Plant Pigments - Bioenergetics - and Lights

Plant Pigments and
plastids
Hopkins & Huner, 2009

Today’s Overview
1) Plant pigments
– Biological, physical and chemical character of plant
pigments
2) Energy transformation  Bioenergetics
3) Role of sunlight and pigment interaction
– The nature of lights: Concept, and units in the
measurement of light
– Light reactions (How do plants capture light?)
– Light, leaves, and photosynthesis.

Learning objectives
Student will be able to:

• Explain biological, physical and
chemical character of plant pigments
• Explain the roles of pigments in
plants

Plant leaves have many types of cells

Plant Cells

Plastids
There are several forms of plastids:
1. Proplastids - precursor of all plastids, found

in meristems
2. Etioplasts - form in shoots of dark-grown
plants, distinctive internal structure
3. Chloroplasts
4. Amyloplasts - prominent in roots, store starch,
colorless
5. Chromoplasts - in mature fruit, lots of
carotenoids, little chlorophyll
From U. Wisconsin Botany Dept.
Plastids
• Contain
pigments or
storage
products
1. Chloroplasts
2. Chromoplasts
3. Amyloplasts
Cells of a red pepper

The photograph below is an Elodea leaf 100x.
Individual cells are clearly visible. The tiny green
structures within the cells are chloroplasts
this is where photosynthesis happens.

Amyloplasts store Starch

Plastid development & plastids functions

Isolated Spinach chloroplast
thylakoid membrane envelope
stroma From Hoober

Young chromoplast from developing tomato fruit
From Gunning and Steer
Stars mark lycopene crystals; many plastoglobuli

Plastid development is plastic & mostly under
nuclear control.
Shoots:
light
proplastids etioplasts chloroplasts
chromoplasts
Roots:
proplastids amyloplasts

Chloroplasts make the sugars!

Chloroplasts
make the
oxygen too!

Chloroplasts
• A chloroplast contains:
– stroma, a fluid
– grana, stacks of thylakoids
• The thylakoids contain chlorophyll
– Chlorophyll is the green pigment that captures
light for photosynthesis

The location and structure of chloroplasts
Chloroplast
LEAF CROSS SECTION MESOPHYLL CELL
LEAF
Mesophyll
CHLOROPLAST Intermembrane space
Outer
membrane
Granum Inner
membrane
Grana Stroma Thylakoid
Stroma Thylakoid compartment
WHY ARE LEAVES GREEN?
Are they always green?
• Leaves are green
because they
contain the
pigment
• Leaves have a
large surface area
to absorb as much
light as possible
WHY ARE PLANTS GREEN?
Reflected
Light light
Absorbed
• Plants are green because the light
green wavelength is reflected, Transmitted Chloroplast

light
not absorbed.
Chloroplast Pigments
• Chloroplasts contain several pigments
– Chlorophyll a
– Chlorophyll b
– Carotenoids
– Xanthophyll
• Carotenoids are pigments that are

either red or yellow.

Pigments
Chlorophyll pigments harvest energy (photons)
by absorbing certain wavelengths (blue-420
nm and red-660 nm are most important).
• Chlorophyll a is the main photosynthetic pigment

• Accessory pigments, such as chlorophyll b,
broaden the spectrum used for photosynthesis
• Accessory pigments called carotenoids absorb
excessive light that would damage chlorophyll

Absorption spectrum

Chlorophyll
• 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.

Chlorophyll Molecules
Chlorophyll a & b
•Chl a has a methyl
group
•Chl b has a carbonyl

group
Porphyrin ring
delocalized e-
Phytol tail
Photosynthetic Pigments:
The Light Receptors
• Pigments are substances that absorb visible light

• Different pigments absorb different wavelengths
• Wavelengths that are not absorbed are reflected
or transmitted
• Leaves appear green because chlorophyll
reflects and transmits green light

Energy transformation
BIOENERGETICS

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.
• Understand the role of oxidation-reduction reactions in
biological energy transformations.
• Understand the structural features of two energy-
transducing organelles – the chloroplast and the
mitochondria.
• Understand the chemiosmotic model for the synthesis of ATP
in chloroplasts and mitochondria.
Bioenergetics
• 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.

Bioenergetics
• 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.
Bioenergetics
• 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.

Bioenergetics
• 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
entropy.
– The opposition of entropy requires energy.
Bioenergetics
• 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.
Bioenergetics
• 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.

Bioenergetics
• 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.
Bioenergetics
• Figure 5.1

Bioenergetics
• The relationship between G and the
equilibrium constant (Keq) of a reaction can
be expressed as:
G = Gº' + RT ln Keq
• Or in a form showing the displacement of

a reaction from equilibrium:
Keq
G =  2.3 RT 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
example:
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
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
homeostasis.
coupled reactions
• Figure 5.2
Adenosine triphosphate (ATP).

(A) The ATP molecule consistsof
adenine (a nitrogenous base),
ribose (a sugar), and three
terminal phosphate groups. (B)
Hydrolysis of ATP yields ADP
(adenosinediphosphate) plus an
inorganic phosphate molecule

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.

• Figure 5.3
The chemical structures of some common biological
redox agents in oxidized and reduced states. (A)
Nicotinamide adenine dinucleotide (NAD) and
nicotinamide adenine dinucleotide phosphate (NADP).
Note that only the nicotinamide ring is changed by the
reaction. The nicotinamide ring accepts two electronsbut
only one proton. Arrow indicates where the electrons are
added to the nicotinamide ring. (B) Flavin adenine
dinucleotide (FAD) consists of adenosine (adenine plus
ribose) and riboflavin (ribitol plus isoalloxazine). Flavin
mononucleotide (FMN) consists ofriboflavin alone.
Reduction occurs on the isoalloxazine moiety, which
accepts two electrons and twoprotons. (C)
Quinones. A quinone ring is attached to a hydrocarbon
chain composed of five-carbon isoprene units. The value
of n is usually 9 for plastoquinone, found in chloroplast
thylakoid membranes, and 10 for ubiquinone, found in
the inner membrane of mitochondria. Reduction of the
quinone ring is a two-step reaction. The transfer of one
electron produces the partially reduced, negatively
charged semiquinone (not shown). Addition of a second
electron plus two protons yields
the fully reduced hydroquinone form.

• 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.
• The free energy of a redox reaction can be
determined from the redox potentials.
Gº' = -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.
• 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 is the movement of ions across a
semipermeable membrane, down their electrochemical
gradient. An example of this would be the generation of
adenosine triphosphate (ATP) by the movement of
hydrogen ions across a membrane during cellular
respiration or photosynthesis.

• Figure 5.4
Electron micrograph ofa

mesophyll chloroplastof
maize (Zea mays). S,
stroma; G, granum; P,
peripheral reticulum; E,
envelope membrane;
CW, cell wall

• 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.
• The stroma of the chloroplast is largely protein,
most of which is the photosynthetic enzyme
Rubisco.
• 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.
• Figure 5.7A

• 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
membranes
– The matrix inside the inner membrane
• Plant mitochondria have inner membrane

formed into a system of tubes and sacs instead
of cristae.
• Figure 5.7b

• 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
“reservoir”.
– 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.

Outside
inside
• Figure 5.9
ATP synthase is an enzyme

that creates the energy
storage molecule adenosine
triphosphate (ATP). ATP is
the most commonly used
"energy currency" of cells
for most organisms.
Active site ATP sythesis

• The proton circuit which synthesizes ATP in the
chloroplast is a light-dependent process called
photophosphorylation.
• The chemiosmotic synthesis of ATP in the

mitochondrial, drive by aerobic respiration, is
called oxidative phosphorylation.
• ATPase proton pumps are proteins related to

ATP synthases, but create proton gradients
across membranes.
Role of Sunlight and plant
pigment interaction

Learning objectives
• Understand the nature of light and its
interaction with matter.
• Understand the light environment of plants.
• Understand the nature of plant pigments and their
role in the capture of light.
• Understand what occurs in the light-dependent
and light- independent reactions of photosynthesis
• Understand the principal products of the reactions

Sunlight
• Sunlight is a source of energy which drives
photosynthesis.
• 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 photobiology.

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

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.
c
=

– The frequency () is the number of wave crests per
second.
– The wavelength () is the distance between crests of
the wave.
– The speed of light is c.
The nature of light
• Figure 6.2
Wave nature of light.
Electric vectors (E) and
magnetic vectors (H)
oscillate at 90◦ to each other.

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
principle.
• A molecule that absorbs light is a pigment.

• 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.
• 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
molecule.
• 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.
• 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

• Light quantity is measured in terms of the
fluence.
– Photon fluence is the total number of incident
photons.
– Energy fluence is the total amount of incident
energy.
– These fluence terms can also be expressed as the
photon fluence or energy fluence rate.
– The energy fluence rate is also referred to as
irradiance.
– Visible light relevant to photobiological processes is
broadly defined as photosynthetically active
radiation (PAR).
• 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.
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.

• Figure 6.6

• Ultraviolet radiation absorbed by
molecules produces highly reactive
molecules.
• If a living organism absorbs UV light,

the reactive molecules produced can
be deleterious.

• 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
sunlight.

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).

• 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.

• Figure 6.8
Absorption spectra
of chlorophyll a
(broken
line) and
chlorophyll b(solid
line) in acetone.

• 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.
• An important phycobiliprotein in plants 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.

• 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
photooxidation.
• Figure 6.12
Absorption spectra of
α-carotene (solidline)
and β-carotene
(broken line)

• Blue light and UV-A radiation is perceived
by cryptochrome and phototropins.
– The chromophore for cryptochrome is a
flavin, such as riboflavin or its derivatives
flavin mononucleotide and flavin adenine
dinucleotide (FAD).
– While these flavins can form flavoproteins that
participate in light absorption, most flavins
acts as cofactors in cellular redox
reactions.
– 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.

• 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
anthocyanins.
• 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.

– Because of the absorbance in the UV range,
flavonoids provide plants with a natural sunscreen.
– Other flavonoids serve as an attractant for
insect pollinators.
– 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.

Funneling of excitation from the antenna
system toward the reaction center.

Further reading
• Hopkins & Huner 2009 Introduction to Plant
Physiology 4th. ed: Chapter 5 Bioenergetics
and ATP synthesis & Chapter 6 The dual
role of sunlight: Energy and Information

Plant Pigments - Bioenergetics - and Lights

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Plant Pigments and

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Student will be able to:

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

1. Proplastids - precursor of all plastids, found

Cells of a red pepper

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

thylakoid membrane envelope

stroma From Hoober

From Gunning and Steer

Stars mark lycopene crystals; many plastoglobuli

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

CHLOROPLAST Intermembrane space

green wavelength is reflected, Transmitted Chloroplast

• Carotenoids are pigments that are

Hopkins & Huner, 2009

• Chlorophyll a is the main photosynthetic pigment

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

•Chl b has a carbonyl

• Pigments are substances that absorb visible light

Hopkins & Huner, 2009

Hopkins & Huner, 2009

• Bioenergetics is the study of the energy

• There are two broad strategies by which

Hopkins & Huner, 2009

• In the biological context, there are

• Bioenergetics is the application of

Hopkins & Huner, 2009

– H is the total heat energy (enthalpy)

Hopkins & Huner, 2009

Hopkins & Huner, 2009

• Or in a form showing the displacement of

• Coupled reactions are spontaneous if the net

ATP  ADP + Pi Gº’=-32.2 kJ mol-1

Adenosine triphosphate (ATP).

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009

• This mechanism by which this occurs is called

• These double-membrane structure of

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Electron micrograph ofa

Hopkins & Huner, 2009

• The network of grana and stroma thylakoids

• The lumen of the thylakoids play a key role in

Hopkins & Huner, 2009

• Plant mitochondria have inner membrane

Hopkins & Huner, 2009

Hopkins & Huner, 2009

Hopkins & Huner, 2009