The PCR has three stages:

– Carboxylation
– Reduction
– Regeneration

• To balance the stoichiometry, three “turns” of the

cycle (i.e., three CO2 molecules fixed) are
required to generate a net increase of one triose
phosphate molecule.
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.6
The photosynthetic carbon
reduction (PCR) cycle
• During the carboxylation stage:
– CO2 is combined with the 5-carbon molecule
ribulose-1,5- bisphosphate (RuBP) by the
enzyme Rubisco.
– The 6-carbon intermediate spontaneously
breaks down to two molecules of 3-
phosphoglycerate (3-PGA).
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.7
The photosynthetic carbon
reduction (PCR) cycle
• During the reduction stage:
– ATP is expended to convert 3-PGA to 1,3-
bisphosphate glycerate.
– NADPH is expended to reduce 1,3-
bisphosphate to glyceraldehyde-3-
phosphate (G3P).
– While about 5/6 of the G3P formed
contributes to the regeneration phase, 1/6 of
the G3P is converted to dihydroxyacetone
phosphate (DHAP) and exported for
carbohydrate synthesis.
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.8
The photosynthetic carbon
reduction (PCR) cycle
• The regeneration phase uses 5/6 of the G3P
formed to regenerate the RuBP needed for the
carboxylation stage.
– Two G3P molecules (3 C each) combine to form
fructose-1,6-bisphosphate, which is de-
phosphorylated to fructose-6-phosphate (6 C).
– Fructose-6-phosphate (6 C) combines with the third
G3P (3 C) and then is broken down to one molecule
of xylulose-5-phosphate (5 C) and one molecule of
erythrose-4-phosphate (4 C).
The photosynthetic carbon
reduction (PCR) cycle
• The regeneration phase uses 5/6 of the
G3P formed to regenerate the RuBP
needed for the carboxylation stage.
– The erythrose-4-phosphate (4 C) combines
with the fourth G3P (3 C) to form
sedoheptulose-1,7-bisphosphate (7 C).
– The sedoheptulose-1,7-bisphosphate (7 C)
combines with the fifth G3P to form ribose-5-
phosphate (5 C) and xyulolose-5-phosphate
(5 C).
The photosynthetic carbon
reduction (PCR) cycle
• The regeneration phase uses 5/6 of the
G3P formed to regenerate the RuBP
needed for the carboxylation stage.
– The single 5 C molecule of ribose-5-
phosphate and the two molecules of xylulose-
5-phosphate are converted to three molecules
of ribulose-5-phosphate.
– Three ATP molecules are expended to
convert the three ribulose-5-phophate
molecules to three RuBP molecules.
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.9
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.10
The photosynthetic carbon
reduction (PCR) cycle
• If three turns of the cycle (3 CO2 molecules
fixed) are required to produce one molecule of
G3P, then:
– The fixation of 6 CO2 molecules is required to
produce one hexose sugar.
– The fixation of 12 CO2 molecules is required to
produce one molecule of sucrose.

• Three turns of the cycle requires 6 NADPH and

9 ATP molecules.
The photosynthetic carbon
reduction (PCR) cycle
• The PCR cycle can also accomplish autocatalytic
regeneration of RuBP.

• When RuBP supplies might be limiting, the carbon

diverted from the cycle for sugar synthesis can be put
back into RuBP synthesis.

• The time required to generate an adequate pool of RuBP

is called the photosynthetic induction time.

• When the RuBP pool is sufficient, the extra carbon goes

back into sucrose or starch synthesis.
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.11
The photosynthetic carbon
reduction (PCR) cycle
• The activity of Rubisco and other PCR
enzymes is regulated by light.
– The activation of Rubisco activity requires
Mg2+, CO2 activation, specific pH changes,
and the activity of Rubisco activase.
– At least four other enzymes of the cycle are
– Some of these additional enzymes also
require the excitation of PSI along the action
of thioredoxin and ferredoxin to be activated.
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.12
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.13
The photosynthetic carbon
reduction (PCR) cycle
• Mitochondrial respiration (R), the catabolism of
sugars for energy, releases the CO2 that had
been fixed in these sugars.

• CO2 can also be generated during a

photosynthesis-associated event called
photorespiration (PR).

• This makes the measurement of the rate of

photosynthesis via changes in CO2
concentration difficult.
The photosynthetic carbon
reduction (PCR) cycle
• The rate of apparent photosynthesis
(AP) in the light, or the net amount of CO2
fixed in the leaf, is a function of:
– The amount of CO2 fixed in the light (gross
photosynthesis, or GR)
– Mitochondrial respiration (R)
– Photorespiration (PR)

AP = GP - R - PR
The photosynthetic carbon
reduction (PCR) cycle
• Figure 8.14
The photosynthetic carbon
oxidation (PCO) cycle
• Rubsico can react with O2 (oxygenase activity) as well
as CO2 (carboxylase) activity.

• When Rubisco reacts with oxygen and RuBP, one 3-

PGA molecule and one 2 C molecule of
phosphoglycolate is formed.

• Phosphoglycolate is metabolized by the C2 glycolate

pathway, which releases CO2 and forms 3-PGA.

• This production of CO2 is why the oxygenase activity of

Rubisco in the light, and the resulting formation of
phosphoglycolate, is called photorespiration.
The photosynthetic carbon
oxidation (PCO) cycle
• Figure 8.15
The photosynthetic carbon
oxidation (PCO) cycle
• The recovery of the carbon from
phosphoglycolate via the C2 glycolate
cycle, or the photosynthetic carbon
oxidation (PCO) cycle, involves three
– Chloroplast
– Peroxisome
– Mitochondria
The photosynthetic carbon
oxidation (PCO) cycle
• The PCO cycle involves the following
– The Rubisco-mediated reaction of RuBP with
oxygen forms 3-PGA and phosphoglycolate.
– The phosphoglycolate is dephosphorylated to
glycolate in the chloroplast.
– The glycolate diffuses to the peroxisome
where it is converted to glyoxylate.
– The glyoxylate is transaminated to form the
amino acid glycine.
The photosynthetic carbon
oxidation (PCO) cycle
• The PCO cycle involves the following
– The glycine is transported to the
– Two molecules of glycine are used to form
one molecule of serine.
– The serine is returned to the peroxisome
where it is deaminated, forming
The photosynthetic carbon
oxidation (PCO) cycle
• The PCO cycle involves the following
– The hydroxyglycerate is reduced to glycerate.
– The glycerate is returned to the chloroplast.
– Glycerate is phosphorylated to
phosphoglycerate, where it returns to the
PCR cycle.
The photosynthetic carbon
oxidation (PCO) cycle
• Figure 8.16
The photosynthetic carbon
oxidation (PCO) cycle
• Photorespiration is a competing reaction
with the first step of the PCR.
– The ratio of carboxylation to oxygenation is
about 3:1.
– Factors such as increased temperature and
decreased CO2 concentrations favor
– There is a higher energetic requirement for
the PCO.
– Photorespiration results in a net loss of CO2.
The photosynthetic carbon
oxidation (PCO) cycle
• Despite the apparent disadvantage, there
may be a physiological benefit to the
presence of this pathway.
– The PCO scavenges the glycolate, returning it
into the carbon pool.
– This pathway may contribute the amino acids
glycine and serine to metabolism.
– The pathway may help to minimize photo-
oxidative damage.
The oxidative pentose phosphate
cycle (OPPC)
• This pathway is present in the chloroplast and
cytosol of plants.

• The chloroplastic OPPC is integrated with the

PCR cycle.

• The OPPC provides:

– An additional means of regenerating RuBP.
– A precursor for synthesis of nucleic acid sugars.
– A pool of NADPH for biosynthetic reactions.
The oxidative pentose phosphate
cycle (OPPC)
• The OPPC involves the following steps.
– Glucose-6-phosphate (G-6-P) is oxidized by
G-6-P dehydrogenase to form 6-
– The 6-phosphogluconate is oxidized by 6-
phosphogluconate dehydrogenase to
ribulose-5-phosphate (R-5-P).
– R-5-P can be utilized to:
• Form RuBP for use in the PCR cycle.
• Synthesize ribose and deoxyribose.
The oxidative pentose phosphate
cycle (OPPC)
• The OPPC results in a net release of CO2, which
would seem to compromise the effectiveness of
the PCR.

• The enzymes of the OPPC are active only in the

dark, which is the opposite of the PCR cycle.

• This coordination prevents futile cycling of

The oxidative pentose phosphate
cycle (OPPC)
• Figure 8.17
Allocation, Translocation, and
Partitioning of Photoassimilates
Chapter 9
Learning objectives
• Understand the biochemical pathways that lead
to the synthesis of starch and sucrose.

• Know how carbon provided by photosynthesis is

allocated to starch or sucrose synthesis.

• Understand the nature of the phloem tissue and

its role in the transport of photoassimilates.
Learning objectives
• Know the mechanism of phloem transport
and the importance of source-sink
relationships for transport.

• Recognize that some xenobiotic

compounds can enter the phloem and be
translocated internally.
Starch and sucrose synthesis
• Photosynthesis produces simple hexose sugars
that are used by plants to synthesize starch and

• Whether those sugars are devoted to starch or

sucrose synthesis is called carbon allocation.

• Starch is a storage form of carbon while sucrose

is the primary form in which carbon is
transported over long distances in the plant.
Starch synthesis
• Starch is synthesized in the stroma of
chloroplasts in the leaves.

• There are two principle forms of starch.

– Amylose is a linear glucose polymer
constructed with -(1,4) linkages.
– Amylopectin is similar to amylose except that
it has -(1,6) linkages that create a branched
chain structure.
Starch synthesis
• Figure 9.1
Starch synthesis
• The synthesis of starch begins with the
hexose phosphate pools produced by the
PCR cycle.
– Fructose-6-phosphate is converted to
glucose-1-phosphate by hexose-phosphate
isomerase and phosphoglucomutase.
– The glucose-1-phosphate reacts with ATP to
form ADP-glucose, mediated by ADP-
glucose pyrophosphorylase.
Starch synthesis
• Figure 9.2A
Sucrose synthesis
• The synthesis of the sucrose occurs in the
cytosol of photosynthetic cells by one of
two pathways.

• Unlike starch synthesis where glucose is

activated by ATP, glucose for sucrose
synthesis is activated by uridine
triphosphate (UTP) primarily, but also by
Sucrose synthesis
• Figure 9.2B
Sucrose synthesis
• The principle pathway is mediated by sucrose
phosphate synthase and sucrose phosphate
– UDP-glucose reacts with fructose-6-P to form
sucrose-6-P, releasing UDP.
– Sucrose-6-P is dephosphorylated to form sucrose.

• Sucrose synthase can synthesize sucrose

directly from UDP-glucose and fructose, yielding
free UDP.
– This synthesis reaction is energetically unfavorable
( G = +14 kJ mol-1).
– This enzyme may more often participate in the
catabolism of sucrose.
Sucrose synthesis
• The carbon used to synthesize sucrose in the
cytosol is exported as DHAP from the
chloroplast on the Pi/triose phosphate

• G-3-P and DHAP combine in the cytosol to form


• The fructose-1,6-bisphosphate enters the

cytosolic hexose phosphate pool where it is
converted to glucose-1-phosphate.
Sucrose and starch synthesis are
competing processes
• The principle factor determining the balance
between sucrose and starch synthesis is the
cytosolic enzyme fructose-1,6- bisphosphate
phosphatase (FBPase).

• This enzyme represents a key regulatory point

for the flow of carbon into sucrose.

• FBPase can be inhibited by a regulator

metabolite called fructose-2,6-bisphosphate
Sucrose and starch synthesis are
competing processes
• Figure 9.3
Sucrose and starch synthesis are
competing processes
• F-2,6-BP helps provide a balance between
CO2 assimilation and carbon allocation.
– Under low light conditions, sucrose export
– Decreased export results in an accumulation
of F-6-P, triose phosphates, and F-2,6-BP.
– This accumulation decreases triose
phosphate export from the chloroplast.
– The increases in chloroplastic triose
phosphates and the decreased Pi stimulates
starch synthesis in the chloroplast.
Sucrose and starch synthesis are
competing processes
• There is also a reduction in ATP synthesis
in the stroma.

• This ultimately inhibits photosynthetic

electron transport and therefore CO2

• This type of photosynthetic control is

said to be feedback limited.
Sucrose and starch synthesis are
competing processes
• Figure 9.4
Fructan biosynthesis
• Assimilated carbon can also be allocated to
fructan biosynthesis in the vacuole.
– Sucrose:sucrose fructosyl transferase uses to
sucrose molecules to form glucose and a
trisaccharide called 1-ketose.
– Fructan:fructan fructosyl transferase, a vacuolar
enzyme, extends the fructan polymer.

• Fructans can be synthesized when the rate of

carbon accumulation exceeds the rate of carbon
Long distance transport of
• Early experiments in which trees were
girdled provided some of the first
evidence that the phloem was the tissue
responsible for photoassimilate transport.

• Results from studies with aphids and

radiotracers (e.g., 14C) provided additional
Long distance transport of
• Figure 9.5
Long distance transport of
• Figure 9.6
Composition of the phloem sap
• Phloem sap is a complex mixture of
organic and inorganic compounds.
– Sucrose and other sugars
– Proteins
– Amino acids
– Organic acids
– Anions and cations
– Phytohormones
Composition of the phloem sap
• Some plant species transport other sugars
in addition to sucrose.
– Some plants transport sugars from the
raffinose series.
– Some plants transport sugar alcohols such as
mannitol or sorbitol.

• Plants do not transport reducing sugars

in the phloem.
Composition of the phloem sap
• Figure 9.7
Cellular constituents of the phloem
• The conducting cells of the phloem are the
sieve elements (or sieve tubes).

• The individual cells, or sieve tube members,

are attached end-to-end to form the phloem

• The protoplast of these cells is connected

through sieve areas, bordered between cells by
the sieve plate.
Cellular constituents of the phloem
• The sieve tube members are highly
modified living cells, retaining at maturity
only the ER and mitochondria.

• Associated with each sieve tube member

is a companion cell.

• The companion cells provide metabolic

support to the sieve tube members.
Cellular constituents of the phloem
• Figure 9.8
Cellular constituents of the phloem
• Additional parenchymal cells associated
with the phloem are the transfer cells.

• These cells are likely involved in the

transfer of photoassimilates and other
compounds between mesophyll cells.
Proteins in the phloem
• The phloem contains aggregates of proteins
called P-protein bodies.

• The role of P-proteins in phloem transport is

unclear but may involve plugging the sieve
plates of damaged cells.

• The glucan callose may serve a similar purpose

in sealing off damaged phloem cells.
Directionality of phloem transport
• Phloem transport moves photoassimilates
from sources to sinks.
– A source is an area, such as a storage organ
or photosynthetically active leaf that is
capable of exporting photoassimilates.
– A sink is an area that must import
photoassimilates to support metabolism.

• Sources and sinks within a plant can

change in response to developmental age.
Mechanism of phloem transport
• The currently accepted model for phloem
transport is the pressure flow hypothesis.

• According to this model, phloem sap is

driven by a positive hydrostatic pressure
from source to sink.

• Phloem transport is tightly linked with

transpirational water flow in the xylem.
Mechanism of phloem transport
• The currently accepted model for phloem
transport is the pressure flow hypothesis.
– Phloem loading occurs at the source, as
photoassimilates are transported into the
sieve tube members.
– The addition of these solutes makes the water
potential of these cells more negative.
– Water, following the water potential gradient,
diffuses into the sieve tube members from the
Mechanism of phloem transport
• The currently accepted model for phloem
transport is the pressure flow hypothesis.
– The influx of water creates a positive
hydrostatic pressure driving sap movement.
– At the sink tissue, phloem unloading occurs.
– This unloading makes the water potential of
the sieve tube members less negative.
– This change in water potential causes water
to exit back to the xylem.
Mechanism of phloem transport
• The currently accepted model for phloem
transport is the pressure flow hypothesis.
– The loading at the source and unloading at
the sink creates a differential that maintains
– Fundamentally, the transport of the phloem
sap occurs passively without the direct input
of energy.
Mechanism of phloem transport
• Figure 9.9
Mechanism of phloem transport
• The driving force for phloem transport can
be simulated using osmometers and a
circuit of tubing.

• This system demonstrates that the

mechanism is not only feasible, but more
than adequate to provide the necessary
rates of transport.
Mechanism of phloem transport
• Figure 9.10
Mechanism of phloem transport
• Since the phloem sap moves from source
to sink, and sources and sinks within a
plant change over time, then the phloem
must be bidirectional in its transport.

• This bidirectional transport may occur

through different vascular bundles, or even
through different sieve tubes within the
same bundle.
Phloem loading and unloading
• Source cells (such as photosynthetic cells
in leaves) are generally located within a
few cells of a sieve element-companion
cell complex (se-cc).

• In leaves, sucrose is believed to move

through the symplasm via
plasmodesmata by diffusion to reach the
phloem parenchyma.
Phloem loading and unloading
• There are two possible pathways from the
phloem parenchyma to the se-cc.
– A symplastic pathway may allow for transport directly
into the se-cc.
– Sucrose may also be transported into the cell wall
apoplasm and move via an apoplastic pathway to
the se-cc.

• The contribution of these two pathways has not

been established, but depends on the extent to
which the se-cc are symplastically isolated.
Phloem loading and unloading
• Figure 9.11
Phloem loading and unloading
• The transport of sucrose into the ss-cc
complex from the apoplasm would require
active transport.

• A sugar-H+ co-transport system, mediated

by genes such as SUT1 and SUC2, is
believed to be responsible for this
transport step.
Phloem loading and unloading
• Figure 9.12
Phloem loading and unloading
• Symplastic loading, where it occurs, follows a
polymer trap model.

• Sucrose moving symplastically into the se-cc is

converted to oligosaccharides.

• The synthesis of these oligosaccharides

prevents back-diffusion of sucrose into the
source cells and maintains the concentration
gradient into the se-cc.
Phloem loading and unloading
• Phloem unloading is, in principle, the same as
phloem loading except for the directionality.

• Both symplastic and apoplastic pathways are

believed to occur.

• The symplastic pathway has been observed in

young, developing leaves and root tips, and
involves sucrose diffusion followed by hydrolysis
of the sucrose.
Phloem loading and unloading
• There are two possible apoplastic
pathways for phloem unloading.
– Sucrose released into the apoplast can be
hydrolyzed into glucose and fructose by acid
invertase, and the monosaccharides are then
taken up by sink cells.
– Sucrose can be transported into the apoplasm
by an energy-dependent carrier.
Allocation and partitioning
• While some of the photoassimilates are
retained within the photosynthetic leaves,
the rest can be exported.

• The distribution of those exported

photoassimilates to various processes
involves allocation and partitioning.
Allocation and partitioning
• Allocation is the metabolic fate of

• Photoassimilates may be retained in the

photosynthesizing leaf to support metabolism.

• Some of the photoassimilates are stored in the

photosynthesizing leaves.

• The bulk of the photoassimilates are exported.

Allocation and partitioning
• The distribution of photoassimilates
between sinks is called partitioning.

• The partitioning is determined by

competition between sink tissues.

• The sink strength determines which sink

obtains a larger fraction of the
photoassimilate pool.
Allocation and partitioning
• Sink strength is a function of sink size and
sink activity.
– Sink size refers to the biomass of the sink
tissue (usually as dry weight).
– Sink activity is the rate of uptake of assimilate
per unit biomass per unit time.
Allocation and partitioning
• Sink strength is also a function of:
– Proximity of the sink to the source
– Environmental factors
– Cell turgor
– Hormones
Xenobiotics in the phloem
• Synthetic chemicals, or xenobiotics, with
the appropriate lipophilicity, can also be
transported in the phloem.

• The agrochemical industry has an interest

in understanding this process because it
relates to the internal distribution of
herbicides, pesticides, and growth
Xenobiotics in the phloem
• One example of a phloem-mobile
xenobiotic is the herbicide glyphosate.

• Glyphosate applied to leaves enters the

phloem and is transported to roots where it
interferes with aromatic amino acid
Cellular Respiration: Unlocking
the Energy Stored in
Chapter 10
Learning objectives
• Know the pathways involved in the degradation
of sucrose and starch.

• Know how glycolysis and the alternative

oxidative pentose phosphate pathways convert
hexose sugars to pyruvate.

• Know the pathway by which pyruvate is

metabolized to carbon dioxide and how the
energy liberated is conserved as ATP.
Learning objectives
• Know the unique aspects of electron
transport that are unique to plants.

• Understand the contribution of

gluconeogenesis and carbon skeletons to
plant carbon metabolism.

• Know the impact of environmental factors

on the respiration rate.
Pathways associated with the cellular
respiration of photoassimilates
• Photoassimilates are oxidized by aerobic
organisms to provide energy and carbon
for metabolism.
C 6 H 12 O 6 + 6O 2 6C O 2 + 12 H 2 O
( G º' = -2,869 kJ m ol )

• Photosynthetic carbon fixation was

referred to as carbon reduction, so this
reaction is fundamentally the reverse
chemical process.
Pathways associated with the cellular
respiration of photoassimilates
• Figure 10.1
Pathways associated with the cellular
respiration of photoassimilates
• The oxidation process that releases the energy
stored on photoassimilates involves three
sequential stages.
– Glycolysis
– The citric acid cycle (CAC)
– The respiratory electron transport chain

• Oxygen is required as the terminal electron

acceptor at the end of the respiratory electron
transport chain.
Pathways associated with the cellular
respiration of photoassimilates
• While the summary equation is written for a
hexose sugar, triose sugars, sucrose, starch,
fructans, lipids, and proteins can all be respired.

• A measurement called the respiratory quotient

can be used as an indicator of which substrate is
being used.
m oles C O 2 evolved
RQ =
m oles O 2 consum ed
Starch mobilization
• There are two pathways by which starch
can be converted into a form that can be
utilized in cellular respiration.
– The hydrolytic pathway results in the
production of glucose.
– The phosphorolytic pathway results in the
accumulation hexose phosphates.
Starch mobilization
• The breakdown of the starch molecules
amylose and amylopectin is initiated by the
enzyme -amylase.

• Most of the sugar released consists of the

disaccharide maltose, with smaller amounts of
glucose and limit dextrans produced.

• The enzyme -amylase also cleaves starch.

Starch mobilization
• Figure 10.2
Starch mobilization
• Limit dextrinase cleaves the -(16)
linkage in amylopectin, allowing the
amylase enzymes to continue degrading

• The enzyme -glucosidase splits maltose

into two molecules of glucose.
Starch mobilization
• Starch phosphorylase catalyzes the
phosphorolytic degradation of starch.

starch + nPi n(glucose-1-phosphate)

• The pathway for starch degradation occurs
when the concentrations of inorganic phosphate
is high.

• The enzyme works in conjunctions with -

amylase to degrade starch.
Starch mobilization
• The initial products of starch degradation
must be transported to the cytosol in order
for cellular respiration to begin.

• Specific transporters move the

degradation products to the cytosol.
– Glucose is moved on a hexose transporter.
– Glucose-1-phosphate is converted to a triose-
phosphate and moved on the Pi-triose/
phosphate transporter.
Fructan mobilization
• The enzymes for fructan mobilization are
expressed constitutively.

• Fructans in the vacuoles are hydrolyzed by

fructan exohydrolase.

• Hydrolysis is completed by a vacuolar invertase.

• The free hexoses are transported to the cytosol

and phosphorylated, along with the sucrose
metabolites, to add to the cytosolic hexose
phosphate pool.
Starch and fructan mobilization
• Figure 10.3
• Glycolysis, the first stage of respiratory carbon
metabolism, converts hexose sugars to

• In plants, glycolysis occurs in the cytosol and in

the plastids.

• Glycolysis can be divided into two sets of

– The hexose sugar is converted to a triose-P.
– The triose-P is converted to pyruvate.
• The initial step in glycolysis requires that the
hexose sugars be phosphorylated by ATP.

• These hexose phosphates contribute to the

cytosolic hexose phosphate pool.

• A second phosphorylation step converts hexose

phosphates to fructose-1,6-bisphosphate.

• This molecule is split into two triose phosphates.

• Figure 10.4
• The triose phosphates formed are
dihydroxyacetone phosphate (DHAP) and
glyceraldehyde-3-phosphate (G-3-P).

• The DHAP is converted to G-3-P.

• The G-3-P is converted in a series of

reactions to pyruvate.
• The energy yield of glycolysis includes:
– The formation of reducing potential as
NADH (1 for each G-3-P molecule).
– Substrate-level phosphorylation to form
ATP (2 for each G-3-P molecule).

• The net ATP production from glycolysis is

2 ATP per hexose sugar.
• Figure 10.5
The oxidative pentose phosphate
• The oxidative pentose phosphate
pathway provides an alternate route for
the metabolism of glucose.

• This pathway is closely integrated with

glycolysis, sharing some metabolites.
The oxidative pentose phosphate
• In the first step of this pathway, glucose-6-
phosphate is converted to 6-phosphogluconate,
yielding NADPH.

• The second step removes a CO2 group, forming

ribulose-5-phosphate and NADPH.

• The subsequent reactions form G-3-P and

fructose-6-phosphate, both of which can be
shunted into glycolysis.
The oxidative pentose phosphate
• Figure 10.6
The oxidative pentose phosphate
• This pathway has several functions.
– This pathway generates a pool of reducing
potential in the form of NADPH.
– This pathway also produces pentose
phosphate, which is a precursor for the
nucleic acid sugars ribose and deoxyribose.
– A pathway intermediate, erythrose-4-
phosphate, serves as a precursor for the
synthesis of lignin, flavonoids, and aromatic
amino acids.
The fate of pyruvate
• The subsequent metabolism of pyruvate
depends upon oxygen availability.
– Under aerobic conditions when adequate
oxygen is present to serve as the terminal
electron acceptor, pyruvate is transported to
the mitochondrion and metabolized by the
citric acid cycle.
– Under anaerobic conditions, pyruvate is
metabolized via fermentation.
• There are two general pathways for
– Pyruvate can be converted to lactate by lactate
dehydrogenase (LDH).
– In plants, pyruvate is converted to ethanol and CO2
via alcohol dehydrogenase (ADH).

• The formation of ethanol consumes NADH, but

provides a pool of NAD+ to help carbon
metabolism continue.
• Figure 10.7
Oxidative respiration via the citric
acid cycle
• For the second stage of respiration,
pyruvate must be transported to the matrix
space of the mitochondria.

• The pyruvate is oxidized to CO2 in the

mitochondria by the citric acid cycle
Oxidative respiration via the citric
acid cycle
• The CAC involves the following steps.
– Pyruvate dehydrogenase converts pyruvate
to an acetate group and CO2, forming NADH.
– The acetate is linked to coenzyme A (CoA).
– The acetyl-CoA molecule is linked to
oxaloacetate by citrate synthase and the
CoA is released.
– The citrate form is isomerized into isocitrate,
which is subjected to two decarboxylation
reactions that each form one NADH.
Oxidative respiration via the citric
acid cycle
• The CAC involves the following steps.
– The four carbon molecule formed is bound
initially to CoA.
– Succinyl-CoA is converted to succinate,
providing a substrate-level phosphorylation to
form a molecule of ATP.
– The regeneration of oxaloacetate from
succinate results in the formation of one
molecule of NADH and one FADH2.
– A second turn of the cycle completes the
oxidation of one hexose sugar.
Oxidative respiration via the citric
acid cycle
• Figure 10.8
The mitochondrial electron
transport chain
• Much of the energy harvested from the
catabolism of a hexose sugar is stored as
reducing potential in NADH and FADH2.
– 10 NADH with Gº’ = -222 kj mol-1
– 1 FADH2 with Gº’ = -180 kj mol-1

• In the third stage of respiration, an

electron transport chain is used to
convert this redox energy to ATP.
The mitochondrial electron
transport chain
• The mitochondrial electron transport chain
consists of four multimolecular complexes and
two soluble carriers in the inner mitochondrial
– Complex I is a NADH-ubiquinone oxidoreductase
with an associated flavin mononucleotide.
– A lipid soluble pool of ubiquinone in the membrane is
present between Complexes I and II.
– Complex II is a succinate-ubiquinone
The mitochondrial electron
transport chain
• The mitochondrial electron transport chain
consists of four multimolecular complexes and
two soluble carriers in the inner mitochondrial
– Complex III is a cytochrome c reductase.
– Cytochrome c transfers electrons from Complex III to
Complex IV.
– Complex IV is a cytochrome c oxidase.
The mitochondrial electron
transport chain
• Figure 10.9
The mitochondrial electron
transport chain
• A chemiosmotic mechanism converts the
reducing potential in NADH and FADH2 to ATP.
– Electrons are passed from NADH and FADH2 to
Complex I.
– A pair of protons are picked up at the same time by
Complex I.
– As the electrons are transferred from Complex I to
ubiquinone, the protons are moved into the
intermembrane space against their electrochemical
The mitochondrial electron
transport chain
• A chemiosmotic mechanism converts the
reducing potential in NADH and FADH2 to ATP.
– The electrons flow from the ubiquinone pool to
Complex II, and then to Complex III, and then to
cytochrome c.
– The flow of electrons through Complex III provide
energy to add protons to the proton gradient.
– The flow of electrons to cytochrome c and to Complex
IV and then to oxygen also contributes to the proton
The mitochondrial electron
transport chain
• A chemiosmotic mechanism converts the
reducing potential in NADH and FADH2 to ATP.
– The proton motive force generated by the complexes
is released through ATP synthase.
– The ATP synthases uses the energy released from
the proton motive force to synthesize ATP.
– An adenine nucleotide transporter facilitates the
exchange of ATP synthesized by the ATP synthase
for ADP.
– A phosphate-hydroxyl transporter exchanged
hydroxyl for the Pi needed for ATP synthesis.
The mitochondrial electron
transport chain
• Figure 10.10
Alternative electron transport
• The plant mitochondria have an external
network of dehydrogenases that oxidize
cytosolic NADH and NADPH.

• The electrons from these dehydrogenases also

enter the ubiquinone pool.

• These dehydrogenases do not make the same

contribution to the proton motive force so a
smaller number of ATP are produced.
Alternative electron transport
• Figure 10.11
Alternative electron transport
• Plants also have another NADH dehydrogenase
that is insensitive to the Complex I inhibitors
rotenone and amytal.

• This is called the rotenone-insensitive


• This enzyme oxidizes NADH from the matrix,

with the electrons contributing to the synthesis of
some ATP.
Alternative electron transport
• The plant mitochondria also have an alternative
oxidase that functions as a ubiquinone

• Flow through this oxidase occurs when

cytochrome c oxidase is inhibited, such as in the
presence of cyanide.

• This effect of cyanide is why this pathway is

referred to as the alternative respiratory
pathway or cyanide-resistant respiration.
Alternative electron transport
• Figure 10.12
Alternative electron transport
• The action of the alternative pathway by-passes
the complexes that help establish the proton
motive force, so heat (but little ATP) is produced.

• The role of this pathway is unclear.

– One hypothesis is that the flow of electrons through
the alternative oxidase is important for
– The energy overflow hypothesis suggests that flow
through this pathway is important when there is
excess carbohydrate supply.
– This pathway may also help prevent the
overreduction of the electron transport chain.
Seed oils are carbon sources
• Carbon is frequently stored in seeds as
lipids in the form of oil droplets.

• These lipids are used as a source of

carbon for respiration during germination.

• The carbon has to be converted to a

phloem-mobile form such as sucrose.
Seed oils are carbon sources
• The metabolism of the triglycerides to form
sucrose involves the glyoxysomes,
mitochondria, and the cytosol.
– The triglycerides are hydrolyzed by lipases to
glycerol and free fatty acids.
– The fatty acids enter the glyoxysomes and
undergo -oxidation to form acetyl-CoA.
– The acetyl-CoA combines with oxaloacetate
to initiate the glyoxylate cycle and the
formation of citrate.
Seed oils are carbon sources
• The metabolism of the triglycerides to form
sucrose involves the glyoxysomes,
mitochondria, and the cytosol.
– Two unique enzymes in the glyoxylate cycle
are isocitrate lyase and malate synthase.
– The citrate is broken down to succinate and
glyoxylate, and the succinate is transported to
the mitochondria.
– The glyoxylate is converted to malate.
Seed oils are carbon sources
• The metabolism of the triglycerides to form
sucrose involves the glyoxysomes,
mitochondria, and the cytosol.
– The malate is transported to the cytosol and
converted to phosphoenolpyruvate (PEP) by
the enzyme PEP carboxykinase.
– The PEP can be used in gluconeogenesis.
– The cycling of malate between the
glyoxysome and mitochondria provides a pool
of NADH.
Seed oils are carbon sources
• Figure 10.13
Carbon skeletons
• Cellular respiration also produces
skeletons for the synthesis of important

• These carbon skeletons come from

glycolysis and the citric acid cycle.

• The use of this carbon for synthesis

represents a trade-off with energy
Carbon skeletons
• Figure 10.14
Carbon skeletons
• The diversion of carbon to synthesis also
depletes the oxaloacetate pool.

• The oxaloacetate is replaced through the

action of the cytosolic enzymes malate
dehydrogenase and PEP carboxylase.
PEP + HCO 3 oxaloacetate
oxaloacetate + N A D H m alate + N A D
Carbon skeletons
• The malate is shuttled into the

• Plant mitochondria have high levels of

NAD+-malic enzyme, which converts
malate to pyruvate.

• This means of replacing the oxaloacetate

via malate transport is an example of an
anaplerotic pathway.
Variation in respiratory rate
• Respiration rate is a function of metabolic

• Actively growing young tissues respire

more than older, less active tissues.

• In climacteric tissues, there is also a

respiratory burst associated with
senescence and death.
Variation in respiratory rate
• Figure 10.15
Influence of environmental
conditions on respiration rate
• The influence of light on the respiration
rate is subject of debate.
– Dark respiratory rates for leaves in full sun are
higher than for shade leaves.
– Mature leaves of shade-intolerant plants also
have higher rate than shade-tolerant leaves.
– The ammonium from photorespiration may
decrease the rate of respiration by converting
the mitochondrial pyruvate dehydrogenase
complex to an inactive form.
Influence of environmental
conditions on respiration rate
• Figure 10.16
Influence of environmental
conditions on respiration rate
• The effect of temperature on any process,
including respiration, can be expressed in
terms of a temperature coefficient (Q10).
rate at (t+10)º C
Q 10 =
rate at (t)º C

• Between 5º and ~25ºC there is a doubling

of the respiration rate for every 10ºC
increase in the temperature.
Influence of environmental
conditions on respiration rate
• At temperatures above 30º C, the
respiration rate decreases because
oxygen solubility decreases and enzymes
begin to denature (>50ºC).

• The effect of temperature on respiratory

rate depends upon the climate in which
the plant is acclimated.
Influence of environmental
conditions on respiration rate
• Oxygen availability can limits respiration.
– For bulky tissues with low surface-to-volume
ratios, slow rates of oxygen diffusion may limit
– Oxygen deficit can be experienced during
Nitrogen Assimilation

Chapter 11
Learning objectives
• Have a basic understanding of the
nitrogen cycle and the three major
nitrogen pools

• Understand the processes of nitrogen

fixation and assimilation in plants
The nitrogen cycle
• Global nitrogen supplies are distributed
between three major pools.
– Atmospheric, most of which is dinitrogen
– Soil and groundwater pools
– Nitrogen associated with biomass

• The principle focus of the nitrogen cycle is

the exchange of chemical forms of
nitrogen that occurs in the soil.
The nitrogen cycle
• Nitrogen enters the soil pool primarily as nitrate
(NO3-), a form which can be taken up directly by
plants and microorganisms.

• Nitrate is assimilated in organic form (amino

acids) by living organisms.

• As these organisms excrete wastes and

eventually die, the nitrogen is returned to the soil
The nitrogen cycle
• Decomposing organic forms of nitrogen are
converted to ammonia in a process called

• Most of the ammonia is converted back to nitrate

by chemoautotrophic microorganisms
performing nitrification.

• Denitrifying bacteria convert nitrate to

dinitrogen, returning nitrogen to the atmosphere.
The nitrogen cycle
• Figure 11.1
Nitrogen fixation
• The process of nitrogen fixation is the
pathway by which prokaryotes convert
dinitrogen to an organic form.

• The prokaryotes capable of carrying out

this process are called nitrogen-fixers.

• The principal enzyme complex involved in

nitrogen fixation is dinitrogenase.
Nitrogen fixation
• Many prokaryotes capable of nitrogen
fixation are free-living microorganisms.

• Nitrogen fixation can occur under aerobic

microaerobic, or anaerobic conditions.

• Some nitrogen-fixers are photosynthetic

and some are non-photosynthetic.
Nitrogen fixation
• Legumes form a symbiotic association with
nitrogen-fixing microorganisms in a host-
microsymbiont association.

• Legumes roots form specialized structures

called nodules to provide the nitrogen-fixers
with the microenvironment necessary for
nitrogen fixation.

• The nitrogen-fixers that form the association with

legumes are collectively called rhizobia.
Nitrogen fixation
• Figure 11.2
Nitrogen fixation
• The interaction between the rhizobia and
legume roots is a type of infection that
induces nodule formation by legume roots.
– The rhizobia colonize the rhizosphere and
attach to the root epidermis.
– Nodule initiation begins in the cortex.
– The root hair curls to allow an infection thread
to form.
– The bacteria migrate to the nodulating tissue
and differentiate into specific nitrogen-fixing
Nitrogen fixation
• Figure 11.3
Nitrogen fixation
• The roots use positive chemotaxis to
attract the appropriate rhizobia.

• The chemicals associated with the

attraction of rhizobia are flavonoids.

• The rhizobia respond by synthesizing

NOD factors, which are lipo-chitooligo-
saccharides that induce root hair growth.
Nitrogen fixation
• Figure 11.4
Nitrogen fixation
• The rhizobia also release chemicals that
induce the formation of the primary
nodule meristem and induce pericycle
cell division to create a region where the
nodule will develop.

• The chemical recognition between the

host and rhizobia involves lectins and
Nitrogen fixation
• The rhizobia must penetrate the host cell
wall, typically by releasing wall-degrading

• The rhizobia cause the host cell

membrane to invaginate to form the
infection thread.

• The infection thread elongates until it

reaches the developing nodule.
Nitrogen fixation
• At the developing nodule, the thread
branches so that several host cells
become infected.

• The bacteria are “released” into the host

nodule cells and enlarge into bacteroids
and are surrounded by the peribacteroid

• The infection process is continuous.

Nitrogen fixation
• The bacteria continually infect new nodule
cells, causing the nodule to enlarge and

• The nodule also establishes connections

with the vascular tissue, which provides for
the import of photoassimilates to “feed” the
Nitrogen fixation
• Figure 11.5
The biochemistry of nitrogen fixation

• The enzyme complex used by prokaryotes

to fix dinitrogen is dinitrogenase.
– The complex consists of two proteins.
– The smaller is a dimer called the Fe protein
because it contains Fe4S4 clusters.
– The larger protein is a tetramer called the
MoFe protein and contains Fe4S4 clusters
and two molybdenum atoms.
The biochemistry of nitrogen fixation

• Nitrogen fixation via dinitrogenase requires

the reduction of dinitrogen.
+ -
8H + 8e + N 2 + 16ATP 2NH 3 + 16 ADP + 16Pi

– A primary electron donor such as ferrodoxin

reduces the Fe protein.
– The electrons pass to the MoFe protein.
– The MoFe protein uses the electrons to
reduce dinitrogen to ammonia.
The biochemistry of nitrogen fixation

• Figure 11.6
The biochemistry of nitrogen fixation

• Nitrogen fixation is an energetically

demanding reaction, requiring as many as
25 ATP per dinitrogen atom fixed.

• Nitrogen fixation also requires

carbohydrates to support bacteroid
growth, as much as 12 g carbon per gram
dinitrogen fixed.
The biochemistry of nitrogen fixation

• Figure 11.7
The biochemistry of nitrogen fixation

• The dinitrogenase reaction is rapidly inactivated

by molecular oxygen.

• The half-life of the Fe protein in the presence of

oxygen is 30-45 sec and 10 min for the MoFe

• However, oxygen is required in order for cellular

respiration to produce the ATP required for
dinitrogen fixation.
The biochemistry of nitrogen fixation

• The oxygen level must be carefully

regulated in order to balance these
– Free-living rhizobia are generally anaerobic.
– Nitrogen-fixing cyanobacteria form
heterocysts which balance the demand for
ATP with the consumption of oxygen.
– Host plants provide an oxygen-binding protein
called leghemoglobin to the nodules.
The biochemistry of nitrogen fixation

• Figure 11.8
Hydrogen production by
• The fixation of nitrogen by dinitrogenase also
results in the production of hydrogen.

• As much as 25-30% of the ATP and electrons

supplied to dinitrogenase may be consumed by
hydrogen production.

• Many nitrogen-fixing organisms have an uptake

hydrogenase that couples ATP production to H2
oxidation, recovering some energy.
Genetics of nitrogen fixation
• Synthesis of the dinitrogenase enzyme is
directed by the nif genes.

• Several genes regulate nodulation.

– The nod genes on the Sym plasmid encode
the chitooligosaccharides.
– The nodD gene activates transcription of the
nodABC genes and host-specific nodEFGH
Genetics of nitrogen fixation
• Several genes regulate nodulation.
– Various nod genes in the host cell encodes
nodulins that influence the infection thread
and the onset of nitrogen fixation.
– Leghemoglobin is an example of a late
– The nif and fix genes are also actived late in
Assimilation of ammonia
• Ammonia from nitrogen fixation goes into
equilibrium with ammonium.
+ +
NH 3 + H NH 4

• Ammonium is assimilated by the

glutamate synthase cycle into the amino
acid glutamine by the enzymes
glutamine synthase (GS) and glutamate
synthase (GOGAT).
Assimilation of ammonia
• The initial assimilation of ammonium into
glutamine requires glutamate and ATP and is
catalyzed by GS.
glutam ate + N H 4 + A T P glutam ine + A D P + Pi

• The amino group added to glutamine is

transferred to the -ketogluarate by GOGAT.
glutamine + -ketogluarate + NADH 2 glutamate + NAD
Assimilation of ammonium
• Figure 11.9
Assimilation of ammonium
• The enzyme glutamate dehydrogenase
(GDH) also provides a means of
assimilating ammonium.
+ +
NH 4 + -ketogluarate + N AD H glutamate + N A D

• However, this enzyme more often

catalyzes the reverse reaction.
Assimilation of ammonium
• Nitrogen assimilation via GS-GOGAT is an
interface between carbon and nitrogen

• The carbon and nitrogen status is sensed

by the PII proteins.

• The PII proteins are ubiquitous and highly

conserved across living organisms.
Assimilation of ammonium
• Activity of the PII proteins in regulated
through uridylyation.
– Nitrogen status is sensed through changes in
glutamine bioavailability.
– When glutamine levels are low, UTP is used
to uridylylate PII, forming PII-UMP.
– PII-UMP converts inactive GS-GOGAT to the
active form.
– PII inactivates GS-GOGAT to slow the rate of
ammonium assimilation.
Assimilation of ammonium
• Figure 11.10
Export of fixed nitrogen
• Fixed nitrogen exported from the nodules
can be in the form of:
– Asparagine
– Ureides

• The asparagine is synthesized by

aminotransferases, which transfer an
amino group from an amino acid to a keto-
Export of fixed nitrogen
• Aspartate aminotransferase transfers an
amino group from glutamate to
glutam ate + oxaloacetate -ketogluarate + aspartate

• Asparagine synthetase catalyzes the

synthesis of asparagine.
glutam ine + aspartate + AT P glutam ate + asparagine + AD P
Export of fixed nitrogen
• The asparagine synthesis requires a
sustained supply of oxaloacetate.

• Nodules have high activities of PEP

carboxylase to form oxaloacetate from
PEP and carbon dioxide.
Export of fixed nitrogen
• Principle ureides formed from nitrogen
fixation include allantoin and allantoic

• The advantage of these compounds as

transport forms of fixed nitrogen is that
they provide a favorable C:N ratio better
than that of asparagine.
Export of fixed nitrogen
• Figure 11.11
Assimilation of soil nitrogen
• Nitrate is often the most common form of
nitrogen in soils and can be assimilated into
organic form.

• Root uptake of nitrate occurs by both a

constitutive and inducible mechanism.

• Nitrate transport is sensitive to temperature,

anaerobic conditions, and inhibitors of
respiration and protein synthesis.
Assimilation of soil nitrogen
• Nitrate is first reduced to nitrite in the cytosol by
the enzyme nitrate reductase.
+ - - -
2H + NO 3 + 2e NO 2 + H 2 O

• Nitrate reductase (NR) receives the electrons for

reduction from NAD(P)H.

• NR can be found in roots and shoots, but the

degree to which plant species reduce nitrate at
the root level varies by species.
Assimilation of soil nitrogen
• NR activity is regulated by:
– Nitrate supply
– Light
– Carbohydrate supply
– Regulatory proteins, including protein
kinases, protein phosphatases, and
inhibitor proteins.
Assimilation of soil nitrogen
• Nitrite is rapidly reduced to ammonium in the
plastids by nitrite reductase.
+ - - +
8H + NO 2 + 6e NH 4 + 2H 2 O

• The electrons for nitrite reduction come from

photosynthesis, so nitrogen fixation is a
competing reaction with carbon fixation.

• The ammonium formed is assimilated by GS-

Nitrogen cycling in plants
• Mature leaves of plants contribute to nitrogen
cycling, both importing and exporting nitrogen.

• This export of nitrogen plays a significant role in

seed development.

• The nitrogen exported may come from newly

assimilated nitrogen or from existing proteins
broken down for their nitrogen content.
Nitrogen cycling in plants
• Figure 11.12
Nitrogen and agricultural and
ecosystem productivity
• Nitrogen can be a limiting elements in
terrestrial plant systems.

• For agricultural, the application of nitrogen

is used to overcome this limitation.

• Nitrogen fertilization has a pronounced

effect on yield and is necessary to
maintain annual crop productivity.
Nitrogen and agricultural and
ecosystem productivity
• Figure 11.13
Nitrogen and agricultural and
ecosystem productivity
• Nitrogen in ecosystems is extensively
cycled between pools.

• The return of organic nitrogen to inorganic

pools occurs via mineralization, which
most often involves ammonification.

• Immobilization of this inorganic nitrogen

occurs within decomposing organisms.
Carbon, Nitrogen, and Plant
Chapter 12
Learning objectives
• Understand how carbon gain contributes
to plant productivity

• Understand how carbon balance between

photosynthesis and respiration influence
carbon gain in plants

• Understand how abiotic factors influence

photosynthesis and productivity
Carbon and productivity
• Gross primary productivity is the total carbon
assimilated by photosynthesis.

• Since respiration consumes photoassimilates,

the carbon that contributes to growth is called
net primary productivity.

• Growth therefore depends upon the carbon

balance between respiration and
Carbon and respiration
• Carbon and energy costs of plants can be
considered from two perspectives.
– Growth respiration is the carbon cost of
– Maintenance respiration refers to the carbon
cost of maintaining existing tissues.

• The difference between these two is a

determining factor in growth rate.
Carbon and respiration
• Figure 12.1
Carbon and respiration
• Overall, there is a negative relationship between
respiration and growth rate.

• One interpretation of these results is that the

efficiency of respiratory carbon metabolism also
plays a key role in determining the growth rate of

• The activity of the alternative pathway in

mitochondrial electron transport may also be
important to increasing the growth rate.
Carbon and respiration
• Figure 12.2
Influence of environmental factors
on productivity
• Photosynthesis can be limited by a variety
of variables, including:
– Light.
– CO2 availability.
– Temperature.
– Soil water.
– Nutrient supply.
– Pathological conditions.
– Pollutants.
Influence of environmental factors
on productivity
• The rate of photosynthesis is determined
by the fluence rate.

• Photosynthesis only contributes to

productivity when the fluence rate is above
the light compensation point.

• Photosynthetic rate increases in C3 plants

until saturation is reached.
Influence of environmental factors
on productivity
• Figure 12.3
Influence of environmental factors
on productivity
• Photosynthetic rate is also dependent
upon the intracellular CO2
concentration, showing a saturable
relationship in C3 plants.

• The influence of CO2 concentration of

photosynthesis is related to light intensity.
Influence of environmental factors
on productivity
• Figure 12.4
Influence of environmental factors
on productivity
• Photosynthetic capacity is also
dependent upon the balance between
carboxylation capacity and the electron
transport capacity.
– At low CO2 concentrations, this factor limits
photosynthetic capacity.
– At high CO2 concentrations, photosynthesis is
limited by the capacity of the photosynthetic
electron transport chain.
Influence of environmental factors
on productivity
• Figure 12.5
Influence of environmental factors
on productivity
• The most efficient photosynthetic capacity
is achieved when plants alter stomatal
conductance to maintain intracellular CO2
concentrations in the transition range.

• This insures that there is an adequate

balance of CO2 and electron transport
Influence of environmental factors
on productivity
• Photosynthesis is sensitive to

• The temperature response curve shows

the typical cardinal points, including a
minimum and maximum temperature
and an optimum temperature.
Influence of environmental factors
on productivity
• Figure 12.6
Influence of environmental factors
on productivity
• The relationship between temperature and
a biological process like photosynthesis
can be illustrated by the Q10 value.
R T +10
Q 10 =

– RT is the rate at each temperature.

– Q10 is the magnitude of the change in rate
between two temperatures 10ºC apart.
Influence of environmental factors
on productivity
• Photochemical reactions are largely
insensitive to temperatures from 0º-50ºC.

• The response of photosynthesis to

temperature is related primarily to carbon
metabolism and electron transport.
Influence of environmental factors
on productivity
• The rate of apparent photosynthesis
(AP) in the light, or the net amount of CO2
fixed in the leaf, is a function of:
– The amount of CO2 fixed in the light (gross
photosynthesis, or GR)
– Mitochondrial respiration (R)
– Photorespiration (PR)

AP = G P - (R + PR )
Influence of environmental factors
on productivity
• Figure 12.7
Influence of environmental factors
on productivity
• The components of this relationship
respond differently to temperature.

• Thus, net photosynthesis has a different

optimum temperature than gross
Influence of environmental factors
on productivity
• Figure 12.8
Influence of environmental factors
on productivity
• Photosynthesis rate declines with water
availability, in part due to stomatal closure.

• Low water also reduces leaf expansion,

decreasing photosynthetic surface area.
Influence of environmental factors
on productivity
• Photosynthetic rate is sensitive to the
supply of nutrients, particularly nitrogen.

• Nitrogen is required for synthesis of amino

acids, enzymes, chlorophyll, and redox

• There is an intricate balance between

photosynthesis, respiration, and nitrogen
Influence of environmental factors
on productivity
• Figure 12.9
Influence of environmental factors
on productivity
• Figure 12.10
Influence of environmental factors
on productivity
• Several factors at the leaf level influence
the rate of photosynthesis.

• The capacity of a leaf changes markedly

through development and aging.

• The rate of photosynthesis is also

dependent upon the type of leaf.
Influence of environmental factors
on productivity
• Net primary productivity is also a function
of leaf organization in the canopy.
– There is often a gradient in leaf age and
development along the vertical axis of the
plant with the upper leaves contributing more
to photosynthesis.
– Lower leaves are sacrificed via sequential
senescence to decrease the burden of
maintenance respiration for those leaves.
Influence of environmental factors
on productivity
• Leaf area index (ratio of photosynthetic
leaf area to ground area) is generally
optimized in each plant species to
distribute light intercept across the canopy.

• The leaves of some plants display

heliotropism (solar tracking), which
means that the optimum leaf angle
changes during the day to insure light
maximum light intercept.
Influence of environmental factors
on productivity
• Figure 12.11
Responses of Plants to
Environmental Stress
Chapter 13
Learning objectives
• Understand the basic concepts of stress,
acclimation, and adaptation.

• Understand the impact of excess light


• Understand how water deficit influences

stomatal conductance.
Learning objectives
• Understand how high and low
temperatures influence plant survival.

• Understand how plants withstand freezing.

• Understand how plants respond to abiotic

stresses (e.g., insects and disease).
Stress responses
• As sedentary organisms, plants must
endure stress if they are to survive.

• Plant stress responses are important to

our understanding of crop productivity and
ecological stability.

• The study of plant stress also improves

our understanding of plant physiology.
Plant stress
• Living organisms attempt to maintain
homeostasis to balance the flux of energy.

• Figure 13.1
Plant stress
• A factor which disrupts homeostasis is a
– A biotic stress is caused by a living
– An abiotic stress is caused by a physical or
chemical factor.

• If plants are injured by a stress, there is a

decrease in the rate of one or more
physiological processes.
Plant stress
• Figure 13.2
Plant stress
• There are different strategies to avoid
– Ephemeral plants complete their life cycle
during optimal periods, thereby avoiding the
stress (i.e., stress avoidance).
– Other plants show stress resistance,
acclimating to the stress using one or more
specific strategies.
Plant stress
• Figure 13.3
Light stress
• Under low light conditions, electron flow
initiated by light is the limiting factor for

• Under these conditions, the slope of the

light response curve is a measure of
photosynthetic efficiency.
Light stress
• Figure 13.4A
Light stress
• Under excess light, the photosynthetic
machinery can become light saturated.

• The maximum light saturated rate is a

measure of photosynthetic capacity.

• Under even higher light levels, plants can

suffer from photoinhibition.
Light stress
• Figure 13.4B
Light stress
• Chronic photoinhibition caused by
excess light can affect photosynthetic
capacity, efficiency, and net assimilation.

• The site of photodamage is photosystem

II, and this damage can been seen in a
measure of chlorophyll fluorescence.
Light stress
• Figure 13.5A
Light stress
• Figure 13.5B
Light stress
• Photosystem II is thought to have a limited
functional life span that functions as a
photon counter.

• Damaged photosystems can be repaired

with the aid of the psbA gene through the
D1 repair cycle.
Light stress
• Figure 13.8
Water stress
• Water stress can be caused by excess or
inadequate levels of water.

• Inadequate water supply leads to water deficit

stress, or water stress.

• Drought stress refers to the lack of water due

to inadequate rainfall.

• Desiccation stress occurs when there is

excess transpirational loss from leaves.
Water stress
• Water stress can lead to a decrease in the
integrity of membranes and leakage.

• The function of membrane proteins and

cellular organelles may also be
compromised by water stress.
Water stress
• Water stress also affects photosynthesis.
– Water stress triggers closure of the stomates.
– Changes in the cellular water potential can
affect the photosynthetic machinery.
– Excess light in the presence of decreased
water also leads to damage due to increased
temperature and decreased evaporative
Water stress
• The closure of the stomata during water
stress can be due to two processes.
– Hydropassive closure involves the
dehydration of guard cells, causing them to
lose turgor and close the stomata.
– Hydroactive closure is metabolically-
dependent control of the stomata.
Water stress
• Hydroactive closure is triggered by
decreasing water potential and hormones,
including abscisic acid (ABA).
– Under nominal water conditions, ABA is
stored in mesophyll chloroplasts because the
pH favors formation of protonated ABAH.
– Under water stress, the pH increases, causing
ABA to deprotonate (ABA-).
– ABA- is transported to guard cells where it
triggers stomatal closure.
Water stress
• Figure 13.9
Water stress
• Figure 13.10
Water stress
• The closure of the stomates anticipates
the onset of water stress, even before
there is a decrease in leaf water potential.

• This is a feed-forward mechanism that

involves transport of ABA from roots to
leaves as a signal of drying soil.
Water stress
• Figure 13.11
Water stress
• Figure 13.12
Water stress
• Figure 13.13
Temperature stress
• Low, non-freezing temperatures can
produce chilling stress.

• Symptoms of chilling stress include:

– Reduced leaf expansion.
– Wilting.
– Chlorosis.
– Necrosis.
– Death.
Temperature stress
• The metabolic effects of chilling include:
– Impaired cytoplasmic streaming.
– Reduced respiration.
– Reduced and altered protein synthesis.
– Inhibition of photosynthesis.
– Decreased membrane integrity and fluidity.

• Chilling decreases the fluidity of

membranes when the temperature drops
below the transition temperature.
Temperature stress
• Chilling sensitivity in plants is related to
the proportion of saturated fatty acids in
the membrane phospholipids.

• Chilling resistant plants can acclimate to

lower temperature (i.e., hardening) by
adjusting the fatty acid composition of the
membrane phospholipids.
Temperature stress
• High temperature stress can result in:
– Protein denaturation, particularly among the
membrane proteins in the chloroplast.
– Inhibition of the D1 repair cycle.
– Decreased membrane integrity because of
increased fluidity.
Temperature stress
• High temperatures result in the production
of heat shock proteins and ubiquitin.
– Heat shock proteins function as molecular
chaperones, which assist in the folding of
other proteins.
– Ubiquitin is involved in the tagging of proteins
for proteolytic degradation.
Biotic stresses
• Plants have a hierarchy of responses to
biotic stresses, including:
– Changes in the cell wall properties.
– Synthesis of specific secondary metabolites.

• Collectively, these responses are referred

to as the hypersensitive reaction.
Biotic stresses
• The hypersensitive reaction is mounted in
response to viruses, bacteria, fungi, and
nematodes and includes:
– The activation of pathogenesis-related (PR)
– The activation of phytoalexins.
– Accumulation of lignin, callose, and suberin in
cell walls.
– Programmed cell death.
Biotic stresses
• The hypersensitive response is localized
to the site of infection.

• Resistance to the infection spreads

through the plant, a phenomenon called
systemic acquired resistance (SAR).

• The development of SAR requires

salicylic acid.
Biotic stresses
• Figure 13.14
Biotic stresses
• In response to infection, salicylic acid
increases in proximity to the infection.

• Salicylic acid induces PR genes.

• Salicylic acid is transported to distal

tissues, either in the phloem or as volatile
methyl salicylate, where it prevents
secondary infection.
Biotic stresses
• Figure 13.15
Biotic stresses
• Jasmonates and methyljasmonate
mediate insect and disease resistance.

• Jasmonates induce a resistance pathway

different from that induced by salicylates.

• Jasmonic acid may also function as a

second messenger.
Biotic stresses
• Jasmonates may also be involved in a
range of other physiological processes,
– Seed and pollen germination.
– Root development.
– Tendril coiling.

• Jasmonates may work in conjunction with

Biotic stresses
• Figure 13.16
Stress cross talk
• Both abiotic and biotic stresses may
influence the expression of a common set
of genes and physiological processes.

• This observation is an example of cross

Acclimation to Environmental
Chapter 14
Learning objectives
• Understand plant acclimation and plasticity
as a time-nested phenomenon.

• Understand the role of state transitions in

response to light quality.

• Understand how the xanthophyll cycle

protects plants against photodamage.
Learning objectives
• Understand the mechanisms plants use to
survive water limitations.

• Understand how plants adapt to low

temperature and freezing.

• Understand how excitation pressure

serves as a redox signal to regulate
nuclear genes.
Learning objectives
• Understand how photosynthesis
acclimates to high temperature.

• Understand how O2 serves as an

alternative electron acceptor during
photosynthetic acclimation.
Plant acclimation
• Plants experience stress in response to a
change in environmental conditions.

• Plant acclimation to that stress is a time-

dependent phenomenon.

• Acclimation involves the establishment of

a new homeostasis in the presence of the
Plant acclimation
• Figure 14.1
Plant acclimation
• If the stress is removed, plants may return
to their initial homeostatic level.

• The acclimation process may require

changes in multiple physiological
processes over several time scales.

• Acclimation is a time-nested response to

the stress.
Plant acclimation
• Figure 14.2
Plant acclimation to light
• Short-term responses are the first stage of

• For example, during photosynthesis, the

various processes may not be balanced
and there may be excess energy fed into
the photosystems.
Plant acclimation to light
• State transitions can be used to regulate
energy distribution across photosystems.
– Plants in state 2 are in a condition where
preferential excitation of PSII has caused a
build up of reduced plastoquinone (PQH2).
– PQH2 activates phosphorylation of LHCII.
– LHCII dissociates from PSII.
– The dissociation causes PSI to enter state 1,
oxidizing PQH2 to PQ.
Plant acclimation to light
• Figure 14.3
Plant acclimation to light
• Carotenoid pigments play a role in
– Chronic photoinhibition produces reactive
oxygen species (ROS), such as singlet
excited O2 (1O2).
– Carotenoid pigments function in the
xanthophyll cycle to provide
nonphotochemical quenching (NPQ) of
Plant acclimation to light
• Carotenoids play a role in photoprotection.
– Violaxanthin can be converted to zeaxanthin via
stepwise de-epoxidation.
– The de-epoxidation removes radicals.
– The activity of the cycle can be assessed by
measuring the de-epoxidation state of the
carotenoid pool.
Z+ A
DEPS = 2
Plant acclimation to light
• Figure 14.4A
Plant acclimation to light
• Figure 14.4B & C
Plant acclimation to light
• The processes that protect photosystems from
excess light act over different time scales.
– Dynamic photoinhibition of the PSII reaction
centers is rapidly reversible by NPQ.
– Chronic photoinhibition of the PSII reaction centers
is slowly reversible through the D1 repair cycle.

• Both photodamage and photoprotection may

decrease photosynthetic efficiency.
Plant acclimation to light
• Figure 14.5A
Plant acclimation to light
• Figure 14.5B
Plant acclimation to water stress
• In response to water stress, plant cells
exhibit a decrease in osmotic potential
called osmotic adjustment.

• This increase in solute concentration is

due to both the dehydration of the cell and
the synthesis of compatible solutes.
Plant acclimation to water stress
• Examples of compatible solutes include:
– Proline
– Sorbitol
– Betaine

• Plants capable of synthesizing compatible

solutes to counter water stress are called
osmotic adjusters.
Plant acclimation to water stress
• Figure 14.6
Plant acclimation to temperature
• The viscosity of biological membranes can
decreases as the decreases to the
transition temperature.

• The proportion of unsaturated fatty acids

in the membranes increases in response
to low temperature.

• Unsaturated fatty acids help maintain

Plant acclimation to temperature
• Low temperature also induces the
expression of genes for the late
embryogenesis active (LEA) proteins.

• Promoters for these genes contain

dehydration responsive elements
(DRE), which are activated by C-repeat
binding factors (CBFs).
Plant acclimation to temperature
• Abscisic acid may also be involved.
– ABA increases under low temperature.
– Application of ABA to plants can increase cold
– ABA induces the synthesis of new proteins.

• The specific role for ABA has not been

Plant acclimation to temperature
• Plants can suffer from temperature stress
if they are subjected to temperatures that
lead to thermal denaturation.

• Plant respiration shows a linear increase

as temperatures decrease from 40 to 0ºC.
– At low temperatures, CO2 evolution and O2
consumption are reduced.
– At moderate to high temperatures, the
efficiency of respiration rate decreases.
Plant acclimation to temperature
• Figure 14.7
Long term acclimation to light
• Photoacclimation describes the
adjustments made to the photosynthetic
machinery in response to changes in
growth irradiance.

• These adjustments can include a

decrease in total chlorophyll per leaf area.
Long term acclimation to light
• Photoacclimation changes the nature of
the photosynthetic light response curves.
– Plants grown under high light have a higher
rate of light saturated net photosynthesis.
– Plants grown under high light have a higher
rate of dark respiration due to a higher growth
– Plants grown under high light have a lower
gross photosynthetic efficiency.
Long term acclimation to light
• Figure 14.8
Long term acclimation to light
• In algae, photoacclimation involves a
change in the size and composition of the
LHCII associated with PSII.

• The content of the LCHII decreases as

growth irradiance increases, but the core
antenna complex is not affected.

• Some herbicides produce the same effects

on photosynthesis.
Long term acclimation to light
• Figure 14.9A
Long term acclimation to light
• Figure 14.9B
Long term acclimation to light
• High light creates an imbalance in plant
energy budgets.

• This manifests as an over-reduction of the

PQ pool and over-excitation of PSII.

• This creates excitation pressure and

induces retrograde gene regulation.
Long term acclimation to light
• Retrograde regulation influences the
expression of nuclear genes.

• A similar pattern of regulation can be

induced by the mitochondrial UQ pool.

• The chloroplast and mitochondria exhibit a

cross talk in response to light called
Long term acclimation to light
• Figure 14.10
Long term acclimation to light
• Photosynthetic organisms also show
adaptations to changes in light quality as
well as intensity.
– In some plants, changes in light wave length
(e.g., red or blue light) have effects similar to
changes in light fluence rate.
– Cyanobacteria alter the composition of their
phycobilisomes through complementary
chromatic adaptation (CCA).
Long term acclimation to light
• Figure 14.11
Acclimation to drought
• Acclimation to drought can include:
– A reduction in vegetative growth.
– A decrease in cell enlargement.
– Leaf area adjustment.
– Reduced stomatal frequency.
– An increase in the root:shoot ratio.
Acclimation to cold
• The acclimation to cold includes elements
similar to those for photoacclimation.

• While cold temperatures can enhance

freezing tolerance of cold tolerant plants,
the sensitivity to photoinhibition also
Acclimation to cold
• Figure 14.12A
Acclimation to cold
• Figure 14.12B
Acclimation to cold
• In cold tolerant winter crop varieties, low
temperature stimulates photosynthetic capacity.
– Cold enhances expression of genes associated with
carbon metabolism.
– Enhanced sink activity increases carbon export from
– Photorespriation is suppressed.

• Green algae do not show the same responses

as they cannot regulate photosynthesis in the
same manner as plants.
Acclimation to cold
• Cold acclimation in plants may also
involve a change in the leaves.

• Cold stress and acclimation can induce

freezing tolerance.

• Light in conjunction with low temperature

is required for maximum freezing
Acclimation to cold
• Plants synthesize antifreeze proteins
(AFPs) in response to low temperature.

• These proteins are synthesized in the

cytosol and are released to the apoplasm.

• AFPs inhibit the growth of ice crystals.

Acclimation to cold
• Woody species demonstrate tolerance to
freezing if they enter a period of
dormancy prior to the cold stress.

• Dormancy induction involves:

– Perception of shorter days in the autumn.
– A response to the first frost event.
– Metabolic changes in carbon metabolism,
such as the accumulation of protective
glycoproteins in the cytosol.
Acclimation to cold
• Figure 14.13
Acclimation to high temperature
• Plants that can acclimate to high
temperatures are called thermotolerant.

• One aspect of the acclimation to

temperature involves a shift in the
temperature optima for photosynthesis.

• How the optimal temperature shifts

depends upon the plant species.
Acclimation to high temperature
• Figure 14.14
Oxygen and stress acclimation
• While produced as a by-product of
photosynthesis, oxygen can also act as an
electron acceptor.

• PSI can photoreduce oxygen via the

Mehler reaction forming superoxide (O2-).

• Superoxide dismutase (SOD) converts

O2- to hydrogen peroxide.
Oxygen and stress acclimation
• Hydrogen peroxide can react with O2- to
form the hydroxyl radical (OH-).

• The Asada-Halliwell pathway converts

the hydrogen peroxide to water to prevent
OH- formation.
Oxygen and stress acclimation
• Figure 14.15A
Oxygen and stress acclimation
• Oxygen can also be photoreduced in the
chloroplast by the chlororespiratory

• This pathway involves a plastid terminal

oxidase that accepts electrons from PQ.

• This pathway helps prevent the over-

reduction of the PQ pool.
Oxygen and stress acclimation
• Figure 14.15B
Adaptations to the
Chapter 15
Learning objectives
• Understand how plants adapt to low and high
light environments

• Understand how C4 photosynthesis represents

an adaptation to high temperature

• Understand how CAM photosynthesis provides

an adaptation to desert environments

• Understand how plant physiology affects biomes

Adaptations to sun and shade
• Plants are classified as sun or shade
plants based upon how they respond to
changes in irradiance.

• For example, obligate shade plants are

adapted to survival in extreme shade.
Adaptations to sun and shade
• Shade leaves tend to have:
– Thinner leaves with higher chlorophyll content
than sun leaves.
– Higher stacks of thylakoids.
– Lower ratios of chlorophyll a to b.

• Sun leaves have:

– A greater capacity to use light for
– A greater sensitivity to low light.
Adaptations to sun and shade
• Figure 15.1
Adaptations to sun and shade
• Sun and shade plants both suffer if they
are growing in light conditions below the
light compensation point.

• The light compensation point is the

irradiance at which photosynthesis rate
equals respiration rate.
C4 photosynthesis
• C3 photosynthesis forms 3-
phosphoglyceric acid as the first stable

• C4 photosynthesis is an alternate
mechanism for assimilating CO2.

• In C4 photosynthesis, the first stable

product is oxaloacetate (OAA).
C4 photosynthesis
• There are specific anatomical features in
plants displaying the C4 syndrome.
– There are two distinct photosynthetic tissues.
– These tissues show Kranz anatomy.
• The vascular bundles are close together, often in
• The bundles are surrounded by bundle sheath
• The loosely packed mesophyll cells lie between
the bundle sheath cells.
C4 photosynthesis
• Figure 15.2
C4 photosynthesis
• C4 plants are often found in sub-tropical
and tropical environments.

• C4 plants are found in 18 different families

of angiosperms.

• C4 plants are also more resistant to

drought conditions.
C4 photosynthesis
• The advantage to C4 photosynthesis is
that it provides a CO2 concentrating
mechanism that reduces photorespiration.

• The key enzyme is phosphoenol

pyruvate carboxylase (PEPcase), which
carboxylates PEP with bicarbonate.

• This reaction produces OAA.

C4 photosynthesis
• The OAA is rapidly converted to aspartate
or malate and shuttled to the bundle
sheath cells.

• The malate or aspartate is decarboxylated,

with the CO2 entering the PCR cycle.

• The C3 acid (pyruvate or alanine) released

is returned to the mesophyll.
C4 photosynthesis
• The pyruvate is phosphorylated by
pyruvate phosphate dikinase to
regenerate PEP.

• The PEP can pick up another bicarbonate

to continue the cycle.

• This cycle concentrates CO2 in the bundle

sheath cells.
C4 photosynthesis
• This CO2 concentration mechanism increases
the overall rate of carbon fixation.

• However, C4 photosynthesis has a higher

metabolic cost than C3 photosynthesis.

• C4 photosynthesis has the same energy

requirements as C3 photosynthesis, plus two
additional ATP to regenerate PEP.
C4 photosynthesis
• Figure 15.3
C4 photosynthesis
• The anatomy of C4 leaves augments the
efficiency of C4 photosynthesis.
– The C4 leaf is thinner with only one type of
– The cells are more closely packed and there are
fewer air spaces.

• This structure reduces the diffusion path for CO2

because all bundle sheath cells are closely
adjacent to a mesophyll cell.
C4 photosynthesis
• C4 photosynthesis:
– Has higher rates of photosynthesis.
– Is less inhibited by O2 (less photorespiration).
– Has a low CO2 compensation point, which is
the point where CO2 uptake for
photosynthesis is the same as CO2 evolution
during respiration.
C4 photosynthesis
• C4 photosynthesis has a higher temperature
optimum than C3 photosynthesis.

• As temperatures increase, C4 quantum yield

remains steady while C3 quantum yield

• C4 plants also have a greater sensitivity to lower

C4 photosynthesis
• Figure 15.4
C4 photosynthesis
• C4 photosynthesis also provides an
advantage in terms of:
– Increased water use efficiency (WUE).
m oles C O 2 assim ilated
m oles H 2 O transpired

– Decreased transpiration ratio (TR).

m oles H 2 O transpired
TR =
m oles C O 2 assim ilated
C4 photosynthesis
• C4 plants have higher rates of light-
saturated photosynthesis than C3 plants,
giving them greater productivity.

• At lower temperatures or at lower

irradiance, C3 plants can exceed the
productivity of C4 plants.
C4 photosynthesis
• Figure 15.5
CAM photosynthesis
• Another CO2 concentrating mechanism is
crassulacean acid metabolism (CAM).

• CAM photosynthesis is found in 23 different

families of angiosperms, typically those
growing in xerophytic environments.

• CAM plants are also often succulent plants.

CAM photosynthesis
• The most notable feature of CAM
photosynthesis is that the stomatal cycle is
– Stomates are open at night for gas exchange.
– Stomates are closed during the day to limit
evaporative water loss.

• CAM plants accumulate malate during the

night, which is a “stored” form of CO2.
CAM photosynthesis
• The malate is stored in the vacuole.

• During the day, the malate is transported to

the cytosol and decarboxylated.

• The CO2 is transported to the chloroplast

for assimilation via the PCR cycle.
CAM photosynthesis
• As in C4 photosynthesis, PEP carboxylase
helps concentrate the CO2.

• For CAM plants, PEP carboxylase forms

OAA, but the OAA is converted to malate.

• NAD-malic enzyme decarboxylates the

malate to release the CO2 for fixation.
CAM photosynthesis
• Figure 15.6
CAM photosynthesis
• C4 and CAM photosynthesis share several
– Both utilize PEP carboxylase to form a C4 acid.
– Both concentrate CO2.

• There are also important differences.

– In CAM plants, both C4 carboxylation and the
PCR cycle occur in the same cell.
– The CAM cycle is a cycle in time.
CAM photosynthesis
• CAM photosynthesis provides a significant
conservation of water.

• CAM plants have a lower transpiration rate

that C3 and C4 plants.

• However, daily carbon assimilation is

much lower than C3 and C4 plants.
CAM photosynthesis
• CAM plants can reassimilate respired CO2
much more readily than C3 and C4 plants.

• CAM photosynthesis can also be

facultative, meaning that it is utilized as
the pathway for photosynthesis only when
it is needed.
CAM photosynthesis
• C4 and CAM photosynthesis require a tight
regulation of starch metabolism in order to
provide PEP and retrieve malate.

• The isozymes of PEP carboxylase show higher

activity than in C3 plants and are regulated by
light-dark transitions.

• Since PEP is also an intermediate in glycolysis,

photosynthesis and respiration need to be
CAM photosynthesis
• PEP carboxylase in C4 plants is regulated
via feedback inhibition by malate in the

• In CAM plants, malate exhibits feedback

inhibition in the dark, but not in the light.

• PEP carboxylase activity is also regulated

by a protein kinase.
Plant physiology and biomes
• Another perspective from which to
examine physiology is ecophysiology.

• Ecophysiology is the physiology of a plant

community or ecosystem.

• Biomes represent a collection of

ecosystems with distinct vegetation.
Tropical rain forests
• Tropical rain forests are found between
latitudes of 23º 30’ N and S.

• The zone experiences a combination of

high irradiance and high temperature.

• There are also small variations in light

quantity and photoperiod.
Tropical rain forests
• Rainfall is typically high.

• Hence, plant productivity is very high.

• The three main rain forests are:

– The Amazon basin.
– The African rain forest.
– The Malaysian rain forest.
Tropical rain forests
• There is tremendous plant diversity in rain
forests, which include:
– Emergents
– Epiphytes
– Lianas

• Detrivores are also present and rapidly

degrade leaf litter.
Tropical rain forests
• The evapotranspiration carried out by rain
forest plants contributes considerable amounts
of water to the hydrologic cycle.

• This water vapor and the water vapor from

oceans create considerable cloud cover that
contributes to weather patterns.

• This water movement also drives a latent heat

flux that redistributes energy from ground level
to the troposphere.
Tropical rain forests
• Figure 15.7
Desert plants
• There are both hot and cold deserts, both of
which are characterized by episodic rainfall
and limited water availability.

• In deserts, the potential is for evapotranspiration

to exceed rainfall.

• Limited water availability and high heat load are

the problems with desert environments.
Desert plants
• Desert perennial have several adaptations
to deal with these conditions.
– Some plants show seasonal leaf
polymorphism, displaying anatomically
different leaves in response to the seasons.
– Some plants also have leaf trichomes, which
are leaf hairs that help reflect light.
– Other plants have high root:shoot ratios.
– Some desert plants are succulents.
– Leaves of some plants are vertically oriented.
Desert plants
• Annual plants are ephermeral in deserts,
completing their life cycle only during brief
periods when moisture is available.
– The life cycle is very rapid.
– The plants shown high growth rates.
– The plants have high shoot:root ratios.
– Stomatal conductance is high.
– Photosynthetic rate is high.
Plant Development:
An Overview
Chapter 16
Learning objectives
• Make the distinction between plant growth,
differentiation, and development.

• Know the nature of plant meristems and

their contribution to growth and

• Understand the events associated with

seed development and germination.
Learning objectives
• Know the pattern of development from
plant embryo to adult plant.

• Understand senescence and programmed

cell death as the final stage of plant
Development: An overview
• Plant development involves a series of
highly ordered events.

• These events span the time from

fertilization to senescence and death.

• These genetically-programmed events

control the progression of a plant through
its life cycle.
Growth, development, and
• Development refers to all changes that a cell,
tissue, organ, or organism goes through during
its life cycle.

• Growth involves irreversible, quantitative

changes in cell number, size, and/or volume.

• Growth can be measured quantitatively with

either fresh weight or dry weight.
Growth, development, and
• Cell division and cell enlargement in plants are
separate events, either of which can occur in the
absence of the other.

• Differentiation refers to changes in cells,

tissues, and organs other than size.

• Differentiation involves qualitative changes in

cells, tissues, and organs.

• Like cell division and enlargement, growth and

differentiation need not occur concurrently.
Growth, development, and
• Differentiation in plants can be dictated by
cell lineage and by cell position.

• Differentiation in plants is also reversible

and cells can revert to an embryonic form.

• For example, cells isolated from plants can

be induced to de-differentiate, producing a
mass of cells called a callus.
Growth, development, and
• Figure 16.1
Growth, development, and
• The ability of cells to revert to the embryonic
state without passing through a reproductive
stage is called totipotency.

• Most plants cells are totipotent, with the

exception of highly specialized cells modified too
highly to de-differentiate.

• The genetic program that controls cell

differentiation is influenced by neighboring plant
Plant meristems
• Plant growth is restricted to discrete
regions of cell division called meristems.

• There are two apical meristems, located

at the tip of the root and tip of the stem.

• The growth provided by the apical

meristems, which is predominantly
vertical, is called primary growth.
Plant meristems
• The root apical meristem (RAM) is a
cluster of dividing cells located behind the
root cap.

• The roles of the root cap include:

– Secretion of mucigel to lubricate the root tip
as it moves through the soil and enhance
recovery of mineral nutrients
– Perception of gravity
Plant meristems
• As each cell of the RAM divides, one remains to
continue cell division and the other elongates to
push the root tip through the soil.

• At the center of the RAM is an area of slowly

dividing cells called the quiescent center.

• Cell division in the quiescent center produces

new root tissues and cells for the root cap.
Plant meristems
• Figure 16.2
Plant meristems
• The shoot apical meristem (SAM) is more
complex than the root because of the diversity of
cells and tissues that must be produced to
achieve shoot growth.

• The SAM of dicots is a dome-shaped structure,

organized into two regions.
– The tunica has cells that undergo anticlinal divisions,
providing surface growth and peripheral stem tissues.
– The inner corpus layer generates most of the shoot.
Plant meristems
• Figure 16.3
Plant meristems
• Leaves develop from nodes on the SAM
called primordia.

• The pattern of primordia on the shoot

depends upon the plant species.

• The development of the primordia gives

rise to the typical flattened shape of
Plant meristems
• If a tissue is derived from an apical meristem it is
called a primary tissue.

• In woody plants, a meristem called the vascular

cambium produces secondary tissues which
increase in diameter of the plant.

• The secondary growth provided by the

vascular cambium adds secondary xylem and
phloem to the plant stem.
Plant meristems
• Figure 16.4
Seed development
• In flowering plants, the formation of a zygote
during fertilization occurs in the maternal organs
of the flower.

• Subsequent growth and differentiation of the

zygote results in an embryo and the
encasement of the embryo in a seed.

• A mature seed maintains the embryo in a

dormant state until conditions are favorable for
Seed development
• A flower has a basic design consisting of
four whorls, or circles of tissue.
– The two outer whorls are vegetative tissues
that comprise the sepals and petals.
– The two inner whorls are the stamen and the
– The inner whorls contain the reproductive
tissues of the flower.
Seed development
• Figure 16.5
Seed development
• The pistil contains the female reproductive
– The ovary of the pistil contains one or more
– There is a megaspore mother cell within each
ovule that undergoes mitosis to form four
megaspore cells.
– One megaspore undergoes meiosis to
produce an embryo sac.
– One cell of the sac becomes the egg while
two more fuse to become the endosperm.
Seed development
• Figure 16.6
Seed development
• The male reproductive structures are
contained within the stamens.
– The anther contains microspore mother cells
that divide by meiosis, forming microspores.
– The anther is supported by the filament.
– The microspores divide mitotically to produce
a tube cell and a generative cell, which
collectively comprise a pollen grain.
Seed development
• When pollen grains are deposited on a
pistil (i.e., pollination), the pollen grain
begins to form a pollen tube.
– The pollen tube grows down into the pistil to
reach the embryo sac and the ovule.
– The generative cell divides once to form two
sperm nuclei.
– The sperm nuclei migrate down the pollen
tube to fertilize both the polar nuclei and the
egg (double fertilization).
Seed development
• Figure 16.7
Seed development
• The development of a seed is initiated after the
formation of a zygote.

• Subsequent cell divisions increase the number

of cells in the embryo and the endosperm.

• The first division of the zygote establishes the

polarity of the embryo.
– The upper cell will be the embryo.
– The lower cell is the connection to the embryo sac.
Seed development
• As the embryo of a typical dicot grows, it
grows through several clear stages.

• When the embryo reaches the “heart-

shape” stage, the apical meristems begin
to organize.
Seed development
• Figure 16.8
Seed development
• During embryonic development, the maternal
plant allocates nutrients into the endosperm or

• The endosperm and cotyledons will provide

resources necessary for the embryo during
– If the endosperm is retained at seed maturity, the
seeds are termed endospermic.
– In nonendospermic seeds, the cotyledons enlarge
and the size of the endosperm is greatly reduced.
Seed development
• In monocot seeds, the endosperm is surrounded
by the aleurone layer which provides enzymes
needed to mobilize nutrients during germination.

• For both monocots and dicots, the embryo

becomes dormant and desiccated at maturation.

• The seed is also surrounded by a hard seed

coat (integuments) derived from maternal
Seed development
• Figure 16.9
Seed development
• Plant hormones play a key role in the
development of seeds.
– Cytokinin concentrations are highest during
peak periods of cell division in early embryo
– Auxin and gibberellin concentrations increase
and cytokinin concentrations decrease during
periods of cell enlargement in the embryo.
– Abscisic acid concentrations peak at seed
maturity and contribute to the dormancy and
desiccation tolerance of the embryo.
Seed development
• Figure 16.10
Seed germination
• Because of the dehydration imposed on
mature seeds, they are quiescent.

• The breaking of quiescence and

subsequent germination of seeds depends
upon a combination of factors:
– Adequate water to rehydrate the seed
– Sufficient oxygen to support aerobic
– A physiological temperature (25-45º C)
Seed germination
• The rehydration of the seed in the
presence of water is called imbibition.
– Imbibition is driven by matric forces.
– The imbibition pressure generated helps
rupture the seed coat.
– After imbibition, there is an increase in seed
metabolism, which leads to:
• The release of hydrolytic enzymes to mobilize
nutrient reserves
• Cell division and enlargement in the embryo.
Seed germination
• The seeds of some plant species have
additional requirements for germination.
– Some seeds must be subjected to
scarification to break the seed coat.
– Oxygen may be required for the oxidative
degradation of germination inhibitors.
– Water may be required to leach inhibitors,
hormones, and other compounds from the
seed coat.
Seed germination
• Germination is considered complete when
the radicle emerges.

• Radicle emergence is driven by cell

enlargement and imbibition pressures.

• Once the radicle has emerged, water and

nutrients from the media can be used to
support further growth.
From embryo to adult
• After the radicle emerges from the seed,
branching lateral roots are produced.

• Lateral roots emerge from the pericycle, a

ring of meristematic cells inside the
endodermis of the stele.

• The lateral root must break through the

root cortex and epidermis to reach the soil.
From embryo to adult
• The shoot axis does not begin to elongate
until after the radicle has emerged.

• In some dicots, the hypocotyl hook

emerges and elongates to protect the
plumule, which consists of the first leaves
and the shoot tip.

• This called epigeal germination.

From embryo to adult
• In other dicots, the hypocotyl is short and
the cotyledons are kept below ground.

• Instead, the are above the cotyldens (the

epicotyl) elongates pulling the plumule
from the ground.

• This called hypogeal germination.

From embryo to adult
• For some plants, such as cereal grains,
the plumule is encased in a sheath-like
structures – the coleoptile and
– The coleorhiza emerges from the pericarp
first, which allows the radicle to elongate.
– The coleoptile protects the mesocotyl as it
pushes toward the soil surface.
From embryo to adult
• Figure 16.11
From embryo to adult
• After germination, the shoot axis is pushed
upward by cell division and elongation.

• This growth is controlled by several

factors, including:
– Nutrition
– Hormones
– Light
– Temperature
From embryo to adult
• The increase in shoot height is determined
by the degree of internode elongation.

• Different plant species show different

patterns of internode elongation.

• Internode elongation is reduced when the

concentration of gibberellins, a plant
hormone, is low.
From embryo to adult
• Figure 16.12
Senescence and programmed
cell death
• Senescence, the final stage of development,
involves specific changes to plant cells, tissues,
and organs.
– Increased respiration
– Decrease photosynthesis
– Catabolism of macromolecules
– Sugar synthesis via gluconeogenesis

• The changes help the plant to recover nutrients

and molecules from tissues that have reached
the end of their useful life.
Senescence and programmed
cell death
• These processes are governed by two
groups of senescence-associated genes
– One group controls catabolic processes, and
include various enzymes, ubiquitin, and
– The second group controls the initiation and
progression of senescence.

• Senescence is a normal, genetic

consequence of plant aging.
Senescence and programmed
cell death
• Senescence is one form of programmed
cell death (PCD), which refers to a
proactive, controlled initiation of cell death.

• PCD is a normal process for growth and

development, including examples such as:
– Maturation of xylem tracheary elements
– Formation of aerenchyma during anoxia
– Development of unisexual flowers
– The response of some pathogens
Plant Development:
Growth and Development of
Chapter 17
Learning objectives
• Know the chemical composition of plant
cell walls.

• Understand the events associated with cell

division in plants.

• Know the process that must occur for cell

walls and cells to elongate.
Learning objectives
• Understand the signals involved in the
control of plant development and the
crosstalk that occurs between signalling

• Understand the different signal

transduction pathways that may be
activated when plant cells perceive
developmental or environmental signals.
Growth and development of cells
• The growth and development of plants is
driven primarily at the cellular level.

• The growth and development of cells is

controlled by a complex series of internal
and external signals.
Plant cell walls
• The outer surface of plant cells consists of
a complex extracellular matrix (ECM),
most of which comprises of the cell wall.

• There are two types of cell walls.

– The primary cell wall around young, actively
growing cells.
– The secondary cell wall deposited around
mature cells.
Plant cell walls
• The primary cell wall consists primarily of
a network of cellulose microfibrils, cross-
linked with glycans.
– The microfibrils are long, bundled arrays of up
to 3,000 -14 linked cellulose molecules.
– Neighboring cellulose chains are linked by
hydrogen bonds, making the microfibril highly
– Microfibril orientation in the primary wall is
generally random.
Plant cell walls
• Figure 17.1
Plant cell walls
• Figure 17.2
Plant cell walls
• The microfibrils themselves are cross-
linked by non-cellulosic polysaccharides
called glycans.
– The glycan cross-linking creates a semi-rigid
– In dicots and many monocots, the glycans are
xyloglycans, which are glucose chains with a
xylose sugar at carbon-6.
– In other plants, the xylose may be by
arabinose, galactose, or glucoronic acid.
Plant cell walls
• Figure 17.3
Plant cell walls
• Figure 17.4
Plant cell walls
• The cellulose-glycan complex is imbedded
in a matrix of pectin and protein.
– Pectin is heterogeneous mixture of non-
cellulosic polysaccharides.
– Free acid groups on the galacturonic acid
molecules cross-link with calcium ions, which
provides stability to the matrix.
– Pectins are the principle component of the
middle lamella that cements cells walls of
neighboring cells to one another.
Plant cell walls
• The cellulose-glycan complex is imbedded
in a matrix of pectin and protein.
– The matrix of primary cell walls contain
extensin, a gylcoprotein rich in
– Contrary to its name, extensin is believed to
help lock the wall into shape, contributing to
its strength.
– Other cell wall proteins are rich in proline,
glycine, and threonine.
Plant cell walls
• Cellulose microfibrils are assembled by a
plasma-membrane bound cellulose
– The enzyme is a multimeric complex of six
– The complex synthesizes the cellulose chains
and assembles them into microfibrils.
– The cellulose is synthesized from uridine
Plant cell walls
• Figure 17.5
Cell division in plant cells
• The division of eukaryotic cells like those
in plants consists of two primary steps:
– Mitosis (a.k.a. karyokinesis) is the division
of the genetic material.
– Cytokinesis is the division of the cytoplasmic

• The events of cell division and the

intervening events between cell division
comprises the cell cycle.
Cell division in plant cells
• The cell cycle is divided into phases.
– The mitotic (M) phase
– A gap, or resting period, after mitosis (G1)
– The DNA synthesis (S) phase
– A second gap (G2) after the S phase but prior
to the M phase

• The G1, S, and G2 phases collectively are

referred to as interphase.
Cell division in plant cells
• Figure 17.6
Cell division in plant cells
• The timing of the cell cycle is controlled by
a variety of enzymes, including the cyclin-
dependent kinases (CDKs).
– Cyclin is a subunit of CDKs that activates the
entire CDK complex.
– The four classes of plant cyclins, designated
as A, B, D, and H, allow for a specificity in the
regulation of the cell cycle.
– Phosphatases and CDK inhibitors also play a
key role in controlling the cell cycle.
Cell division in plant cells
• Cytokinesis divides the cytoplasm of plant
cells by constructing a new membrane and
ECM from the inside of the cell outwards.
– New cell walls begin forming in late M phase.
– The mitotic spindle fibers disassemble and
then reassemble into the phragmoplast.
– The phragmoplast helps orient secretory
vesicles released by the Golgi apparatus.
– The vesicles fuse to form the cell plate, which
separates the parent cell into two daughter
Cell division in plant cells
• Figure 17.7
Cell division in plant cells
• While a cell plate is formed, some
connections, called plasmodesmata, are
maintained between the daughter cells.

• These plasmodesmata allow a continuity

of the symplast to be maintained.

• Symplastic transport allows for the

exchange of molecules between cells
without the need to cross membranes.
Cell division in plant cells
• Figure 17.9
Cell walls and cell growth
• In order for cells to grow, the connections
between xyloglucans and cellulose
microfibrils must be loosened, increasing
the extensibility of the wall but without
compromising integrity.

• The subsequent expansion of a cell is

driven by turgor pressure resulting from
the uptake of water.
Cell walls and cell growth
• The relationship between turgor pressure
and cell expansion is described by:

m (P -Y )
– “dV/dt” is the change in volume with time
– “Y” is the yield threshold for expansion
– “m” is the wall extensibility
– “P” is the turgor pressure in excess of Y
Cell walls and cell growth
• Figure 17.10
Cell walls and cell growth
• Cell wall expansion is stimulated by low
pH, a phenomenon termed “acid growth”.

• Figure 17.11
Cell walls and cell growth
• Two cell wall proteins, called expansins,
stimulate expansion at low pH.

• Expansins are highly active proteins that

act rapidly.

• These proteins are highly expressed in

growing, differentiating tissues, consistent
with their role in cell expansion.
Cell walls and cell growth
• Two possible mechanisms have been
proposed for the action of expansins.
– Expansins may hydrolyze the cross-linkages
between glycans and other wall components,
but there is no direct evidence for this role.
– Alternately, expansins may weaken the non-
covalent bonds which cross-link glycans to
the cellulose microfibrils.
Secondary cell walls
• When a cell ceases to enlarge and begins
to mature, a second cell wall is deposited
inside the existing primary cell wall.

• The secondary cell wall is thicker and

more rigid than the primary wall and
consists of higher proportions of cellulose
and lower amounts of glycans and pectins.
Secondary cell walls
• Secondary cell walls frequently contain
lignin, a polymer that further strengthens
the wall.

• The combination of cellulose microfibrils

and lignin create the strength and
durability seen in woody tissues.
Signalling pathways associated
with plant development
• The various plant hormones regulate a variety
of processes in plants, including growth and

• The classes of plant hormones include:

– Auxins
– Gibberellins
– Cytokinins
– Abscisic acid
– Ethylene
– Brassinosteroids
Signalling pathways associated
with plant development
• Growth and development can also be
modulated by external factors such as:
– Light and photoperiod
– Gravity
– Moisture
– Mechanical stimuli (e.g., wind, touch)
– Magnetic fields
– Biotic factors (e.g., herbivores and pathogens)
– Anthropogenic compounds (e.g., pollutants)
Signalling pathways associated
with plant development
• In order to influence growth and development, a
signal must be perceived and then transduced
(i.e., transmitted) through the cell.

• There are two mechanisms for signal perception

and transduction.
– The signal binds to a receptor protein on the plasma
membrane and initiates a cascade of events that
ultimately alter metabolism or gene expression.
– The signal travels to the nucleus and directly alters
gene expression.
The G protein system
• The G protein system is a common
receptor system in cells.
– G protein receptors are guanosine
triphosphate (GTP) proteins that bind
hormones and other signalling molecules.
– The receptor system consists of the G protein
on the cytosolic side of the membrane and the
transmembrane G protein coupled receptor
(GPCR) protein.
The G protein system
• The G protein system is a common
receptor system in cells.
– The G protein systems acts as an on/off
switch controlling cellular processes.
– In the absence of a signal, the three subunits
of the G protein ( , , and ) assemble into a
single inactive complex.
– The inactive complex is associated with a
molecule of GDP.
The G protein system
• The G protein system is a common
receptor system in cells.
– When a ligand, or signal, binds to the GPCR,
the G protein binds to the GPCR and the GDP
is replaced with a GTP molecule.
– The active G protein dissociates from the
GPCR and the G subunit dissociates from
the G protein.
– The G and G are each active effectors.
– The reassembly of the G protein complex
returns the system to the inactive state.
The G protein system
• Figure 17.12
Signal transduction
• After perception of a signal, a series of
signal transduction events occur that
trigger the cell’s response.

• If the signal does not cross the membrane,

the signal is relayed within the cell by
secondary messengers such as:
– Protein kinase enzymes
– Calcium ions
– Phospholipid derivatives
Protein kinase secondary
• Protein kinases are enzymes that activate
other proteins via phosphorylation.

• Weak signals can be amplified if a series

of kinases (a protein kinase cascade) act
to progressively activate other proteins.

• The action of protein kinases is balanced

by phosphatase enzymes.
Phospholipase secondary
• Phospholipases create second
messengers by hydrolyzing membrane

• There are four different phospholipases:

– A1 (PLA1)
– A2 (PLA2)
– C (PLC)
– D (PLD)
Phospholipase secondary
• Figure 17.13
Phospholipase secondary
• An example of a lipid-based signalling is the
inositol triphosphate system.
– When the receptor binds the signal, the signal-
receptor complex activates PLC.
– PLC causes the release of inositol triphosphate (IP3)
and diacylglycerol (DAG) from phosphatidylinositol
bisphosphate (PIP2).
– IP3 activates the calcium channels and the release of
internal calcium.
– DAG is converted to phosphatidic acid (PA), and the
PA regulates a range of transporters and enzymes.
Phospholipase secondary
• Figure 17.14
Calcium ions as secondary
• Divalent calcium ions (Ca2+) regulate
numerous processes in plant cells.

• Ca2+ is stored in the ER, vacuole, and

mitochondria but when released into the
cytosol acts as a secondary messenger.

• Ca2+ ATPases and channels act to

regulate Ca2+ concentration in the cytosol.
Calcium ions as secondary
• Figure 17.15
Calcium ions as secondary
• The Ca2+ receptor in cells in a protein
called calmodulin (CAM).

• The Ca2+-CAM complex is capable of

activating target proteins, including:
– NAD+ kinases
– Protein kinases
– Ca2+-ATPases
Transcription-based signaling
• Transcription-based signaling involves the
binding of the signal to a nuclear receptor.

• This signalling may involve interaction with

specific transcription factors that may
induce or repress gene expression.
Crosstalk among signaling
• Signaling pathways are not isolated from each
other, but are an integrated network of
interconnected pathways.

• When signaling pathways interact or use

common second messengers, there is said to be
crosstalk between pathways.

• Crosstalk allows for a greater coordination of

developmental signals.
Plant Hormones I: Auxins

Chapter 18
Learning objectives
• Understand the concept of hormones,
particularly with respect to plant hormones

• Recognize the range of chemical

compounds considered to be “auxins”

• Know the tryptophan dependent and

independent pathways for auxin synthesis
Learning objectives
• Know the roles for auxins, particularly with
respect to plant growth and development

• Understand how auxins activate auxin

responsive genes

• Know how auxins are transported in plants

and the relationship of auxin transport to
auxin function and to plant development
Hormones: General background
• Multicellular organisms require
mechanisms to coordinate the activity of
the different cell types in the organism.

• The principle means of providing

coordination, communication and control
are chemical compounds called
Hormones: General background
• Hormones were initially discovered in
animals as glandular secretions into the
bloodstream that influenced physiology.

• The search for comparable compounds in

plants began as early as the mid 1700’s,
but was pioneered others, including
Charles Darwin.
Hormones: General background
• Hormones, in the animal context, have the
following chemical characteristics:
– Naturally occurring organic molecules
– Synthesized in discrete organs or tissues
– Transported from the site of synthesis to the
site of action
– Bioactive at low concentrations but control
physiological processes in a concentration-
dependent manner
Hormones: General background
• The “hormones” in plants differ in the
following ways:
– Hormone synthesis can be more diffuse,
occurring in many cell types simultaneously
– Plant hormones may act in the same cells or
tissues where they are produced
– The relationship between hormone
concentration and the degree and type of
bioactivity is not always linear
Auxins: Background
• Auxins were the first of the plant hormones to
be discovered.

• Auxin has been termed the “master” hormone

because of the importance of auxins and their
numerous functions.

• Auxins synthesis occurs throughout the plant,

but primarily in actively growing regions such as
the apical meristem, rapidly growing leaves, etc.
Auxin compounds in plants
• Auxins are not a single compound but a group of
structurally similar compounds that can elicit the
same biological effect.

• The most common, widely-distributed auxin is

indole-3-acetic acid (IAA).

• IAA concentrations in plants are generally from 1

to 100 g kg FW-1 in leaves, but even higher in
Auxin compounds in plants
• Figure 18.1
Auxin compounds in plants
• Other natural auxins include:
– Indole-3-ethanol
– Indole-3-acetaldehyde
– Indole-3-acetonitrile
– Indole-3-butyric acid (IBA)
– 4-chloroIAA
– Phenyl acetic acid (PAA)
Auxin compounds in plants
• As auxin activity is based upon structure, several
synthetic auxins have been made, including:
– Naphthalene acetic acid (NAA)

• The auxinic activity of synthetic compounds can

also be manipulated to create herbicides:
– 2,4-D
– 2,4,5-T
– Dicamba
Auxin compounds in plants
• Figure 18.2
Auxin synthesis
• Auxin (IAA) synthesis occurs by two primary
pathways in plants.
– A tryptophan-dependent pathway
– A tryptophan-independent pathway

• The tryptophan-dependent pathway is generally

a three step pathway in plants.

• There are variations in some plant species that

allow auxin synthesis from tryptophan via
different intermediates.
Tryptophan-dependent synthesis
• Figure 18.3
Tryptophan-independent synthesis
• The pathway for tryptophan-independent
synthesis has not been fully described, but
some details have been determined:
– Indole-3-acetonitrile is the precursor of IAA.
– The source of the indole-3-acteonitrile is not
known, but is derived from the glucosinolate
glucobrassicin in some plants.
Control and storage of auxins
• The active concentration of auxins in plant
cells is controlled by several processes:
– de novo synthesis
– Inactivation by conjugation with
• Sugars
• Amino acids
– Inactivation by oxidation via IAA oxidase
– Transport away from target cells
Control and storage of auxins
• Figure 18.4
Biological functions of auxins
• The principal function of auxins is the promotion
of cell elongation.

• This cell elongation contributes not only to

typical vertical growth, but to the directional
growth associated with phototropism and
gravitropism (see Ch. 23).

• The cell elongation response to auxin increase

with concentration but is saturable.
Biological functions of auxins
• Figure 18.5 (individual panels in four
Biological functions of auxins
• Auxins promote the cellular differentiation of
vascular tissue, particularly in shoots.

• The regeneration of vascular tissue after

wounding is also mediated by auxin.

• The differentiation of vascular tissue is

concentration dependent:
– Phloem sieve tubes differentiate under low auxin
– Xylem differentiation occurs with higher auxin
Biological functions of auxins
• Figure 18.6
Biological functions of auxins
• Auxins establish apical dominance over the
axillary buds on the stem.

• The auxins produced by the apical meristem are

transported down the stem, where they slow or
suppress mitosis and cell expansion in the buds.

• Removing the apex of the plant, such as when a

plant is pruned, releases the axillary buds from
inhibition, allowing their growth until one of the
buds establishes itself as the new apical
Biological functions of auxins
• Figure 18.7
Biological functions of auxins
• Auxins promote cell expansion.

• The effect of auxins is related to the pH

decrease observed during cell
Biological functions of auxins
• The role of auxins in cell wall extensibility
is currently described by the acid-growth
– A docking protein anchors a membrane-
bound auxin binding protein (or ABP1)
receptor to the plasma membrane.
– When auxin binds to ABP1, a signal
transduction cascade is activated which
activates enzymes, including phospholipase
A2 (PLA2).
Biological functions of auxins
• The role of auxins in cell wall extensibility
is currently described by the acid-growth
– The products of PLA2, lysophospholipids and
fatty acids, trigger a protein kinase cascade.
– The protein kinase cascade activates the
proton ATPase, which releases protons into
the cell wall space.
Biological functions of auxins
• The role of auxins in cell wall extensibility
is currently described by the acid-growth
– The decreased pH is optimal for the function
of cell wall-loosening enzymes such as
– When expansins loosen the walls, the turgor
pressure within the cell causes the cell to
Biological functions of auxins
• Figure 18.8
Sustaining growth with auxins
• The acid-induced growth • Figure 18.9
of plants is transient,
ceasing with 30 to 60

• The maintenance of
growth is also mediate by
auxins, but through
different mechanisms.

• A component of these
mechanisms is the
induction of gene
expression by auxins.
Auxin-induced gene expression
• Auxins induce the transcription of a set of genes
called the primary auxin responsive genes,
which include:
– Small upregulated auxin RNAs (SAUR)

• SAUR genes are produced rapidly (<3 min.) in

tissues in response to auxin, sometimes
asymmetrically in association with gravitropic
Auxin-induced gene expression
• AUX/IAA genes are induced over longer time
frames by auxin (up to 30 min.)

• The members of this gene family act as

transcriptional regulators, influencing
transcription through interaction with auxin
response factors (ARFs).

• A repressor protein called Transport Inhibitor

Response 1 (TIR1) is also involved and acts to
derepress transcription of auxin responsive
Auxin-induced gene expression
• The activation of a auxin responsive gene
occurs via the following steps:
– TIR1 has a binding site that accepts both
auxin and the AUX/IAA protein.
– When auxin and AUX/IAA bind, the TIR1
complex binds to the SCF complex.
– The AUX/IAA protein is ubiquinated, tagging it
for degradation by the ubiquitin-26S
proteaosome pathway.
Auxin-induced gene expression
• The activation of a auxin responsive gene
occurs via the following steps:
– The degradation of the AUX/IAA protein
derepresses the gene.
– The gene is transcribed, with the resulting
mRNA translated into an auxin-responsive
– The ability of a molecule to bind with TIR1
and derepress gene expression is one of the
defining factors that makes a molecule an
Auxin-induced gene expression
• Figure 18.10
Polar transport of auxins
• The transport of auxin from sites of
synthesis contributes to the control of plant
growth and development.

• The transport of auxin in the shoot is

basipetal and occurs by two mechanisms:
– Some auxin moves in the phloem.
– Most auxin is transport be a complex cell-to-
cell polar transport mechanism.
Polar transport of auxins
• Figure 18.11
Polar transport of auxins
• Transport of auxins in roots occurs in both
– An acropetal stream of auxin travels through the
xylem parenchyma in the stele to the root tip.
– A basipetal stream reverses the direction of auxin
flow upwards through the cortical region.

• The gradients of auxin created by polar transport

contribute to numerous developmental
Polar transport of auxins
• The mechanism of polar auxin transport
involves a carrier-mediated, secondary
active transport mechanism.

• Evidence for this transport mechanism

comes in part from inhibitor studies,
including those with phytotropins such as
TIBA, morphactin, and NPA.
Polar transport of auxins
• Figure 18.12
Polar transport of auxins
• The current chemiosmotic model for polar
auxin transport has the following features:
– A proton motive force serving as the driving
force for secondary active transport of IAA.
– An IAA influx carrier at the top of the auxin-
transporting cell.
– An efflux carrier at the base of the auxin-
transporting cell.
Polar transport of auxins
• The steps involved in the transport of IAA
into and out of the cell are as follows:
– In the cell wall space at the top of the
transporting cell, the slightly acidic pH causes
~80% of the IAA to deprotonate to form IAA-.
– The IAA- enters the cell via the influx carrier
(encoded by the AUX1 gene), with a smaller
amount of the protonated IAAH entering by
simple diffusion.
Polar transport of auxins
• The steps involved in the transport of IAA
into and out of the cell are as follows:
– As the cell cytoplasm is near pH 7.0, all of the
IAA will deprotonate to form IAA-.
– The efflux carriers that mediates the transport
of IAA- from the cell (encoded by genes of the
PIN family) are located only at the cell’s base.
– The specific positioning of the efflux carrier
insures that IAA moves in a polar direction.
Polar transport of auxins
• Figure 18.13
PIN genes in plant development
• The PIN genes contribute not only to polar auxin
transport, but contribute to other aspects of plant
development as well.

• During embryogenesis, the localization of PIN

proteins in the cell membrane help establish the
apical-basal axis.

• Patterns of PIN protein distribution also

contribute to lateral root initiation and tropic
growth responses (Ch. 23).
Plant Hormones II:
Chapter 19
Learning objectives
• Recognize the range of chemical
compounds considered to be “gibberellins”

• Recognize the range of compounds,

including gibberellins, that are part of the
terpene family of secondary compounds

• Know the general pathway for the

synthesis of terpenes
Learning objectives
• Understand how gibberellins are synthesized
from terpene precursors and where within the
cell synthesis occurs

• Know the roles for gibberellins, particularly with

respect to plant growth and development

• Understand how gibberellins induced gene

Gibberellins: Background
• Gibberellins are part of a diverse group of
secondary compounds called terpenes.

• Gibberellins are plant hormones with

notable effects on:
– Stem elongation
– Seed germination
– Reproductive processes, such as flower and
fruit development
Gibberellins in plants
• Gibberellins are a large groups of
compounds with more than 135 members.

• Only a few of these compounds have

biologically activity.

• Most compounds in this groups are

intermediates in biosynthesis or
inactivated gibberellins.
Gibberellins in plants
• Gibberellins are diterpenes (19 or 20-
carbon compounds) with the basic ent-
gibberellane structure.

• The identification system for gibberellins is

based upon the order of their discovery:
– GA1 = the first gibberellic acid discovered in
– GA3 = a natural fungal gibberellic acid
– GA4 = another bioactive plant gibberellin
Gibberellins in plants
• Figure 19.1
Gibberellins in plants
• Subtle differences in gibberellin structure
influence their degree of bioactivity:
– A carboxyl group present at carbon-7 is
common to all bioactive gibberellins
– C19 gibberellins have more bioactivity than C20
– Gibberellins with more potent bioactivity have:
• 3- -hydroxylation or 3- -1,3-dihydroxylation
• 1,2-unsaturation
• Both hydroxylation and unsaturation (highest
Gibberellin synthesis: Background
• There are three principle sites of
gibberellin synthesis in plants:
– Developing seeds and fruits
– Young leaves of developing apical buds and
elongating shoots
– Root apex

• Cell-free preparations can also show

gibberellin synthesis.
Gibberellin synthesis: Background
• While gibberellin synthesis by reproductive
tissues has been clearly demonstrated,
evidence for synthesis in vegetative
tissues is more limited.

• It is clear that terpene precursors of

gibberellins are derived from chloroplasts,
and perhaps other plastids as well.
Terpene synthesis
• The terpenes from • Figure 19.2
which gibberellins are
derived are polymers
of isoprene.

• Terpenes are also

referred to as
Terpene synthesis
• Isoprene is phosphorylated to form two
basic subunits for terpene synthesis:
– Iso-pentyl pyrophosphate (IPP)
– Dimethylallyl pyrophosphate (DMAP)

• IPP and DMAP are synthesized by two

– A cytoplasmic pathway
– A chloroplast pathway
Terpene synthesis
• The cytoplasmic pathway for IPP/DMAP
synthesis is the mevalonic acid pathway.
– Synthesis begins with three molecules of
acetyl-CoA condensing to form
– The subsequent, irreversible step requires
NADPH to form mevalonic acid.
– Mevalonic acid is phosphorylated by ATP to
form mevalonic acid pyrophosphate.
Terpene synthesis
• The cytoplasmic pathway for IPP/DMAP
synthesis is the mevalonic acid pathway.
– Decarboxylation and dephosphorylation of
mevalonic acid pyrophosphate yields IPP.
– IPP is reversibly isomerized to form DMAP.
Terpene synthesis
• Figure 19.3A
Terpene synthesis
• The chloroplastic pathway for IPP/DMAP
synthesis involves several steps.
– Pyruvate and glyceraldehyde-3-phosphate
condense with the loss of CO2 to form
– Methylerythritol-4-phosphate is
phosphorylated with ATP to form IPP.
– IPP is reversibly isomerized to form DMAP.
Terpene synthesis
• Figure 19.3B
Terpene synthesis
• IPP serves as the precursor for a variety of
different compounds.
– Various terpenes
– Gibberellins
– Three other plants hormones, the cytokinins,
brassinosteroids, and abscisic acid
– Plastiquinones
– Chlorophyll

• Synthesis of specific compounds is restricted to

either the cytoplasm or the chloroplast.
Terpene synthesis
• Terpenes synthesized in the cytoplasm are:
– Cytokinins
– Sesquiterpenes (C15)
– Brassinosteroids

• An intermediate in the cytoplasmic pathway,

farensyl pyrophosphate, is a branch point for
the synthesis of the sesquiterpences and the
phytosterol percursors of brassinosteroids.
Terpene synthesis
• Figure 19.4, cytosolic half
Terpene synthesis
• Terpenes synthesized in the chloroplast are:
– Monoterpenes (C10)
– Gibberellins
– Abscisic acid
– Plastoquinones
– Chlorophyll

• An intermediate in the chloroplastic pathway,

geranylgeranyl pyrophosphate (GGPP), is a branch
point for the synthesis of the C20 and C40 terpenes.
Terpene synthesis
• Figure 19.4, plastid half
Gibberellin synthesis
• Gibberellins are synthesized from GGPP:
– The first two cyclization reactions result in the
formation of ent-kaurene.
– C19 undergoes three oxidations, converting
the methyl group to a carboxyl group.
– NADPH-dependent cytochrome P450
monooxygenases are responsible for the
synthesis of GA12-7-aldehyde.
Gibberellin synthesis
• Figure 19.5
Gibberellin synthesis
• All other gibberellins are synthesized from
– The oxidation of GA12-7-aldehyde to GA12 is a
common step in all plants.
– The conversion of GA12 to other bioactive
gibberellins varies by species and tissue.
• The bioactive gibberellins GA20 and GA1 are
synthesized in seeds and shoots.
• GA9 is synthesized only in shoots.
Control of gibberellin bioactivity
• The bioactivity of gibberellins is controlled
through deactivation.
– The primary mechanism if hydroxylation of C2.
– Bioactive GA1 is converted to the inactive
GA8, and possibly to GA4, GA5, GA6, GA37, or

• In seeds, GA8 can be conjugated to form

glucosyl esters.
Gibberellin synthesis and control of
gibberellin bioactivity
• Figure 19.6
Growth retardants
• The synthesis of gibberellins can be blocked by
synthetic compounds called antigibberellins.

• Antigibberellins have important commercial

uses, such as in the production of ornamental

• Gibberellins themselves also have a number of

important commercial uses.
– Fruit production
– Barley malting
– Sugarcane yield
Gibberellin transport
• Little is known about the transport of gibberellins
in plants.

• Gibberellins have been detected in phloem,

moving with source-sink patterns.

• Gibberellins may be transport in the xylem,

either from sites in synthesis in the roots or as a
means of redistributing gibberellins transport via
the phloem.
Biological effects of gibberellins
• The discovery of gibberellins and their role
in stem elongation came from the study of
rice plants who displayed hyperelongation
of the stem due to a fungal gibberellin.

• Subsequent studies demonstrated that the

application of gibberellins can rescue
some plants displaying dwarfism, but
generally has no effect on normal plants.
Biological effects of gibberellins
• Figure 19.7
Biological effects of gibberellins
• Some examples of dwarfism, which can be
rescued by exogenous gibberellins, are
due to mutations in genes associated with
gibberellin biosynthesis.

• Through study of these mutants it was

determined that the role of gibberellins in
enhancing stem growth was through
internode elongation.
Biological effects of gibberellins
• Additional evidence for the role of
gibberellins in internode elongation came
from the study of rosette plants.

• The application of gibberellins to rosette

plants causes hyperelongation of stems,
such as that associated with bolting and
the shift to reproductive growth.
Biological effects of gibberellins
• Figure 19.8
Biological effects of gibberellins
• In vivo, the environmental signals that
trigger flowering trigger the conversion of
inactive gibberellins (e.g., GA19) to active
gibberellins (e.g., GA20).

• The formation of bioactive gibberellins

promotes elongation of the stems.
Biological effects of gibberellins
• Figure 19.9
Biological effects of gibberellins
• Gibberellins also promote the mobilization of
nutrients stored in the endosperm.

• Gibberellins are essential for germination

because the seeds of some gibberellin mutants
cannot germination unless exogenous
gibberellins are applied.

• The role of gibberellins complements the role of

auxins and brassinsteroids in seed germination.
Biological effects of gibberellins
• The role of gibberellins in germination
involves the activation enzymes.
– Following imbibition, the seed embryo begins
to synthesize gibberellins.
– The gibberellins diffuse to the aleurone layer
of the seed where they induce the synthesis
of -amylases and proteases.
– These enzymes break down the nutrient
reserves in the seed to provide the embryo
with the resources to maintain growth.
Biological effects of gibberellins
• Figure 19.10
Biological effects of gibberellins
• Figure 19.11
Gibberellin-induced gene expression

• The induction of -amylase production by

gibberellins occurs at the gene level.

• This activation of genes leads to a

significant increase in -amylase mRNA
and protein abundance.
Gibberellin-induced gene expression

• Figure 19.12
Gibberellin-induced gene expression

• Some genes involved in the response to

gibberellins have been identified.

• The slender rice1 (slr1) mutant has a mutation

that confers a constitutive gibberellin phenotype
and insensitivity to gibberellins.
– The mutant behaves as if saturated with gibberellins
and elongates continually.
– However, the gibberellin content is lower than wild-
type plants.
Gibberellin-induced gene expression

• The gibberellic acid insensitive mutant (gai)

mutant in Arabidopsis shows the same

• The SLR1 and GAI genes encode transcription

regulators called DELLA proteins.

• The proteins are repressors of gibberellin

signalling, and hence when defective due to
mutation, lead to insensitive gibberellin mutants.
Gibberellin-induced gene expression

• The GID gene family is also associated

with the response to gibberellins.
– The three GID genes encode nuclear
– These three genes show subtle differences in
their role in growth and seed germination.
– The phenotype of the mutant depends upon
specific combinations of genes with
Gibberellin-induced gene expression

• The control of gene expression by

gibberellins includes the SLR1 DELLA
protein and the GID1 receptor.
– A complex forms between gibberellins, SLR1,
and GID1.
– The formation of this complex promotes the
degradation of the SLR1 protein by the 26S
proteasome pathway.
– Degradation of SLR1 allows gibberellin to
derepress gibberellin responsive genes.
Gibberellin-induced gene expression

• This model also explains the phenotype of

a gibberellin insensitive mutant.
– The protein encoded by the mutated GAI
gene cannot bind the gibberellin-GID1
– In the absence of binding, the gibberellin-
responsive gene remains repressed.
– With the gene repressed, gibberellin cannot
enhance growth.
Gibberellin-induced gene expression

• Figure 19.13
Plant Hormones III:
Chapter 20
Learning objectives
• Understand the synthesis of cytokinins
from adenine and the location within the
plant where synthesis occurs

• Know mechanisms for controlling cytokinin


• Know how cytokinins are transported

within plants
Learning objectives
• Know the roles for cytokinins, particularly
with respect to cell division and

• Recognize the receptors for cytokinins and

the signalling pathway activated by
Cytokinins: Background
• Plant cytokinins are derivatives of adenosine
monophosphate (AMP).
– If the side chain is related to isoprene, then the it is an
isoprenoid cytokinin.
– If the side chain contains an aromatic ring, then it is
an aromatic cytokinin.

• Natural isoprenoid cytokinins include:

– N6-(D2-isopentenyl)-adenine (iP)
– Trans-zeatin (tZ)
– Dihydrozeatin (DZ)
Cytokinins: Background
• A natural aromatic cytokinin is
benzyladenine (BA).

• The first cytokinin discovered was the

synthetic derivative kinetin.

• Kinetin has not been detected in plants but

has been reported in human urine.
Cytokinins: Background
• Figure 20.1
Cytokinin synthesis
• The synthesis of cytokinins begins with
adenosine-5’-monophosphate (AMP).
– Adenosine phosphate-isopentenyl transferase
(IPT) catalyzes the transfer a DMAP group to
the 6-position of AMP, forming iPRMP.
– As the IPT-catalyzed step is rate-limiting,
biotechnology has been used to alter this
reaction to influence cytokinin synthesis.
Cytokinin synthesis
• The synthesis of cytokinins begins with
adenosine-5’-monophosphate (AMP).
– The two subsequent steps remove phosphate
and ribose to form an active cytokinin (iP).
– In a parallel reaction, the isopentenyl side
chain can be hydroxylated along with the
removal of phosphate and ribose to form
– Cytokinins can be converted from the free
base form to ribosides and ribotides, which
may alter their specificity.
Cytokinin synthesis
• Figure 20.2
Control of cytokinin activity
• One process for controlling cytokinin
activity is through conjugation to glucose
or amino acids.
– The O-glycosides of cytokinins are inactive
and serve as storage forms.
– The conjugate can be hydrolyzed by a
glucosidase, restoring cytokinin activity.
– Conjugation can also occur to a nitrogen atom
in the purine ring, forming an N-glycoside.
Control of cytokinin activity
• One process for controlling cytokinin
activity is through conjugation to glucose
or amino acids.
– Conjugation can also occur to a nitrogen atom
in the purine ring, forming an N-glycoside.
– The N-glycosides cannot be hydrolyzed and
serve as a means of permanently inactivating
– Conjugation to alanine also permanently
inactivates cytokinins.
Control of cytokinin activity
• Figure 20.3
Control of cytokinin activity
• The second mechanism for controlling
activity is via degradation by cytokinin
oxidase/dehydrogenase (CKX).
– Degradation is the primary mechanism for
controlling cytokinin activity.
– Only cytokinins with a double bond in the
isoprenoid side chain is degraded by CKX.
– Over-expression of CKX is another means of
controlling cytokinin activity.
Sites of cytokinin synthesis
• Cytokinins are transported in the xylem
from their primary site of synthesis at the
root tips.

• High concentrations of cytokinins are also

found in immature seeds and developing
fruits, which may indicate synthesis of
cytokinins or that cytokinins are
preferentially transported to these tissues.
Biological effects of cytokinins
• The role of cytokinins in the regulation of
cell division is well known.
– Cytokinins were first identified as the “cell-
division factor” requires for cell proliferation.
– Cytokinins only stimulate cell division in the
presence of auxins.
– The specific role of cytokinins is to regulate
the progression of the cell cycle.
Biological effects of cytokinins
• The role of cytokinins in the regulation of
cell division is well known.
– In absence of either auxin and cytokinin, cell
cultures remain in the G1 or G2 phases of
– The presence of cytokinins are needed to
activate cyclin-dependent kinases (CDK).
– The activation of CDK by cytokinins allows
cells to transition from the G2 phase to
Biological effects of cytokinins
• Figure 20.4
Biological effects of cytokinins
• The role of cytokinins in the regulation of
cell division is well known.
– Cytokinins also regulate the level of D-type
cyclins in Arabidopsis.
– D-type cyclins control the transition from the
G1 phase to the S phase of interphase.
Biological effects of cytokinins
• The interaction between auxin and cytokinin
regulates the formation of root and shoot tissues
in cell culture.
– Both hormones are required to maintain cells in
culture as an undifferentiated callus.
– If the ratio of auxin to cytokinin is too high, only plant
roots form.
– If the ratio of cytokinin to auxin is too high, only shoots
– If the proper ratio of auxin and cytokinin are provided,
the callus can be regenerated into an intact plant.
Biological effects of cytokinins
• Figure 20.5
Biological effects of cytokinins
• Cytokinins also antagonize the effect of
auxin on apical dominance.
– Exogenous auxin applied to either normal
plants, or plants over-producing auxin, can
overcome apical dominance.
– Such results illustrate that the ratio of auxin to
cytokinin dictates apical dominance.
– The phenomenon of “witch’s broom” is
caused by parasites which stimulate
overproduction of cytokinins, releasing axillary
buds from their dormancy.
Biological effects of cytokinins
• Figure 20.6
Biological effects of cytokinins
• Cytokinins are involved in the formation of
crown gall tumors in plants.
– Gall tumors are caused by the bacterium
Agrobacterium tumifaciens.
– These bacteria carry a tumor-inducing (Ti)
plasmid which contains genes responsible for
inducing neoplastic growth of gall tumors.
– This plasmid is transferred to the plant cells
following A. tumifaciens infection.
Biological effects of cytokinins
• Figure 20.7
Biological effects of cytokinins
• Cytokinins are involved in the formation of crown
gall tumors in plants.
– Transferred DNA (T-DNA) from the plasmid is
incorporated into the host plant genome.
– The T-DNA contains three genes.
• Two of the genes are necessary for the synthesis of auxins
and cytokinins.
• The third gene causes the plant to produce opines, which are
a nutrient amino acid for the bacteria.
– The natural ability of A. tumifaciens to genetically
reprogram plants can been adapted to facilitate the
transfer of other genes into plants.
Biological effects of cytokinins
• Cytokinins are inhibitors of senescence.
– Exogenous cytokinins delay senescence.
– Similarly, there is a linear relationship
between the decrease in endogenous
cytokinins and the onset of senescence.
– When expression of the Agrobacterium gene
for cytokinin synthesis is placed under the
control of a heat shock promoter, treatment
with heat causes a direct increase in zeatin
concentrations and delayed senescence.
Biological effects of cytokinins
• Figure 20.8
Biological effects of cytokinins
• Cytokinins influence the distribution of
nutrients in tissues.
– When cytokinins are applied to leaves, for
example, nutrients migrate to the spot where
the application was made.
– It is believed that this migration occurs
because cytokinins stimulate metabolism,
thereby causing the local cells to become
sinks for nutrients.
Biological effects of cytokinins
• Figure 20.9
Biological effects of cytokinins
• Cytokinins have a role in maintaining the
shoot meristem.

• Reducing in vivo cytokinin concentrations

results in:
– Retarded shoot development
– Dwarf, late flowering plants
– Reduced size of the shoot meristem
– Slowed formation of leaf primordia
– A reduced number of leaf cells
Biological effects of cytokinins
• Cell growth is arrested in cells where
cytokinin degradation is up-regulated or in
mutants lacking in cytokinin synthesis or

• The lonely guy (LOG) gene encodes a

phosphoribohydrolase that regulates
meristem activity by converting inactive
cytokinins to the active free base form.
Biological effects of cytokinins
• Figure 20.10
Biological effects of cytokinins
• A suite of master control genes regulate
cytokinin concentrations in the meristem.
– Cell differentiation in living organisms is
controlled by genes containing homeobox or
homeodomain sequences.
– Homeobox genes have a fundamental role in
controlling cell development and fate.
– Plant homeobox proteins are KNOX proteins.
– The KNOX genes regulate the synthesis of
gibberellins and cytokinins.
Biological effects of cytokinins
• Mutations in KNOX genes have specific effects
on development.
– KNOX genes are normally expressed in the cells of
the shoot apical meristem, but not in leaf primordia or
developing leaves.
– A dominant, gain-of-function mutation causes
expression of KNOX genes in developing leaves,
causing “knots” of cells or ectopic shoots to form.
– These effects result because the accumulation of
KNOX proteins causes cells to continue dividing,
rather undergoing differentiation.
Biological effects of cytokinins
• Mutations in KNOX genes have specific
effects on development.
the same expression pattern as LOG genes.
– Mutations in the STM gene produce loss-of-
function mutants.
– A defect in STM prevents the formation of an
apical meristem during embryogenesis.
Biological effects of cytokinins
• Figure 20.11
Biological effects of cytokinins
• KNOX proteins are transcription factors that
regulate the transition from indeterminate growth
to differentiation.

• The KNOX proteins :

– Up-regulate IPT genes for cytokinin synthesis
– Suppress the GA20-oxidase gene in gibberellin

• KNOX proteins help maintain the high

cytokinin/low gibberellin ratio needed for
formation and maintenance of shoot meristems.
Cytokinin receptors and signalling
• The cytokinin receptor in plants was
discovered using the hypocotyl test.
– Application of cytokinin to explants normally
causes cell proliferation and shoot formation.
– In the cytokinin response 1 (cre1) mutant,
there is no response to applied cytokinin
because the receptor is not present.
– A mutation in the WOODENLEG (WOL) gene
retards root growth because of a defect in
Cytokinin receptors and signalling
• The cytokinin receptor is a two-
component regulatory system.
– The system consists of a receptor and a
response regulator.
– The CRE1 cytokinin receptor protein is a
histidine kinase (HK) with three domains.
– The sensor domain consists of two
membrane-spanning regions.
– The histidine kinase domain is on the
cytoplasmic side of the membrane.
Cytokinin receptors and signalling
• Figure 20.12
Cytokinin receptors and signalling
• The cytokinin receptor is a two-
component regulatory system.
– Of the numerous histidine kinase genes in
plants, only three are cytokinin receptors.
• CRE1
• AHK2
• AHK3

– Some receptors are also ethylene receptors

and others are osmosensors.
Cytokinin receptors and signalling
• Cytokinin signalling involves transfers of
phosphate groups to response regulators.
– Cytokinin binding to the sensor domain results
in the phosphorylation of the histidine
residues of each protein in the dimer.
– The phosphoryl group is spontaneously
transferred to the Db receiver domain.
– The phosphoryl group is then transferred
through a series of histidine-
phosphotransfer proteins (HPTs).
Cytokinin receptors and signalling
• Cytokinin signalling involves transfers of
phosphate groups to response regulators.
– Phosphorylated HPTs migrate to the nucleus.
– The phosphoryl group is transferred from the
HPTs to one of two classes of response
– Phosphorylation of the B-type regulators,
which are transcription factors, induces the
transcription of the A-type regulators.
Cytokinin receptors and signalling
• Cytokinin signalling involves transfers of
phosphate groups to response regulators.
– The phsophorylation of the A-type regulators
modulate cytokinin activity at the metabolic
– Cytokinin signalling is controlled by the
activity of phosphatases, which remove
phosphoryl groups.
Cytokinin receptors and signalling
• Figure 20.13
Plant Hormones IV:
ABA, Ethylene, and
Chapter 21
Learning objectives
• Know the pathways for the synthesis of
abscisic acid, ethylene, and

• Understand the physiological effects of

these three plant hormones.

• Understand the signalling pathways by

which these hormones exert their effects.
Abscisic acid
• Unlike auxin, cytokinins, and gibberellins,
only one molecule represents the hormone
abscisic acid (ABA).

• This hormone was named based upon the

erroneous assumption that it was
responsible for the abscission of leaves
and other tissues.
Abscisic acid
• Figure 21.1
Abscisic acid
• The primary functions of ABA include:
– Prevention of precocious germination
– Initiation and maintenance of seed dormancy
– Stomatal control
– Protection of cells from desiccation

• Other functions may include:

– Induction of storage proteins in seeds
– Heterophylly
– Initiation of secondary roots
– Flowering and senescence
ABA synthesis
• ABA is synthesized from the -carotene
violaxanthin, typically in mature leaves.

• Synthesis begins in the chloroplast,

beginning with G3P and pyruvate, and
ending with xanthoxin.

• Synthesis in completed in the cytosol,

where xanthoxin is converted to ABA.
ABA synthesis
• Figure 21.2
ABA synthesis
• Based upon the expression of genes
encoding enzymes involves in ABA
synthesis, there is also evidence that ABA
is synthesized in:
– Guard cells
– Phloem parenchyma
– Xylem parenchyma
Transport and storage of ABA
• ABA is highly mobile within plants.

• ABA tends to accumulate in sink tissues,

including seeds.

• During periods of water stress, ABA can

be stored in roots.
Transport and storage of ABA
• ABA may also be stored in chloroplasts.
– In the cytosol, the pH favors the protonated
form of ABA (i.e., ABAH)
– In a chloroplast not undergoing
photosynthesis, the stromal pH of 7.5 favors
the formation of deprotonated ABA (i.e. ABA-),
trapping the ABA in the chloroplast.
– During photosynthesis, the stromal pH
decreases to a value of 6.5, facilitating the
formation of ABAH and the release of ABA to
the cytosol.
Transport and storage of ABA
• Figure 21.4
Control of ABA activity
• ABA is metabolized quickly in plants.

• One pathway to control ABA activity

involves the formation of a glucose ester.

• The primary pathway involves the

oxidation of ABA to phaseic acid (PA)
followed by reduction to dihydrophaseic
acid (DPA).
Functions of ABA
• ABA regulates the maturation of the
embryo and the germination of seeds.
– During embryogenesis, ABA levels peak
during the maturation stage.
– ABA imposes dormancy on the embryo,
preventing vivipary (precocious germination).
– ABA also induces desiccation of the seed,
which also contributes to seed dormancy.
Functions of ABA
• ABA also has important roles in the
response to water stress.
– ABA accumulates in water-stressed leaves
where it inhibits stomatal opening.
– Some of the ABA comes from storage pools in
the cell apoplast.
– The acidification of the chloroplast caused by
water stress allows stored ABA to be released
and transported to the guard cells.
– Increased rates of ABA synthesis help to
maintain stomatal closure during water stress.
Functions of ABA
• Figure 21.5
Functions of ABA
• ABA also has important roles in the
response to water stress.
– The transport of ABA from roots to shoots is
triggered by decreases in soil moisture.
– This feed-forward signal initiates stomatal
closure before there is a change in leaf water
– The presence of ABA reduces stomatal
conductance, helping to preserve water.
Functions of ABA
• Figure 21.6
Functions of ABA
• Figure 21.7
Functions of ABA
• Additional roles for ABA include:
– Lateral or secondary root development.
– A possible role in the suppression of flower
ABA signalling
• One possible ABA receptor that has been
identified is the ABAP1 protein, located in
the plasma membrane of aleurone cells.

• Three other ABA receptors may include:

– The chloroplast protein magnesium
protoporphyrin-IX chelatase H subunit.
– The flowering-time control protein FCA.
– A G-protein identified as GCR2.
ABA signalling
• The signalling pathway for ABA includes
the following components:
– Ca2+ is an important second messenger,
especially in guard cells, where it activates
membrane anion channels.
– Transcription factors known as ABA response
element binding factors activate ABA-induced
genes that promote the synthesis of
osmolytes, or compatible solutes.
ABA signalling
• The signalling pathway for ABA includes
the following components:
– ABA may regulate specific aspects of gene
expression in seeds.
– Protein phosphorylation, via kinases and
phosphatases, is regulated by ABA.
ABA signalling
• Figure 21.8
• Ethylene is a small molecule that has key
roles in plant growth and development.

• Ethylene can influence root and shoot

growth, but is primarily associated with
stress, senescence, and ripening.

• Ethylene can be found in all plant tissues,

although the concentration can vary.
Ethylene synthesis
• Ethylene is synthesized by a three step
– The precursor methionine is converted to S-
adenosylmethionine (SAM) by the enzyme
SAM synthetase.
– SAM is converted to 1-aminocyclopropane-
1-carboxylic acid (ACC) by ACC synthase.
– ACC is converted to ethylene by ACC
Ethylene synthesis
• Sustained synthesis of ethylene requires
the sulfur-containing by-product of ACC
synthesis to be recycled to methionine.

• The recycling of methionine occurs via the

Yang cycle.
Ethylene synthesis
• Figure 21.9
Ethylene synthesis
• Ethylene synthesis is influenced by:
– Auxin
– Wounding
– Water stress
– Temperature
– Inhibitors of RNA and protein synthesis
– Ethylene autocatalysis

• The effects of these factors on synthesis occurs

at the transcriptional level via ACC synthase.
Control of ethylene activity
• Ethylene activity can be controlled by:
– Oxidation to carbon dioxide
– Conversion to ethylene oxide
– Conversion to ethylene glycol

• Ethylene activity can simulated with 2-

chloroethylphosphonic acid (ethephon),
which decomposes to form ethylene.
Functions of ethylene
• Ethylene is involved in the ripening and
senescence of fruits.

• The synthesis of ethylene in fruits differs

between climacteric and non-climacteric fruit.

• Ethylene stimulates the elongation of

aboveground vegetative tissues but inhibits root

• Gibberellins can antagonize the effects of

ethylene on root and shoot growth.
Functions of ethylene
• Ethylene is involved in epinasty, a downward
curvature of leaves caused by excessive cell
elongation on the adaxial (upper) side of the

• Epinasty is a typical response for flood-sensitive


• Ethylene also:
– Promotes seed germination
– Inhibits bud break
– Reduces apical dominance
Ethylene receptors and signalling
• A well known effect of ethylene is the triple
response observed in etiolated seedlings.
– Inhibited hypocotyl and elongation
– Radial swelling of hypocotyl
– Exaggerated curvature of plumular hook

• The various triple response mutants that

exist were useful in determining the
ethylene signalling pathway.
Ethylene receptors and signalling
• Figure 21.10
Ethylene receptors and signalling
• The ethylene receptors are a family of
membrane-associated two-component
histidine kinases.
– The ETR1 receptor is located in the ER
– Ethylene is a repressor of the system, turning
off the signalling cascade when present.
Ethylene receptors and signalling
• According to the general model for
ethylene signalling:
– The Constitutive Triple Response 1 (CTR1)
protein, in the absence of ethylene, interacts
with ETR1.
– Associate with ETR1 results in the
phosphorylation of CTR1.
– The phosphorylated CTR1 is a kinase that
initiates signal transduction that activates
transcription factors which maintain the
constitutive expression of genes.
Ethylene receptors and signalling
• According to the general model for
ethylene signalling:
– The binding of ethylene to CTR1 prevents the
association with ETR1.
– The binding of ethylene therefore prevents the
activation of target genes.
Ethylene receptors and signalling
• Figure 21.11
• As the name implies, brassinosteroids are
steroid hormones, that were first identified as the
active substances (brassins) in pollen from rape
(Brassica napus).

• The principle brassinosteroid in plants is

brassinolide (BL).

• The effects of brassinosteroids are similar to

those of gibberellins and mediate some of the
same functions as auxins.
• Figure 21.13
• Brassinosteroids mediate a wide range of
functions including:
– Stimulation of stem and pollen tube
– Stimulation of cell division (with auxin and
– Seed germination
– Leaf morphogenesis
– Apical dominance
– Inhibition of root elongation
• Brassinosteroids mediate a wide range of
functions including:
– Vascular differentiation
– Accelerated senescence
– Programmed cell death
– Responses to biotic and abiotic stress
Brassinosteroid synthesis
• Brassinosteroids are synthesized from a
terpene precursor.
– The terpene squalene undergoes a cyclization
reaction to form cycloartenol.
– Cycloartenol can be used to synthesized a
wide range of plant sterols.
– Cycloartenol can be converted to
campesterol, which serves as the precursor
for brassinolide.
Brassinosteroid synthesis
• Figure 21.14
Control of brassinosteroid activity
• There are multiple routes for controlling
brassinosteroid activity.
– Esterification with fatty acids
– Glucosylation
– Cleavage of the side chain
– Conjugation at one or more hydroxyl positions
Brassinosteroid receptors and signalling

• The current model for brassinosteroid

signalling involves the following elements:
– The brassinosteroid receptor is a
heterodimer protein comprised of:
• A serine/threonine kinase referred to as
– When a brassinosteroid binds to BRI1, an
inhibitory protein (BKI1) dissociates, allowing
BRI1 to dimerize with BAK1.
Brassinosteroid receptors and signalling

• The current model for brassinosteroid

signalling involves the following elements:
– Dimerization with BAK1 leads to the
autophosphorylation of BRI1.
– The phosphorylated dimer initiates a
signalling pathway, which may include the
1 (BZR1).
Brassinosteroid receptors and signalling

• The current model for brassinosteroid

signalling involves the following elements:
– If BZR1 phosphorylated by the regulatory
protein BIN2, BZR1 stays in the cytosol.
– When dephosphorylated by the signalling
pathway, BZR1 migrates to the nucleus where
it acts as a transcription factor.
Responding to light
Chapter 22
Learning objectives
• Know how light regulates plant growth and
development (photomorphogenesis).

• Understand the role of photoreceptors in

the perception of light.

• Know how phytochromes respond to red

and far red light.
Learning objectives
• Know how cryptochromes respond to blue and
UV-A light.

• Understand the developmental processes that

are mediated by phytochromes and

• Understand the signalling pathways by which

phytochromes and cryptochromes initiate
signalling cascades.
Photomorphogenesis: Growth
responses to light
• Light is an important environmental signal
that plants use to regulate their growth and

• Both the quality and quantity of light are


• The regulation of plant development by

light is called photomorphogenesis.
Photoreceptors in
• Photoreceptors are used by plants to
acquire and interpret light signals.

• When photoreceptors absorb light, the

conformational change that occurs helps
initiate a signal transduction pathway.

• The signal transduction pathway ultimately

triggers a developmental response.
Photoreceptors in
• There are four classes of plant photoreceptors.
– Phytochromes absorb red and far red light.
– Cryptochromes detect blue and UV-A light.
– Phototropins also detect blue and UV-A light.
– A newly-identified class of photoreceptors that
responds to low levels of UV-B light.

• The first three photoreceptors are

chromoproteins, meaning that they are a
complex (holoprotein) consisting of a pigment
(chromophore) and a catalytic protein
• Phytochromes are found in all plants, with at
least three distinct versions present (e.g., phyA,
phyB, phyC, etc.).

• While the chromophore for each version is the

same, the apoprotein differs.

• Each version of a phytochrome has two

chemical states.
– One state responds to red light (R) at 660 nm.
– A second responds to far red (FR) light at ~730 nm.
• Figure 22.1
• The photoreversibility of phytochrome is a
unique aspect of phytochrome.

• Plant responses to red light can be nullified with

an immediate treatment with far-red light.

• A classic example of a photoreversible,

phytochrome-mediated response is seed
– Red light stimulates germination.
– Far-red light “switches” germination back off.
• Photoreversibility occurs because the two
forms of phytochrome are in a
photoequilibrium created by light.
– When exposed to red light, the red-light
absorbing form (Pr) is converted the
biologically active far-red absorbing form
– Exposure to far-red light causes the far-red
absorbing form (Pfr) to be converted back to
the red light absorbing form (Pfr).
• Figure 22.3
• The dynamic relationship between the Pr and Pfr
forms can be seen clearly in etiolated (dark-
grown) plants.
– In the dark, Pr levels are held steady as the rates of
synthesis and degradation are equal.
– When etiolated plants are given a brief pulse of red
light, Pr is converted to Pfr.
– After plants are returned to darkness, the Pfr
concentration decreases rapidly as does the total
phytochrome concentration.
– Both the Pr and Pfr forms of phytochrome are subject
to irreversible chemical degradation.
• Figure 22.4
• Figure 22.5
• The photoequilibrium ( is described
mathematically by:
P fr
Where PTOT is the sum of the Pr and Pfr forms

• Light conditions dictate the specific ratio.

– Under pure red light, = 0.8 (80% pFr).
– Under pure far-red light, = 0.03 (3% pFr).
– In sunlight, the value of will change through the day.
• Phytochrome responses are grouped
based upon their fluence requirement.
– Low fluence responses (LFRs) are
mediated by phyA and stimulated by light
doses in the 1 – 1,000 mole light m-2.
– Very low fluence responses (VLFRs) are
irreversible responses to light levels of 10-6 to
10-3 mole light m-2.
– High irradiance reactions (HIRs) are those
that respond to sustained exposures to light.
• Specific characteristics of HIRs include:
– A requirement for prolonged exposure to high
irradiance, far-red enriched light to initiate a
– A response that varies in magnitude with the
fluence rate and duration.
– Responses that are irreversible.
• Cryptochromes mediate the growth
responses to blue and UV-A light.

• Examples of blue light photoreceptors

– Cryptochrome 1 (cry1), a receptor which
binds flavins such as FAD.
– Cryptochrome 2 (cry2).
Developmental responses mediated by
phytochrome and cryptochrome
• Seed germination is influenced by light.
– Seeds whose germination is stimulated by
light are positively photoblastic seeds.
– Seeds that negatively photoblastic have
their germination inhibited by high fluence rate
light exposures.
– Phytochrome acts as a sensor that provides a
means for the seed to determine its depth in
the soil.
Developmental responses mediated by
phytochrome and cryptochrome
• Specific changes occur when dark-grown
plants are exposed to light (de-etiolation).
– Hypocotyl growth stops and the hook
straightens so vertical growth can occur.
– The leaves unfold and enlarge.
– Chloroplasts mature and the synthesis of
chlorophyll causes leaves to green.
Developmental responses mediated by
phytochrome and cryptochrome
• Figure 22.6
Developmental responses mediated by
phytochrome and cryptochrome
• Shading triggers changes in plant growth.
– The responses that manifest are termed the
shade avoidance syndrome.
– One response involves increasing specific
leaf area and/or chlorophyll levels to
increased the capacity to harvest light.
– Another involves changes in growth and/or
morphology to alter the position of leaves to
increase access to light.
Developmental responses mediated by
phytochrome and cryptochrome
• Shading triggers changes in plant growth.
– Shading responses are initiated because the
light environment is far-red enriched.
– Cryptochrome and phytochromes (phyB,
phyD, and phyE) are used to discriminate
between shading and full light conditions.
– The effect of shading can be described in
terms of the Pr/Pfr ratio, symbolized by ,
which can be further related to .
Developmental responses mediated by
phytochrome and cryptochrome
• Figure 22.7
Developmental responses mediated by
phytochrome and cryptochrome
• Shading triggers changes in plant growth.
– Light conditions can be experimentally
controlled to allow aspects of morphogenesis
to be related specifically to .
– Results with Chenopodium album, for
example, showed that when exposed to far
red light, there was an increase in stem
extension rate.
– Consequently, a linear relationship was
observed between logarithmic stem extension
rate and
Developmental responses mediated by
phytochrome and cryptochrome
• Figure 22.8
Developmental responses mediated by
phytochrome and cryptochrome
• Phytochrome is the receptor that helps
plants detects end-of-day signals.
– At dawn and dusk, the value is lower that
during the rest of the day.
– If the is manipulated experimentally to mimic
end-of-day conditions, changes in
development (e.g., increased stem and
petiole extension, decreased leaf expansion)
are observed.
– Such experiments suggest a role for
phytochrome in time measurement.
Developmental responses mediated by
phytochrome and cryptochrome
• Biosynthesis of the red-blue anthocyanin
pigments are mediated by light.
– Anthocyanin synthesis is a response to high
– This is an example of a phytochrome LFR,
except that photoreversibility is limited.
Developmental responses mediated by
phytochrome and cryptochrome
• Some phytochrome responses occur
within a matter of seconds to minutes and
typically involve membrane-based
changes in bioelectric potential or ion flux.

• The different forms of phytochrome likely

have different fundamental roles in the
perception of light.
– PhyA may only be involved in light detection.
– Other forms likely interpret light quality.
Mode of action of phytochrome
• The chromophore for phytochrome is
– The difference between the Pr and Pfr forms involves
a rotation of the double bond between rings C and D.
– Red light triggers the conversion of the bond to the
bioactive trans isomer.
– Far-red light of dark reversion converts the molecule
back to the cis isomer.
– A change in the conformation of the chromophore
also changes the conformation of the apoprotein.
Mode of action of phytochrome
• Figure 22.9
Mode of action of phytochrome
• The apoprotein for phytochrome is a small
– The peptide has a photosensory domain on
the N-terminus and a regulatory domain at
the C-terminus.
– The regulatory domain contains a sub-domain
with characteristics of a histidine kinase.
– Phytochrome, in a sense, acts as a two-
component regulatory system like those
involved in hormone sensing.
Mode of action of phytochrome
• Figure 22.10
Mode of action of phytochrome
• The mechanism by which phytochrome
mediates plant development involves three
important factors.
– Phytochromes act as serine/threonine kinases
that autophosphorylate and phosphorylate
other proteins.
– The active Pfr form is imported into the
– Phytochrome responses involve significant
changes in gene expression.
Mode of action of phytochrome
• Phosphorylation is key to the signalling
role of phytochromes.
– Phytochrome is preferentially phosphorylated
in the Pfr form.
– The transfer of the phosphate group initiates
signalling cascades.
• Phytochrome kinase substrate 1 (PKS1) binds to
phyA and phyB and is phosphorylated in red light.
• Nucleoside diphosphate kinase 2 (NDPK2)
phosphorylation is stimulated by red light
Mode of action of phytochrome
• The migration of phytochrome to the
nucleus also provides control of gene
– The Pr form is cytosolic but the Pfr form can
be recognized by the nuclear import
– The far-red elongated hypocotyl 1 (FHY1)
protein is required for Pfr import.
– Phytochromes in the nucleus form nuclear
bodies (also called speckles).
Mode of action of phytochrome
• The migration of phytochrome to the
nucleus also provides control of gene
– Phytochrome in the nucleus may interact with
phytochrome-interacting transcription factors.
– These transcription factors act as repressors.
– The interaction with Pfr triggers the
degradation of the transcription factors,
leading to gene activation.
Mode of action of phytochrome
• Figure 22.11
Mode of action of phytochrome
• Figure 22.12
Mode of action of cryptochrome
• The structure of cryptochromes is similar
to that of DNA repair enzymes.
– Most plant cryptochromes are proteins with two
recognizable domains.
• The N-terminal domain shows, termed a
photolyase-related domain, can bind FAD and
redox factors called pterins.
• The role of the C-terminal domain is unclear.
– Microbial photolyases, which are involved in the
repair of UV-damaged DNA, are thought to be the
evolutionary precursor of cryptochrome.
Mode of action of cryptochrome
• Figure 22.13
Mode of action of cryptochrome
• Figure 22.14
Mode of action of cryptochrome
• The mechanism by which cryptochrome
elicits developmental responses has not
been fully characterized.
– Cryptochromes are typically present in the
nucleus, making the signalling pathway short.
– Cryptochrome interacts with COP1
1) in the nucleus.
– As COP1 is a repressor of gene expression,
this interaction induces gene expression.
Mode of action of cryptochrome
• The mechanism by which cryptochrome
elicits developmental responses has not
been fully characterized.
– Some experiments have shown that phyA
may phosphorylate cry1.
– Thus there are phytochrome-dependent and
independent pathways by which the
phosphorylation of cryptochromes may initiate
signal transduction.
Plant responses to UV-B light
• Examples of UV-B responsive process in
plants include:
– An increase in anthocyanin production
– An increase in flavonoid biosynthesis,
triggered by phytochrome, cryptochrome, and
another UV-B receptor.
Interactions between phytochrome
and cryptochrome
• De-etiolation responses in Arabidopsis
involve an interaction between phyA,
phyB, and cry1.
– If phyB is defective, hypocotyl elongation is
– If phyA is also deficient, the hypocotyls are
even longer than in etiolated plants.
– In a triple mutant which includes a defect in
cry1, the hypocotyl hook does not straighten
and the cotyledons do not unfold.
Interactions between phytochrome
and cryptochrome
• Figure 22.15
Tropisms and Nastic
Chapter 23
Learning objectives
• Know the physiological basis of tropic
movements such as phototropism and

• Know the physiological basis of nastic

movements such as nyctinasty and
Plant “movements”
• There are two categories of movement in
– Irreversible growth movements
– Reversible turgor movements

• Within each category, there are three

types of movements.
– Nutations
– Tropisms
– Nastic movements
Plant “movements”
• Nutations are time-lapse movements that
occur slowly with time.

• Tropic responses are directional growth

responses with respect to a stimulus.

• Nastic responses are plant movements

dictated by inherent directionality in the
plant tissue not the stimulus.
• Phototropism is the phenomenon that
occurs when plants bend toward the light.

• Phototropism is a positive tropism in that

the plant grows toward the stimulus.

• Other tropisms are negative tropisms.

• Figure 23.1
• The directionality of phototropic responses
are dictated by the nature of the organ.
– Coleoptiles, hypocotyls, stems, and aerial
organs are generally positively phototropic.
– Tendrils of climbing plants are negative.
– Leaves are plagiotropic, oriented at angles
relative to the light.
– Roots are non-phototropic.
• Phototropism is a response to a light

• Light fluence differences of as little as 20

percent will induce bending.

• The optical properties of the plant tissue

influences the light gradient and its
• Figure 23.2
• Phototropism is a blue-light response, with
an action spectra showing peaks at 475
and 450 nm.

• Light in the UV-A region at 370 nm, and in

some species at 280 nm, also induces

• The receptor for phototropisms is a

flavoprotein called phototropin.
• Figure 23.3
• Unlike other blue-light responses, phototropism
orients growth and leaf angle to incident light.

• This orientation maximizes the light intercept for


• Blue light also influences the positioning of

chloroplasts in leaf cells, causing them to align
parallel to the light in low light conditions, and
anticlinal under high light conditions.
• Figure 23.4
• The relationship between the fluence rate
and phototropic response shows a
complicated relationship.
– There is an initial first positive curvature
with increasing fluence.
– The first negative curvature follows and
may result in a negative phototropism.
– A second positive curvature then occurs.
– This alternating cycle may continue for some
plants with additional levels of curvatures.
• Figure 23.5
• The first positive curvature obeys the
Bunsen-Roscoe reciprocity law in that
long exposures to a low fluence have the
same effect as a short exposure to a high

• The subsequent curvatures do not

because the second positive curvature is
time dependent.
• The Cholodny-Went hypothesis states
that the bending that results from photo-
tropism is due to a lateral distribution of
endogenous auxin.
– In response to a unilateral light source, auxin
is distributed to the side of the plant away
from the light.
– The auxin stimulates the elongation of the
cells on that side of the plant, causing the
plant to bend toward the light source.
• The Cholodny-Went hypothesis was
based upon agar diffusion experiments.
– The apices of oat coleoptiles exposed to
unilateral light were removed.
– The apices were split and placed on agar
blocks so the auxin diffused into the blocks.
– The agar blocks were then assayed by the
Avena (oat) curvature test.
– The results showed that the block from the
shaded half of the plant induced bending.
• Further evaluation of this hypothesis
provided additional support.
– Coleoptile tips were excised before the plants
were exposed to light.
– The tips were split and transferred to agar.
– If the tips were partially split, attached at the
apex, unilateral light caused the auxin
concentration on the light side to decreased
and the shaded side to increase.
– The total amount of auxin was the same,
indicating that redistribution occurred.
• Figure 23.6
• The photoreceptor for phototropism is a
flavoprotein called phototropin.

• Phototropin is a plasma membrane bound

kinase with two flavin mononucleotide

• There are two phototropins which control

different aspects of the positive curvature.
• Figure 23.7
• Neochrome is a similar photoreceptor
from the fern Adiantum capillus-veneris.

• This photoreceptor is regulated by both

red and blue light.

• This plant also has the two phototropins,

but the second is only involved in
chloroplast avoidance under high light.
• The signalling chain associated with
phototropin has recently been determined.
– A phosphorylation cascade is initiated by the
autophosphorylation of phototropin.
– Phototropin may regulate genes such as
NPH3 and CPT1 that have domains
consistent with transcriptional regulation or
protein degradation.
– Phototropin disrupts polar auxin transport,
preventing the vertical transport out of the tip.
• The understanding of how phototropism
works in light-grown plants is under study.

• In some plants, shading one cotyledon can

induce bending to the opposite side.

• In light-grown cucumber, the phototropic

response is induced by red light, not blue,
in a phytochrome-mediated response.
• Figure 23.8
• Gravitropism helps orient plant tissues
with respect to the directionality of gravity.
– The alignment of the primary vertical axis of
the plant to gravity is orthogravitropic.
– Roots show positive gravitropism while the
shoot displays negative gravitropism.
– Plant structures that grow at right angles to
gravity are diagravitropic.
– Organs that grow at an angle relative to
gravity are plagiogravitropic.
– Some tissues are agravitropic.
• Gravitropic responses insure that
germinating seeds establish the proper
orientation for growth.

• Gravitropic responses also insure that

plants efficiently distribute roots and
shoots throughout the available space.
• Figure 23.10
• The gravitational stimulation is a function
of the intensity and duration.
dose = time x acceleration due to gravity

– The minimum dose to induce a gravitropic

response is the threshold dose.
– The minimum time is the presentation time.
– The minimum stimulus intensity is the
threshold intensity.
• Root gravitropism occurs in four phases.
– Perception occurs during the first second.
– Transduction occurs within the first 10
– Transmission occurs from 10 seconds to 10
minutes after the stimulus.
– The growth response, like phototropism, is
caused by a subsequent unequal distribution
of auxin.
• Figure 23.11
• Perception occurs in the root cap.
– The root cap consists of a central group of
columnella and outer peripheral cells.
– The root cap functions in protection and
mucilage secretion as well as gravitropism.

• The role of the root cap (particularly the

columnella) in gravitropism was
established by experiments in which the
cap was removed, abolishing the effect.
• Figure 23.12
• Figure 23.13
• According to the starch-statolith
hypothesis, perception involves the
displacement of starch-filled amyloplasts.
– Statenchyma tissues contain statocytes,
cells with sedimentable starch grains.
– An amyloplast is a group of starch grains
within a membrane.
– Amyloplasts are mobile only in tissues that
have a high gravitropic sensitivity.
• Figure 23.14
• The evidence for this hypothesis involves
the following observations.
– Gravitropism is absent when starch grains or
amyloplasts were absent.
– The presentation time is correlated with the
rate of starch sedimentation.
– Loss of starch leads to loss of gravitropism.
– Amyloplasts can be displaced by a high-
gradient magnetic field.
• The general conclusion is that the
movement of statoliths applies pressure to
some cellular component, such as the ER
or plasma membrane.

• This “pressure” induces gravitropic growth.

• This contention is supported by electron

micrographs of sedimented amyloplasts.
• During the transmission and response phases
there is differential auxin redistribution.
– The flow of auxin to the root tip is described by the
auxin fountain model.
– Auxin transported from the shoot reaches the root tip
and is redistributed basipetally.
– In a horizontal root, there is greater auxin distribution
to the lower side of the root.
– The auxin inhibits elongation of the lower side while
the upper side continues elongating, which results in
a downward curvature.
• Figure 23.15
• Gravitropic induction involves several
messengers and transport proteins.
– Within seconds of being turned horizontally,
the columnella cells on the lower side of the
root depolarize and those on the other
– These membrane effects are related to the
ctyoskeleton because they are sensitive to the
inhibitor cytochalasin D.
• Gravitropic induction involves several
messengers and transport proteins.
– Specific pH changes in the root cap cells
precede the role of auxin in gravitropism.
– Calcium migration through the mucilage at the
root tip also influences gravitropism.
– Changes in the distribution of the auxin efflux
facilitators PIN1, PIN2, and PIN3 alter the
distribution of auxin in the root.
• Figure 23.16
• Figure 23.17
Nastic movements
• Nastic movements do not relate to any
vectorial component of the stimulus.

• Some nastic movements are reversible but

others are not.

• Some nastic movements involve growth

responses while others are turgor driven.
Nastic movements
• Nastic movements involving differential
growth responses include:
– Epinasty, an auxin-mediated downward
bending of an organ independent of gravity.
– Hyponasty, the opposite of epinasty.
– Thermonasty, the repeated opening and
closing of flower petals.
Nastic movements
• The turgor-driven movements can be
separated into three categories.
– Slower movements are nyctinastic.
– A few rapid responses are seismonastic.
– Thigmanastic or thigmotropic curling occurs
in climbing plants.

• Nyctinastic and seismonastic movements

involve a motor organ called a pulvinus.
Nyctinastic movements
• Nyctinastic movements are most often
associated with plants whose leaves take
up different positions during night and day.

• Leaves are in an “open” position during

the day and a “sleep” position at night.

• The secondary pulvinus makes a

significant contribution to this movement.
Nyctinastic movements
• Figure 23.18
Nyctinastic movements
• Figure 23.19a
Nyctinastic movements
• Nyctinastic movements are based upon
reversible turgor changes in the pulvinus.
– The outer cortex of the pulvinus are motor
cells with thin elastic walls that change shape
to provide movement.
– The opposite sides of the of the pulvinus are
the extensor and flexor regions.
– The extensor cells are cells that lose turgor
during the “closure” movement.
Nyctinastic movements
• Nyctinastic movements are based upon
reversible turgor changes in the pulvinus.
– The flexor motor cells increase turgor during
movement closing and decrease turgor during
– The swelling of extensor motor cells and the
shrinkage of flexor cells straightens the
pulvinus to “open” the leaves.
Nyctinastic movements
• Figure 23.19b
Nyctinastic movements
• The changes in turgor in the motor cells
are driven by the redistribution of K+ ions
between the symplast and apoplast.
– Turgid extensor cells have high protoplasmic
K+ concentrations but low apoplastic K+.
– The exchange of K+ is mediated by channels.
– Changes in the pH gradient between the
apoplast and symplast of both the flexor and
extensor cells also influences turgor.
Nyctinastic movements
• Figure 23.20
Nyctinastic movements
• The current model for motor cell
movement includes the contribution of K+
channels and H+ pumps.
– Light signals activate phytochrome or
cryptochrome, increasing the turnover of
inositol phosphate.
– This increases the concentration of second
messengers such as diacylglycerol and IP3.
– The second messengers increase cytosolic
Ca2+ and protein phosphorylation.
Nyctinastic movements
• The current model for motor cell
movement includes the contribution of K+
channels and H+ pumps.
– These events stimulate H+-ATPases.
– Inward-rectifying K+ channels, then inward-
rectifying Cl- channels, open.
– The change in osmotic potential of the cytosol
induces an influx of water.
– Cytosolic Ca2+ is restored by Ca2+-ATPases.
Nyctinastic movements
• Figure 23.21
• Seismonastic movements occur in
response to mechanical stimulation,
wounding, and intense heat.

• Thigmonastic movements are movements

in response to touch.

• The best studies seismonastic response is

that of Mimosa pudica.
• Figure 23.22
• There are three essential characteristics of
seismonastic responses.
– The response is extremely rapid.
– The response is an “all-or-none” response,
the response is not proportional to stimulus.
– Excitation is propagated from the point of
• The phloem may conduct electrical impulses.
– The symplastic connections between cells of the
phloem provide a continuous network for the
transmission of impulses.
– The signal can induce a depolarization of target cells
caused by changes in proton flux.
– The action potential stimulates K+ and sugar transport
to the apoplast, changing the water potential of the
motor cells.

• Turgorin may also be involved in propagating

the action potential like a neurotransmitter.
Photoperiodism and
Endogenous Clocks
Chapter 24
Learning objectives
• Understand aspects of photoperiodism
and its contribution to floral stimulation

• Know about the endogenous rhythms in

plants that create a biological clock

• Understand the genetic basis for circadian

rhythms in plants
Learning objectives
• Know the significance of photoperiodism in
nature, particularly for the latitudinal
distribution of plants
• Plants are capable of sensing the passage
of time as they have an innate biological

• The ability to sense the passage of time

during a 24-hr period is photoperiodism.
• Photoperiodism influences many aspects
of plant development, including:
– The shift from vegetative growth to flowering
– Tuber development
– Leaf fall
– Dormancy

• The role of photoperiodism in flowering

has received the most attention.
Photoperiodism and flowering
• There are three categories of
photoperiodic responses
– Short-day plants (SD plants) flower when
day length is shorter than a designated
– Long-day plants (LD plants) flower when
day length exceeds a designated length.
– The flowering of day-neutral plants (DNP) is
independent of day length.
Photoperiodism and flowering
• For SD and LD plants, there are obligate and
facultative requirements.

• Obligate plants must have the required

photoperiod in order to flower while facultative
plants will flower eventually, but flowering is
enhanced by the appropriate photoperiod.

• These requirements can be influenced by

environmental factors such as temperature.
Photoperiodism and flowering
• Figure 24.1
Photoperiodism and flowering
• Figure 24.2
Photoperiodism and flowering
• There are other flowering patterns.
– Long-short-day plants (LSD plants) flower if
a certain number of short days are preceded
by a certain number of long days.
– Short-long-day plants (SLD plants) have
the reverse flowering pattern.
– Intermediate-daylength plants flower in
response to days of intermediate length, but
remain vegetative in short or long days.
Photoperiodism and flowering
• There are other flowering patterns.
– Amphophotoperiodism shows a flowering
pattern opposite of the intermediate-daylength
– There are also other subtle variations in some
plant species.
Photoperiodism and flowering
• Figure 24.3
Photoperiodism and flowering
• The photoperiodic response to flowering
depends upon its behavior relative to the
critical daylength.

• Some plants can be induced to flower by

only a single exposure to the necessary
photoperiod (or inductive treatment).

• Induction can also occur in degrees.

Photoperiodism and flowering
• Plants measure daylength by sensing the
duration of the dark period.
– When Xanthium plants were grown under 24-
hr light-dark cycles, flowering occurred when
the dark periods exceeded 8.5 hrs.
– When the total length of the light-dark cycles,
or the ratio of light-dark length was changed,
the relative length of the night and day did not
influence photoperiodism.
Photoperiodism and flowering
• Plants measure daylength by sensing the
duration of the dark period.
– Interruption of the duration of the dark period
prevented flowering.
– The length of the dark period is determined by
the timing of light-off and light-on signals.
Photoperiodism and flowering
• Figure 24.4
Photoperiodism and flowering
• The observation in SD plants that red light
inhibition of flowering could be reversed
with far-red light suggested phytochrome

• The same is not true for all LD plants.

• Some evidence suggests that PhyA

promotes flowering in LDP plants, while
PhyB inhibits flowering.
Photoperiodism and flowering
• There is also evidence that blue light
controls photoperiod.

• Blue light promotes flowering in

Arabidopsis, suggesting the involvement
of cryptochromes.

• The cryptochrome gene CRY2 is known to

be involved in flowering.
Photoperiodism and flowering
• The initiation of flowering occurs in the apical
meristem and the axillary buds.

• Experiments where leaves and the apical

meristem were differentially illuminated showed
that the photoperiodic signal is perceived by the

• The signal to induce flowering could still be

transmitted by leaves that had been illuminated
although detached from the plant.
Photoperiodism and flowering
• Figure 24.5
Photoperiodism and flowering
• The sensitivity of leaves for inducing
flowering increases with decreasing leaf

• The leaves initiate a signal chain, perhaps

with a diffusable floral stimulus.

• This signal can move at a rate of up to 2.5-

3.5 mm hr-1.
Photoperiodism and flowering
• The term florigen has been used to
describe the transmissable signal that
induces flowering.

• Grafting experiments have indicated that

the signal is similar across plant species.

• The chemical identity of florigen has long

been a mystery.
Photoperiodism and flowering
• Figure 24.6
Photoperiodism and flowering
• While the hormone gibberellin induces flowering
in some plants, it is not “florigen”.

• Studies in Arabidopsis suggest that the gene

CONSTANS is involved in the generation of the
phloem-mobile signal.

• The FLOWERING LOCUS T gene is a possible

candidate for florigen because it is phloem
mobile and induces floral meristem identity
Photoperiodism and flowering
• Figure 24.7
Photoperiodism and flowering
• A preceding period of light makes the
inductive dark period for SD plants more
effective at inducing flowering.

• High fluence light following the dark

exposure is also important as it may
stabilize or prevent inactivation of the floral
The biological clock
• The endogenous biological clock is an
internal time-measuring system in plants.

• This clock contributes to the nyctinastic

movements of plants.

• Processes regulated by this clock differ

from simple diurnal phenomenon.
The biological clock
• Figure 24.10
The biological clock
• The rhythms driven by biological clocks
– Persist in the absence of external cues.
– Be reset by external signals such as light or
– Function independently of temperature.
The biological clock
• Endogenous free-running rhythms will persist
for several diurnal cycles under constant

• The length of a cycle is the period ( ) and the

period of a rhythm dictates its type.
– A circadian rhythm is a 24 hr period.
– A lunar rhythm is a 28 hr rhythm.
– An annual rhythm is a period of one year.
– An ultradian rhythm is less than 24 hrs in length.
The biological clock
• Figure 24.11
The biological clock
• The amplitude of the rhythm is the
difference between the maximum and
minimum of a peak.

• The amplitude of a free-running rhythm

usually diminishes under constant
conditions until it disappears.

• The cycle and its amplitude can be reset

by an external signal.
The biological clock
• Circadian rhythms can operate under
solar time and circadian time (CT).
– Solar time is a 24 hr day.
– Circadian time is the internal time based on
the free-running period.

• The phase of a free-running cycle that

corresponds to normal day is the
subjective day and to night is the
subjective night.
The biological clock
• Entrainment involves training a circadian
rhythm to a regular external signal.

• The signal that entrains the rhythm is

called a zeitgeber.
The biological clock
• Entrainment adjusts plants to circadian
rhythms to changes in photoperiod during
the course of the year or to periods longer
or shorter than 24 hrs.

• The rhythms can be shifted by short light

pulses, producing a phase jump that can
be seen in a phase response curve.
The biological clock
• Figure 24.12
The biological clock
• Figure 24.13
The biological clock
• The circadian rhythm is subject to temperature

• If plants are shifted from one temperature

regime to another, the period of the rhythm shifts
for a few cycles.

• However, the plant returns to its original period

after adjusting to the current temperature
The biological clock
• The circadian clock contributes to
– Chenopodium and other plants can be
induced to flower by a single dark period.
– A light pulse during the first 8-10 hrs inhibits
– The subsequent capacity of the plant to flower
as a function of the length of the dark period
shows a rhythmic pattern for 3+ cycles.
The biological clock
• The circadian clock contributes to
– Lemna purpusilla can be grown in the dark
with supplemental glucose.
– This allows photoperiod to be controlled by
skeleton photoperiods (15 min. pulses).
– When taken from continuous light to a 13 hr
schedule with skeleton photoperiods, the
plant flowered only when a long dark period
preceded a shorter dark period.
The biological clock
• Figure 24.14
The biological clock
• Figure 24.15
The biological clock
• The integration of photoperiodic time with
the biological clock has been explained in
terms of the external coincidence model.
– Time has two interacting components.
• The circadian clock
• A clock-regulated daylength measurement system
– The circadian clock sets a light-sensitive
phase within the light-dark cycle.
– A regulator controlling the cyclic output
increases in concentration until late afternoon.
The biological clock
• The integration of photoperiodic time with
the biological clock has been explained in
terms of the external coincidence model.
– In LD plants, the regulator activates flowering
genes if activated by light.
– This coordinates flowering with daylength.
– For SD plants, the regulator reaches
maximum at the beginning of the dark period.
– The regulator in SD plants may therefore act
as an inhibitor rather than initiator.
The biological clock
• Figure 24.16
The biological clock
• The plant circadian clock has three
– The phytochrome/cryptochrome input
– A central oscillator
– The output pathways, mediated by clock-
controlled genes
The biological clock
• Figure 24.17
The biological clock
• Examples of clock-controlled genes are:
– Chlorophyll a/b binding proteins (CAB)
– The Rubisco small subunit
– Rubisco activase
– PEP carboxylase kinase
The biological clock
• CCA1 and TOC1 provide a negative
feedback loop for the central oscillator.

• ELF3 helps to reset the clock.

• CONSTANS is part of the output pathway,

which initiates the floral signalling
The biological clock
• Figure 24.18
Photoperiodism in nature
• Photoperiodism allows plants to synchronize the
life cycle to track the change in seasons.

• Physiological ecotypes of plants can

genetically adapt to latitudinal photoperiods to
allow them to complete their life cycle.

• The latitudinal adaptation of plant

photoperiodism can directly affect humans, such
as in the case of common ragweed.
Photoperiodism in nature
• Figure 24.19
Flowering and Fruit
Chapter 25
Learning objectives
• Understand the molecular genetic basis of
flower initiation and development

• Know the contribution of vernalization to

the flowering response

• Understand the basic principles

associated with fruit set and development
Flower initiation and development
• Floral initiation and development involves
three sets of sequentially activated genes.
– Flowering-time genes determine when
flowering is initiated.
– Floral-identity genes shift vegetative tissues
to reproductive development.
– Organ-identity genes control the
development of the four whorls of floral
Flowering-time genes
• Flowering-time genes connect the florigen signal
to the production of floral organs.

• These genes have roles in:

– The leaf tissues producing the signal.
– The translocation of the signal to the apex.
– The activity of the signal in the apex.

• Mutations in these genes delay flowering, but

redundant pathways insure that it does occur.
Flowering-time genes
• One set of genes comprise the
autonomous pathway for floral initiation.

• The long-day pathway includes the GI

and CO genes and the floral stimulus FT.

• There is a gibberellin pathway and a

group of floral repressor genes
Flowering-time genes
• Figure 25.1
Floral- and organ-identity genes
• There are four known floral-identity genes.

• The expression of these genes in the

apical meristem increases with long days
or with gibberellins.
Floral- and organ-identity genes
• The LFY gene has a central role in
dictating floral meristem identity.

• LFY also activates genes like APETALA1.

• In Arabidopsis, the APETALA genes,

along with PISTILATA, and AGAMOUS all
encode organ identity genes.
Floral- and organ-identity genes
• The ABC model of floral development
describes how these floral-identity genes
interact to dictate the floral whorls.
– Recall that flowers like Arabidopsis have four
whorls: sepals, petals, stamens, and carpels.
– The flower can be divided into fields.
• Field A includes sepals and petals.
• Field B includes petals and stamens.
• Field C includes stamens and carpels.
Floral- and organ-identity genes
• The ABC model of floral development
describes how these floral-identity genes
interact to dictate the floral whorls.
– Sepals are dictated by the AP1.
– Petals are dictated by the AP1, AP3, and PI.
– Stamens are dictated by the AP3, PI, and AG.
– Carpels are dictated by AG.
– AP2 is required for all four whorls.
Floral- and organ-identity genes
• Figure 25.2
Floral- and organ-identity genes
• Figure 25.3
Floral- and organ-identity genes
• Given this model, it is possible to predict
the phenotype of plants with mutations in
one or more genes.

• These genes likely exert their effects on

floral and organ development by acting as
transcription factors that activate other
Floral- and organ-identity genes
• Figure 25.4
Temperature and the flowering
• The flowering of most plants is influenced to
some extent by temperature.

• For some, there is a qualitative or quantitative

relationship between flowering and a low
temperature treatment called vernalization.

• Vernalization allows plants to delay flowering

until the beginning of the next growing season.
• Vernalization occurs primarily in winter
annuals and biennials.
– For example, when the winter strain of rye is
sown in the fall, the germinated seedlings are
vernalized over the winter.
– When they resume growth in the spring, their
flowering is aligned to that of a facultative long
day plant.
• Vernalization occurs primarily in winter
annuals and biennials.
– Biennials are monocarpic plants that flower
and die in the second season following an
over-winter treatment.
– Biennials produce a rosette in the first year.
– After vernalization, the stems begins bolting
and the biennial plant flowers.
• Figure 25.5
• The temperatures required for
vernalization depend upon the plant
species and the duration of exposure.

• Within the effective range, vernalization is

proportional to treatment duration.

• The temperature optimum is higher for

short periods of treatment.
• Figure 25.6
• When most plants are vernalized, they are
left in an induced state.

• Plants can be devernalized by an

appropriate high temperature treatment.

• A neutral temperature prevents either

process from occurring.
• The vernalization signal can only be
perceived by the shoot apex.

• The nature of the vernalization response is

energy dependent but not entirely clear.

• There is also some evidence that the

vernalization signal is transmissible,
perhaps as vernalin.
• Gibberellins may also play a role in
vernalization, with the cold treatment
needed to complete synthesis of this

• Gibberellins can also replace the cold

requirement for some plants, but through a
different pathway.
• In cereals, there are three genes involved
in vernalization.
– VRN1, a transcription factor induced by
– VRN2, a repressor which blocks FT
– VRN3, the cereal equivalent of FT

• These three genes interact to regulate

• In the absence of a low temperature
treatment, VRN2 represses VRN3.

• After the cold treatment is imposed,

expression of VRN1 prevents expression
of VRN2.

• This releases the suppression of VRN3 so

that VRN3 can induce flowering.
• In Arabidopsis, FLOWERING LOCUS C
(FLC) suppresses FT.

• FLC is regulated by low temperature

through a complex derived from VRN1 and
• Figure 25.7
Fruit set and development
• Fruit development has five phases.
– The events from the development of the ovary
prior to fertilization through the decision to
proceed with fruit set
– Cell division in the ovary walls to initiate fruit
– Cell enlargement to increase cell and
therefore fruit size
– Ripening, including the development of color
and flavor
– Senescence and fruit decay
Fruit set and development
• Fruit development involves an interaction
between plant hormones.
– Auxin, cytokinin, and gibberellin are important
during the first and second phases.
– Auxin and gibberellin are involved in the third
– Auxin and ethylene peak during the fourth
Fruit set and development
• Figure 25.8
Fruit set and development
• Fruit development typically requires
fertilization to have occurred.

• Fruit development that occurs in the

absence of fertilization is parthenocarpy.

• Parthenocarpy can be induced by auxin.

Fruit set and development
• The seeds themselves can also provide
auxin necessary for fruit initiation.

• Evidence for this role has come from

studies where:
– Auxin synthesis in the ovary was enhanced
– Auxin regulatory proteins were manipulated
Fruit set and development
• Figure 25.9
• Ethylene triggers ripening in climacteric
fruits such as apple, banana, and tomato.

• Ethylene synthesis, and hence ripening, is

auto-catalytic, which is why some fruits are
picked green and ripened artificially.

• Ethylene synthesis is controlled by the

ACS and ACO genes.
• Figure 25.10
Temperature and Plant
Chapter 26
Learning objectives
• Understand the role of temperature in bud
and seed dormancy

• Understand how temperature influences

the geographical distribution of plants
Plants and temperature
• Like all living organisms, plant growth and
development is sensitive to temperature.

• The range of temperatures over which

plants can function include the three
cardinal temperatures.
– The minimum temperature for function
– The optimum temperature for function
– The maximum temperature for function
Plants and temperature
• The temperature curve for the cardinal
temperatures for plants represents a
composite of the temperature curves for
metabolic processes such as:
– Photosynthesis
– Respiration
Plants and temperature
• Figure 26.1
Plants and temperature
• Plants can be classified according to their
ability to withstand temperature.
– Psychrophiles have a temperature optimum
between 0º and 10ºC.
– Mesophiles have a temperature optimum
between 10º and 30ºC.
– Thermophiles have a temperature optimum
between 30º and 65ºC.
Plants and temperature
• The temperatures of air, soil, and water all
impact plant growth and development.

• Air temperature affects processes such as

photosynthesis and respiration.

• Soil temperature affects processes such

as germination and nutrient uptake.
Bud dormancy
• Temperature has a strong influence on

• Dormancy occurs in several types of plant

tissues that do not grow, even when factors are
favorable for growth.

• Dormancy is a progressive condition and can be

broken by different factors depending upon the
degree of dormancy in the tissue.
Bud dormancy
• There are three dormancy mechanisms.
– Paradormancy is imposed on a tissue by
another tissue within the same plant.
– Ecodormancy is environmentally imposed.
– Endodormancy is inherent to a structure.

• An example of endodormancy is the

dormancy of axillary buds within the bud
Bud dormancy
• Dormancy in tissues like buds is initiated
before the unfavorable conditions emerge.

• Tissues can therefore anticipate the

change in conditions to induce dormancy
and then can perceive when favorable
conditions return.
Bud dormancy
• Photoperiod, often in conjunction with
temperature, are signals that can be used
to signal the need for dormancy.

• The signal to initiate dormancy is

perceived in the leaves and involves
similar genes to those involved in the
response to photoperiod.
Bud dormancy
• While temperature helps induce
dormancy, it primarily breaks dormancy.

• Most buds have a chilling requirement,

particularly those one fruit trees.

• Temperatures near freezing are the most

effective at breaking dormancy.
Bud dormancy
• The duration of the temperature treatment
needed to break dormancy varies by

• The mechanism involved in the breaking

of dormancy in poplar (Populus spp.)
involves inhibition of a FLOWERING
LOCUS C suppressor gene.
Seed dormancy
• Dormancy is also imposed upon seeds.

• Releasing some seeds from dormancy

requires mechanical disruption of the seed
coat through scarification.

• The release of seeds from dormancy also

requires access to water and oxygen,
either through the hilium or a strophiolar
Seed dormancy
• Chemical inhibitors present in seeds may also
impose dormancy on seeds.

• Breaking the seed coat increases the water and

oxygen movement into the seed but also allows
inhibitors to leach out.

• Examples of inhibitors include hormones,

coumarin, ferulic acid, cyanogenic compounds,
and some amino acids.
Seed dormancy
• Depending upon the plant species,
specific patterns of temperature can
release a seed from dormancy.

• After imbibition, most seeds require a

diurnal cycle of temperature.

• Some seeds require stratification, a pre-

chilling treatment different from
Seed dormancy
• The temperature and the duration of
treatment both contribute to the
stratification treatment.

• Stratified seeds undergo metabolic

changes called after-ripening once
dormancy has been broken.

• Gibberellins can substitute to some extent

for the need for stratification.
Seed dormancy
• Figure 26.5
• Thermoperiodism involves a pattern of
diurnal temperature differences that allow
plants to grow and development more
vigorously than at a single temperature.

• Thermoperiodism primarily affects

vegetative growth, which differs from the
photoperiodism effect on flowering.
• In some species, floral movements can be
influence by temperature.

• These movements are a form of

differential growth called thermonasty.

• Opening and closing caused by opposing

effects of temperature on the growth of
abaxial and adaxial surfaces of the tepals.
• Figure 26.6A
• Figure 26.6B
Temperature and plant distribution
• Temperature influences the distribution of
plants across the Earth.

• Biogeography includes the effects of

temperature on plant physiology,
metabolism, and distribution.

• Most plants survive in the temperature

range between 0º and 45ºC, but some can
survive outside this range.
Temperature and plant distribution
• The optimum temperature for plant growth
reflects the temperature of the area where
the plant originated

• Some plants can only survive under the

temperature regime where they originate.

• Some plants can acclimate to different

temperature regimes.
Temperature and plant distribution
• Temperature has a significant effect on the
distribution of C3 and C4 grasses.

• The change in temperature with elevation

(adiabatic lapse) is one example.
Temperature and plant distribution
• Figure 26.7
Secondary Metabolites

Chapter 27
Learning objectives
• Understand the synthesis, physiological
roles, and ecological roles of plant
secondary metabolites, including the
– Terpenes
– Phenolic compounds
– Glycosides
– Alkaloids
Secondary metabolites
• The organic molecules involved in
respiration, photosynthesis, and other
pathways central to the function of plants
are called primary metabolites.

• Plants also divert a significant fraction of

assimilated carbon and energy to
secondary metabolites that are not
essential to cellular function, but are
Secondary metabolites
• Secondary metabolites, or natural
products, are derived from primary
metabolites but are typically found at much
lower concentrations.

• These compounds often have medicinal or

economic value.
Secondary metabolites
• Figure 27.1
• Terpenes are secondary metabolites
synthesized from isoprene subunits.

• Terpenes are grouped into classes based

upon the number of carbon atoms, which
occur in multiples of five.
• Examples of terpenes include:
– Gibberellins
– Carotenoid pigments
– Sterols (e.g., cholesterol)
– Sterol derivatives (e.g., cardiac glycosides)
– Latex
– Essential oils
• Figure 27.2
• Figure 27.2
• Essential oils are ten carbon terpenoids
that create the characteristic odor of mint
and many herbs.

• These are volatile compounds often stored

at or on the leaf surface in glands or cells.

• Ironically, these compounds also

contribute to some aspects of air pollution.
• Figure 27.3
• Figure 27.4
• Figure 27.5
• Steroids and sterols are cyclic terpenoids
with < 30 carbon atoms.

• The most common examples in plants are

stigmasterol and sitosterol.

• There are >150 different examples found

across different plant species.
• Figure 27.6
• The primary function of plant sterols is to
increase the viscosity and enhance the
stability of plant membranes.

• Sterols such as the phytoecdysones

defend against insect herbivores by
emulating plant molting hormones.
• The polyterpenes have >40 carbon atoms.

• The primary example in plants are the

carotenoid pigments.

• Larger polyterpenes are rubber and

• Figure 27.2
• Rubber occurs in small particles in the
latex from plants.

• Latex is produced in the phloem and is

stored in laticifers.

• Gutta is obtained from the desert shrub

guayule (Partenium argentatum).
• Glycosides consist of a sugar condensed with a
molecule with a hydroxyl group.

• Most glycosides are herbivory deterrents.

• Typical examples are the:

– Saponins
– Cardiac glycosides
– Cyanogenic glycosides
– Glucosinolates
• There are three forms of saponins.
– Steroid glycosides
– Steroid-alkaloid glycosides
– Triterpene glycosides

• Saponins also occur as aglycones called


• Saponins have properties of surfactants.

• Figure 27.8
• Saponins, such as avenacin A-1, provide
a chemical defense against fungal attack.

• Saponins react with sterols in the fungal

hyphae to weaken fungal membranes.

• Some fungi produce enzymes, such as

avenacinase, to detoxify the saponin so
the fungi can attack the plant.
• To protect their own membranes from
saponins, plants may store these
compounds as bidesmodic saponin.

• Fungal attack would stimulate the

conversion to the monodesmodic form.

• Saponins have both positive and negative

effects on animals.
• Cardiac glycosides, or cardenolides,
are steroid saponins with a lactone ring
and rare sugars.

• Digitalis, a cardenolide mixture from

foxglove, is composed of the cardenolides
digitoxin and digoxin.

• Foxglove is also the source of digitonin.

• Figure 27.9
• Digitalis influences the ATPase pumps in
the mammalian heart.
– Digitalis is highly toxic to vertebrates.
– Digitalis can be used therapeutically if the
dose is closely monitored.

• Some organisms, like the caterpillars of

the monarch butterfly, store cardenolides
from the foods they eat as a defense.
• Cyanogenic glycosides such as
amygdalin or dhurrin contain cyanide.

• When a herbivore damages the plant, a b-

glucosidase releases the sugar.

• A hydroxynitrile lyase then facilitates the

release of the poisonous cyanide
• Figure 27.10
• Cyanogenic glycosides act principally
against insects, but animals can detoxify
small amounts of cyanide.

• Cyanogenic glycosides can also be found

in many common foods, but can be
removed so the food is safely edible or are
present at low concentrations.
• Glucosinolates are sulfur-containing
compounds (thioglucosides) found
primarily in the mustard family.

• The active form of these compounds are

the mustard oils.

• The presence of glucosinolates influences

the quality of oil from oilseeds like canola.
• Figure 27.11
• Aromatic amino acids are the precursor of the
phenylpropanoids, also called the phenolics
or the polyphenols.

• Some phenolics are involved in plant/herbivore

interactions while others are structural.

• Examples of phenolics include:

– Lignins and tannins
– Flavonoid pigments
• Figure 27.12
• Aromatic amino acids (phenylalanine,
tryptophan, and tyrosine) are synthesized
by the shikimic acid pathway.
– Synthesis begins with erythrose-4-phosphate
and phophoenolpyruvate, forming shikimate.
– Shikimate is converted to chorismate.
– The pathway branches after chorismate so
that one branch leads to phenylalanine and
the other branch to the tyrosine and
• Figure 27.13
• One of the steps involved in the
conversion of shikimate to chorismate is
catalyzed by 3-enolpyruvylshilimate-5-
phosphate synthase (EPSPS).

• The action of this enzyme is inhibited by

glyphosate, the active chemical in
herbicides such as RoundUpTM.
• The synthesis of phenolics involves
phenylalanine ammonia lyase, which
deaminates phenylalanine to form cinnamic

• Cinnamic acid is converted to p-coumaric acid,

and then to caffeic and ferulic acid.

• These phenols are precursors for the remaining

• Figure 27.14
• Figure 27.15
• Coumarins are a diverse group of >1,500
lactones called benzopyranones.

• Coumarins are antimicrobial compounds,

feeding deterrents, and germination

• Derivatives of coumarin, such as

dicoumarol and aflotoxins, can be highly
• Figure 27.16
• Figure 27.17
• Lignin is a large, irregular polymer of

• Lignin synthesis involved peroxidase.

• Lignin is deposited in secondary cell walls

in the xylem for structural support and as a
defensive chemical.
• Figure 27.18
• Flavonoid molecules are involved in:
– Pollinator attraction (anthocyanin pigments)
– Phytoalexins, antibacterial, and antifungal
agents (isoflavonoids)
– Symbiont recognition

• Flavonoids are a diverse groups of >4,500

compounds with a three-ring structure (A,
B, and C rings).
• Flavonoids are derived from malonic acid
and malonyl-CoA.

• Chalcone synthase catalyzes the first

committed step in the biosynthesis of
flavonoids such as naringenin.

• Naringenin is a precursor for flavonols

such as kaempferol and quercitin.
• Another group of flavonoids are the
stilbenes, defensive compounds against
fungal invasion of heartwood.

• Stilbenes are also derived from malonyl-


• Stilbene synthase is the enzyme that

commits the pathway to stilbene synthesis.
• Figure 27.19
• There are two types of tannins.
– Condensed tannins are polymers of flavonoid
units linked by strong carbon bonds.
– Hydrolyzable tannins can be oxidized by
strong acids.

• Tannins are composed of a sugar (usually

glucose) esterified to gallic acid.
• Figure 27.20
• The biological role of tannins is not clear.

• Tannins act as a feeding deterrent to


• Tannins may also reduce the digestibility

of dietary proteins.
Insecticidal and antimicrobial
• Several terpenes and isoflavones have
activity against insects and microbes.

• Pytrethrin is a monoterpene that is toxic

to insects.

• Isoflavones called phytoalexins help limit

the spread of infection.
Insecticidal and antimicrobial
• Figure 27.21
Insecticidal and antimicrobial
• Figure 27.22
Plant “immunity”
• The susceptibility or tolerance to pathogens is
determined by a gene-for-gene model.

• The model predicts that resistance occurs when

the pathogen has a dominant avirulence (Avr)
locus and the plant has a dominant resistance
(R) locus.

• These genes may encode elicitors and

receptors, respectively, involved in the
hypersensitive response.
Plant “immunity”
• Figure 27.23
Plant “immunity”
• The hypersensitive reaction leads to a general
immunity called systemic acquired resistance

• Salicylic acid (SA) and/or methylsalicylate are

the signal molecules for SAR.

• The interaction between regulatory protein NON

transcription factors is facilitated by SA.
Plant “immunity”
• Plant resistance to insects and disease is
also mediated by jasmonic acid and/or

• Jasmonates accumulate in response to

wounding and activate genes associated
the response to fungal infection.
Plant “immunity”
• Jasmonates are synthesized from the
linoleic acid in the membrane

• Jasmonates promote the binding of JAZ

repressors to the E3 ubiquitin ligase,
which degrades this ligase and activates
jasmonate-responsive genes.
• Alkaloids are secondary metabolites that
– Are soluble in water
– Contain nitrogen
– Have high biological activity.

• Alkaloids are generally heterocyclic but

there are some aliphatic examples such as
mescaline and colchicine.
• Many chemicals used as pharmaceuticals are

• The chemicals from opium, including morphine,

codeine, and papaverine, are alkaloids.

• Hemlock contains coniine.

• Peyote contains mescaline.

• Figure 27.24
• Alkaloids are usually synthesized from:
– Tyrosine
– Tryptophan
– Lysine
– Ornithine or argenine

• In contrast:
– Nicotine is synthesized from nicotinic acid.
– Caffeine is derived from a purine derivative.
• Figure 27.25
• The types of alkaloids present are often
specific to the plant species.
– Lupinine, a chemical that poisons livestock,
is found in the seeds of lupines.
– Other poisons that afflict livestock include:
• Senecionine
• Lycotonine
• Scolpamine
• Atropine
• The nightshade plants have alkaloids that
may negatively affect human health.

• Alkaloids such as vinblastine and

vincristine from periwinkle have a health
benefit by fighting cancer.
• Alkaloids are used by plants as defensive
– Their bitter taste is a deterrent to herbivores.
– Most alkaloids show some toxicity to insects
and/or animals.
– Many alkaloids are also antimicrobial.

• Alkaloids tend to accumulate in young

tissues vulnerable to herbivory.