Module 5

Photosynthesis and the Chloroplast

Copyright ©2020 John Wiley & Sons, Inc.

Learning objectives:
By the end of this module, you should be able to:
▪ Explain the roles of autotrophs, cyanobacteria, and chloroplast in the origin of
photosynthesis.
▪ Describe the structure of a chloroplast.
▪ Identify the roles in photosynthesis of the light-dependent reactions and the light-
independent reactions.
▪ Compare the structures, absorption, and functions of chlorophylls and carotenoids.
▪ Identify the functions of chromoplasts.
Which of the following is a usual component found in
the chloroplast stroma?

a) tRNAs

b) eukaryotic-like ribosomes

c) circular DNA

d) Both tRNAs and circular DNA

The Origin of Photosynthesis
▪ Heterotrophs: Organisms that depend on an external source of organic
compounds
▪ Autotrophs: Organisms capable of surviving on CO2 as their principal carbon
source.
• Chemoautotrophs use energy from inorganic molecules (such as ammonia,
hydrogen sulfide, or nitrites) to convert into organic compounds.
• Photoautotrophs use radiant energy to make organic compounds.
• Plants and eukaryotic algae, various flagellated protists, and members of several
groups of prokaryotes.
• Photosynthesis: a process in which energy from sunlight is transformed into
chemical energy that is stored in carbohydrates and other organic molecules.
The Origin of Photosynthesis
▪ Photosynthesis converts energy from sunlight
into chemical energy stored in carbohydrates.
▪ First groups of photoautotrophs, utilized
hydrogen sulfide (H2S) as their source of
electrons for photosynthesis.
light
CO2 + 2H2S → (CH2O) + 2S
where (CH2O) represents a unit of carbohydrate

▪ Nowadays, H2S is neither abundant nor

widespread so green sulfur bacteria are
restricted to habitats such as sulfur springs and
deep-sea vents.
Fig. 6.1 Photosynthetic green sulfur bacteria
The Origin of Photosynthesis

▪ Around 2.7 – 2.4 billion years ago, a new type of photosynthetic prokaryote
appeared on Earth that was able to utilize electrons from water.
light
CO2 + H2O → (CH2) + O2
▪ Cyanobacteria
▪ The use of water also led to the production of a waste product, molecular
oxygen (O2)
The Origin of Photosynthesis

▪ An ancient O2-producing cyanobacteria took up residence inside a

mitochondria-containing, non-photosynthetic, primitive eukaryotic cell.
▪ Cytoplasmic organelle, the chloroplast.

▪ As the chloroplast evolved

▪ Genes were lost or transferred to the plant cell nucleus.

▪ Due to their common ancestry, chloroplasts and cyanobacteria share many

basic characteristics, including similar photosynthetic machinery.
Chloroplast Structure
▪ Photosynthesis in eukaryotes takes place in
the chloroplast, a cytoplasmic organelle.
▪ Chloroplasts are located predominantly in
the mesophyll cells of leaves
▪ 20 - 40 per cell
▪ Chloroplasts arise by fission from preexisting
chloroplasts, or their nonpigmented
precursors (proplastids).
Chloroplast Structure
Chloroplasts have a double membrane:
• Outer envelope membrane contains
several different porins, like mitochondria
outer membranes.
• Inner envelope membrane is highly
impermeable; a variety of transporters.

Fig. 6.3 Internal structure of a chloroplast

Chloroplast Structure
• The internal membrane system is physically
separate from the double-layered envelope.

• The chloroplast internal membrane is organized

into flattened membranous sacs called
thylakoids, arranged in orderly stacks called
grana.

• It contains photosynthetic machinery such as

light-absorbing pigments, a complex chain of
electron carriers, and an ATP-synthesizing
apparatus.

Fig. 6.3 Internal structure of a chloroplast

Chloroplast Structure
• The space inside a thylakoid sac is the lumen.
• The space outside the thylakoid and within the
chloroplast envelope is the stroma that
contains the enzymes responsible for
carbohydrate synthesis.
• The thylakoid membrane contains the
chlorophyll molecules and protein complexes
that comprise the energy-transducing
machinery of the chloroplast.

Fig. 6.3 Internal structure of a chloroplast

Chloroplast Structure
• Stroma components include small, double-stranded
circular DNA molecules and prokaryotic-like
ribosomes.
• Chloroplast DNA is a relic of the genome of an
ancient bacterial endosymbiont.
• Chloroplast DNA contains tRNAs, rRNAs, ribosomal
proteins, or genes involved in photosynthesis.
• Thylakoid membranes have a high protein content
and a high percentage of galactose-containing
glycolipids.
• Membrane fluidity facilitates lateral diffusion of protein
complexes through the membrane during
photosynthesis.

Fig. 6.3 Internal structure of a chloroplast

An Overview of Photosynthetic Metabolism

▪ Photosynthesis is a redox reaction transferring an electron from water to carbon

dioxide:
6 CO2 + 12 H2O → C6H12O6 + 6 H2O + 6 O2
▪ O2 is derived not from CO2 but from the breakdown of two H2O molecules
(absorption of light)
▪ Photosynthesis occurs in two stages:
1. Light-dependent reactions (light reactions) in which sunlight is absorbed,
converting it into ATP and NADPH.
-ATP and NADPH are the cell’s primary sources of chemical energy and reducing power,
respectively.
2. Light-independent reactions (dark reactions) use the energy stored in ATP and
NADPH to produce carbohydrates.
An Overview of Photosynthetic Metabolism

Fig. 6.5 An overview of the energetics of photosynthesis and aerobic respiration

The Absorption of Light
▪ Absorption of photons (light “particles”) by a
molecule makes them go from ground state to
excited state.
▪ In the excited state an electron becomes
sufficiently energetic to be pushed from an inner
to an outer orbital

Fig.6.6 The structure of chlorophyll a

The Absorption of Light

▪ Energy in the photon depends on the wavelength of

light.
▪ Photosynthetic pigments are molecules that absorb
light of particular wavelengths.
▪ Chlorophyll contains:
1. a porphyrin ring that absorbs light
2. a hydrophobic tail embedding it to the photosynthetic
membrane.

Fig.6.6 The structure of chlorophyll a

The Absorption of Light

▪ Several different classes of chlorophyll occur among

photosynthetic organisms, and they differ from each
other in the side groups attached to the porphyrin ring.

▪ The types of chlorophylls are:

• Chlorophyll a - in all O2-producing photosynthetic
organisms but missing from sulfur bacteria.
• Chlorophyll b - in all higher plants and green algae.
• Bacteriochlorophyll - only in green and purple bacteria.

Fig.6.6 The structure of chlorophyll a

The Absorption of Light
▪ The alternating single and double bonds along the porphyrin ring form a
cloud making it a conjugated system (allowing absorption of a range of
wavelengths).
▪ Besides chlorophyll, there are accessory pigments called carotenoids
(absorb light in the blue-green region of spectrum).
▪ Carotenoids produce the characteristic colors of carrots and oranges and the
leaves of some plants during the fall.
▪ They act as secondary light collectors during photosynthesis

Fig. 6.7 Absorption spectrum: three

photosynthetic pigments of higher plants
Green Cells: Chromoplasts
▪ Plant cells also contain a related organelle called
a plastid.
▪ Chromoplasts are a family of plastids whose
primary function is to be colorful.
▪ Many fruits start out green and change color as
they ripen → this is because the plant’s
chloroplasts undergo structural and molecular
changes to make them chromoplasts.
▪ Chromoplast pigments include:
• Carotene (i.e., carrots)
• Lycopene (tomatoes)

Fig. 6.9 Chromoplasts within the cells

of a red pepper
Green Cells: Chromoplasts
▪ When leaves turn color in autumn, the chlorophyll
inside chloroplasts is degraded, leaving behind
the carotenes.
▪ When fall foliage turns colors, chloroplasts turn
into a plastid known as a gerontoplast.
• a plastid that develops from a chloroplast during
the senescing of plant foliage.
There are plastids that lack pigment.
▪ Amyloplast
• It is specialized to synthesize and store starch.
• Potatoes are full of amyloplasts.
• A potato turns green when exposed to the sun for
too long because amyloplasts are turning into
chloroplasts.
Which of the following is a usual component found in
the chloroplast stroma?

a) tRNAs

b) eukaryotic-like ribosomes

c) circular DNA

d) Both tRNAs and circular DNA

d) Both tRNAs and circular DNA

 Module 5b
Photosynthesis and the Chloroplast

Copyright ©2020 John Wiley & Sons, Inc.

Learning objectives:
By the end of this module, you should be able to:
▪ Compare the events of photosystem II and photosystem I.
You are growing algae in culture and exposing them to H2O that
contains radiolabeled oxygen. Where does the radiolabeled
oxygen end up after photosynthesis?

a) water (H2O)

b) gaseous oxygen (O2)

c) carbon dioxide (CO2)

d) carbohydrates
What is the driving force for photolysis?

a) ATP

b) NADPH

c) the very high redox potential of P680+

d) All of these
Photosynthetic Units and Reaction Centers
▪ Each photosynthetic unit contains several hundred
chlorophyll molecules that act together to absorb
light.
▪ One member of the group—the reaction-center
chlorophyll—transfers electrons to an electron
acceptor.
▪ Antenna pigments are responsible for light
absorption rather than the conversion of light energy
• They absorb photons of varying wavelength and very
rapidly transfers that energy (called excitation
energy) to the pigment molecule at the reaction
center.
• Once the energy reaches a reaction-center
chlorophyll, it will be transferring the excited electron
to a primary acceptor.
Fig. 6.10 The transfer of excitation energy
Photosynthetic Units and Reaction Centers
Oxygen Formation: Coordinating the Action of Two Photosynthetic Systems

Photosynthetic light absorption:

▪ Two large pigment-protein complexes called
photosystems act in series to raise
electrons from H2O to NADP+.
1. Photosystem II (PSII) boosts electrons from
below energy level of water to a midpoint.
2. Photosystem I (PSI) boosts electrons to a
level above NADP+.

Fig. 6.11 Overview of the flow of electrons during

the light-dependent reactions of photosynthesis
Photosynthetic Units and Reaction Centers
The reaction center of:
▪ PSII is P680 (Pigment 680), a chlorophyll dimer
that absorbs light most strongly at wavelength
of 680 nm.
▪ PSI is P700 a chlorophyll dimer that absorbs
light most strongly at wavelength of 700 nm.
▪ Electrons are transferred to a primary electron
acceptor.
▪ The flow of electrons from H2O to NADP+ is
referred to as the Z scheme.
▪ Electron flow occurs along three legs:
• from water to PSII
• from PSII to PSI
• from PSI to NADP+ Fig. 6.11 Overview of the flow of electrons during the light-dependent
reactions of photosynthesis
Photosynthetic Units and Reaction Centers
▪ When electrons leave PSI & PSII, the reaction
centers become positively charged and
attract electrons.
• Reaction-center chlorophylls of PSII & PSI are
denoted as P680+ and P700+, respectively.
▪ The primary electron acceptors become
negatively charged.

Fig. 6.11 Overview of the flow of electrons during the light-dependent

reactions of photosynthesis
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I

Photosystem II
▪ PSII uses absorbed light energy to generate a
proton gradient across the thylakoid membrane.
▪ The first step in PSII activation is absorption of
light by an antenna pigment.
▪ Most antenna pigments that collect solar energy
for PSII reside within a separate pigment protein
complex, the light‐harvesting complex II
(LHCII).

Fig. 6.12 Functional organization of photosystem II

Photosynthetic Units and Reaction Centers
Photosystem II: The Flow of Electrons from PSII to Plasto-quinone

▪ Light energy is passed from light‐harvesting complex

II (LHCII) to inner-antenna molecules within PSII
▪ P680 reaction-center chlorophyll a (reaction center)

▪ Step 1: Excited P680 (P680*) transfers energy to an

electron acceptor pheophytin molecule (Pheo); the first
electron acceptor
▪ This first electron transfer generates a separation of
charge in PSII:
▪ P680+ positively charged donor and Pheo-
negatively charged acceptor.

▪ Step 2: Pheo- is transferred to opposite sides of the

thylakoid membrane where Pheo- passes an electron to
plastoquinone (PQ).
▪ D1/D2 proteins associated with the reaction center.
Fig. 6.12 Functional organization of photosystem II
Photosynthetic Units and Reaction Centers
Photosystem II: The Flow of Electrons from PSII to Plasto-quinone

▪ Step 2: Pheo- is transferred to opposite sides of the

thylakoid membrane where Pheo- passes an
electron to plastoquinone (PQ).
▪ Occur near the stroma side of the membrane.
▪ Plastoquinone is a lipid-soluble molecule
similar in structure to ubiquinone.
▪ The acceptance of two electrons (from water)
and two protons (+H from stroma) reduces PQ
(plastoquinone) to PQH2 (plastoquinol).
▪ PQ --- PQa --- PQb- --- PQH2

▪ The reduced PQH2 molecule dissociates from

Fig. 6.12 Functional organization of photosystem II
the D1 protein and diffuses into the lipid bilayer.
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I

The Flow of Electrons from Water to PSII

• The redox potential of P680+ pulls electrons from
water (photolysis).
• Formation of O2 requires four electrons from H2O:
2 H2 O → 4 H + + O 2 + 4 e –
• Protons produced in photolysis are retained in the
thylakoid lumen.
• Oxygen produced is a released as a waste
product into the environment.
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I

From PSII to PSI

1. Production of O2 leads to formation of two
molecules of PQH2.
2. Reduced PQH2 then diffuses through the
thylakoid membrane, binds cytochrome
b6f, and releases protons to the lumen of
thylakoid.
3. Electrons from cytochrome b6f are passed
to another carrier, peripheral membrane
protein, plastocyanin (PC).
Fig. 6.15 Electron transport between PSII and PSI
4. Plastocyanin transfers electrons to P700+.
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I
PSI Operations: The Production of NADPH
▪ Light energy is absorbed by the antenna pigments of
light‐harvesting complex I (LHCI) and passed to the PSI
reaction-center P700 (chlorophyll α dimer)
▪ Step 1: Transfer the electron to A0, the primary electron
acceptor in PSI (P700+ & A0- )
▪ Step 2-4: Electron transfers to different iron-sulfur centers
▪ Step 5: The electron is finally transferred to ferredoxin, a
small iron-sulfur protein (stroma).
▪ Step 6: The reduction of NADP+ to NADPH is catalyzed by
ferredoxin-NADP+ reductase.
▪ Step A: P700+ is reduced by an electron donated by
plastocyanin. Fig. 6.16 The functional organization of photosystem I
Photosynthetic Units and Reaction Centers
An Overview of Photosynthetic Electron Transport

▪ PSII generates a strong oxidizing agent capable of producing

O2 from 2 H2O
▪ PSI generates a strong reducing agent capable of producing
NADPH from NADP+
▪ 2 H2O + 2 NADP+ → O2 + 2 NADPH

Fig. 6.17a Summary of Light dependent reactions

Photosynthetic Units and Reaction Centers
PSI/PSII contribution to proton gradient
▪ Electron transport also produces a proton gradient across the thylakoid membrane.
(1) the splitting of water in the lumen
(2) oxidation of plastoquinol by cytochrome b6f which releases protons into the lumen
(3) reductions of NADP+ and PQ, which remove protons from the stroma.
Photophosphorylation
▪ The machinery for ATP synthesis in a chloroplast is
similar to that of mitochondrial enzymes.
▪ The ATP synthase consists of a head (CF1), and a base
(CF0).
▪ The CF1 heads project outward into the stroma, keeping
with the orientation of the proton gradient.
• contains the catalytic site of the enzyme
▪ CF0 the base, spans the membrane and mediates proton
movement.
▪ The formation of ATP during photosynthesis is known as
noncyclic photophosphorylation because electrons
move in a linear path
You are growing algae in culture and exposing them to H2O that
contains radiolabeled oxygen. Where does the radiolabeled
oxygen end up after photosynthesis?

a) water (H2O)

b) gaseous oxygen (O2)

c) carbon dioxide (CO2)

d) carbohydrates
b) gaseous oxygen (O2)
What is the driving force for photolysis?

a) ATP

b) NADPH

c) the very high redox potential of P680+

d) All of these

c) the very high redox potential of P680+

 Module 5c
Photosynthesis and the Chloroplast

Copyright ©2020 John Wiley & Sons, Inc.

• Exam 1
• Average: 80%

• Quiz 4
• Due on Feb 15th

• Discussion board: Organs in a dish!

• Feb 19th
Learning objectives:
By the end of this module, you should be able to:
▪ Compare the events of photosystem II and photosystem I.
▪ Compare the Calvin cycles of C3 plants, C4 plants, and CAM plants
What enzyme is responsible for fixing CO2 out of the
atmosphere in C4 plants?

a) PEP decarboxylase

b) ATP synthase

c) PEP carboxylase

d) Rubisco
Photosynthetic Units and Reaction Centers
▪ Each photosynthetic unit contains several hundred
chlorophyll molecules that act together to absorb
light.
▪ One member of the group—the reaction-center
chlorophyll—transfers electrons to an electron
acceptor.
▪ Antenna pigments are responsible for light
absorption rather than the conversion of light energy

Fig. 6.10 The transfer of excitation energy

Photosynthetic Units and Reaction Centers
Photosystem II: The Flow of Electrons from PSII to Plasto-quinone

▪ Light energy is passed from light‐harvesting complex

II (LHCII) to inner-antenna molecules within PSII
▪ P680 reaction-center chlorophyll a (reaction center)

▪ Step 1: Excited P680 (P680*) transfers energy to an

electron acceptor pheophytin molecule (Pheo); the first
electron acceptor
▪ This first electron transfer generates a separation of
charge in PSII:
▪ P680+ positively charged donor and Pheo-
negatively charged acceptor.

▪ Step 2: Pheo- is transferred to opposite sides of the

thylakoid membrane where Pheo- passes an electron to
plastoquinone (PQ).
▪ D1/D2 proteins associated with the reaction center.
Fig. 6.12 Functional organization of photosystem II
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I

The Flow of Electrons from Water to PSII

• The redox potential of P680+ pulls electrons from
water (photolysis).
• Formation of O2 requires four electrons from H2O:
2 H2 O → 4 H + + O 2 + 4 e –
• Protons produced in photolysis are retained in the
thylakoid lumen.
• Oxygen produced is a released as a waste
product into the environment.
Photosynthetic Units and Reaction Centers
Photosystem II: The Flow of Electrons from PSII to Plasto-quinone

▪ Step 2: Pheo- is transferred to opposite sides of the

thylakoid membrane where Pheo- passes an
electron to plastoquinone (PQ).
▪ Occur near the stroma side of the membrane.
▪ Plastoquinone is a lipid-soluble molecule
similar in structure to ubiquinone.
▪ The acceptance of two electrons (from water)
and two protons (+H from stroma) reduces PQ
(plastoquinone) to PQH2 (plastoquinol).
▪ PQ --- PQa --- PQb- --- PQH2

▪ The reduced PQH2 molecule dissociates from

Fig. 6.12 Functional organization of photosystem II
the D1 protein and diffuses into the lipid bilayer.
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I

From PSII to PSI

1. Production of O2 leads to formation of two
molecules of PQH2.
2. Reduced PQH2 then diffuses through the
thylakoid membrane, binds cytochrome
b6f, and releases protons to the lumen of
thylakoid.
3. Electrons from cytochrome b6f are passed
to another carrier, peripheral membrane
protein, plastocyanin (PC).
Fig. 6.15 Electron transport between PSII and PSI
4. Plastocyanin transfers electrons to P700+.
Photosynthetic Units and Reaction Centers
The Operations of Photosystem II and Photosystem I
PSI Operations: The Production of NADPH
▪ Light energy is absorbed by the antenna pigments of
light‐harvesting complex I (LHCI) and passed to the PSI
reaction-center P700 (chlorophyll α dimer)
▪ Step 1: Transfer the electron to A0, the primary electron
acceptor in PSI (P700+ & A0- )
▪ Step 2-4: Electron transfers to different iron-sulfur centers
▪ Step 5: The electron is finally transferred to ferredoxin, a
small iron-sulfur protein (stroma).
▪ Step 6: The reduction of NADP+ to NADPH is catalyzed by
ferredoxin-NADP+ reductase.
▪ Step A: P700+ is reduced by an electron donated by
plastocyanin. Fig. 6.16 The functional organization of photosystem I
Photosynthetic Units and Reaction Centers
An Overview of Photosynthetic Electron Transport

▪ PSII generates a strong oxidizing agent capable of producing

O2 from 2 H2O
▪ PSI generates a strong reducing agent capable of producing
NADPH from NADP+

2 H2O + 2 NADP+ → O2 + 2 NADPH

Fig. 6.17a Summary of Light dependent reactions

Photosynthetic Units and Reaction Centers
PSI/PSII contribution to proton gradient
Electron transport also produces a proton gradient across the thylakoid membrane.
(1) the splitting of water in the lumen
(2) oxidation of plastoquinol by cytochrome b6f which releases protons into the lumen
(3) reductions of NADP+ and PQ, which remove protons from the stroma.
Photophosphorylation
▪ The machinery for ATP synthesis in a chloroplast is
similar to that of mitochondrial enzymes.
▪ The ATP synthase consists of a head (CF1), and a base
(CF0).
▪ The CF1 heads project outward into the stroma, keeping
with the orientation of the proton gradient.
• contains the catalytic site of the enzyme
▪ CF0 the base, spans the membrane and mediates proton
movement.
▪ The formation of ATP during photosynthesis is known as
noncyclic photophosphorylation because electrons
move in a linear path
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

▪ The C3 pathway is known as the Calvin

cycle or Calvin–Benson cycle
• Cyanobacteria and all eukaryotic
photosynthetic cells.
▪ Occurs in the stroma
▪ The cycle comprises three main parts:
1. Carboxylation of RuBP to form PGA
2. Reduction of PGA to glyceraldehyde 3-
phosphate (GAP) using NADPH and
ATP from light reactions.
3. the regeneration of RuBP, which also
requires ATP.

Fig. 6.20b Converting CO2 into carbohydrate

Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

Rubisco (Ribulose bisphosphate

carboxylase)
▪ Main enzyme in the C3 pathway
▪ CO2 is condensed with a five-carbon
compound, ribulose 1,5-bisphosphate (RuBP),
to form a six-carbon molecule which then splits
into two molecules of 3-phosphoglycerate
(PGA).

Rubisco
CO2+ RuBP → 2PGA

Fig. 6.20b Converting CO2 into carbohydrate

Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

▪ Step 1: Rubisco fixed CO2 by linkage to ribulose

1,5-bisphosphate (RuBP).
• The product rapidly splits into two molecules of 3-
phosphoglycerate (PGA).
▪ Step 2: The 12 PGA molecules are phosphorylated
via ATP hydrolysis to form 12 1,3-
bisphosphoglycerate (BPG) molecules
▪ Step 3: BPG is reduced by electrons provided by
NADPH to form 12 molecules of glyceraldehyde 3-
phosphate (GAP).

Fig. 6.20b Converting CO2 into carbohydrate

Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

▪ Step 4: 2GAPs are used in the synthesis of

sucrose in the cytosol
▪ Step 5: The other 10 GAPs molecules are
converted into 6RuBP, which can act as the
acceptor for 6 more molecules of CO2
• The regeneration of six RuBPs requires the
hydrolysis of six molecules of ATP.

Note: The NADPH and ATP used in the Calvin

cycle represent the two high-energy products of
the light-dependent reactions.

Fig. 6.20b Converting CO2 into carbohydrate

Carbon Dioxide Fixation and the Synthesis of Carbohydrate
An overview of the various stages of photosynthesis.

▪ For every 6 molecules of CO2 fixed, 12 molecules of GAP are

produced.
1. The GAP molecules can be exported into the cytosol and used
to synthesize sucrose.
2. GAP can also remain in the chloroplast where it is converted to
starch.
▪ Sucrose is the organic building block in plants (similar to
glucose in animals)
▪ Starch is stored in the plant’s leaves and provides it with
sugars at night (similar to glycogen in animals)
▪ 12 NADPH and 18 ATP. This large energy expenditure
reflects the fact that CO2 is the most highly oxidized form in
which carbon can occur.
Fig. 6.21 Overview of various stages of
photosynthesis
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
An overview of the various stages of photosynthesis.

Includes:
▪ the light reactions (light absorption, oxidation of water,
reduction of NADP+, translocation of protons)
▪ phosphorylation of ADP
▪ the Calvin cycle
▪ the synthesis of starch or sucrose

Fig. 6.21 Overview of various stages of

photosynthesis
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Redox Control: Light and dark

▪ Regulator of basic cellular processes, including protein

folding, transcription, and translation
▪ Redox Control is a light-dependent regulator of
chloroplast metabolism.
▪ Several key Calvin cycle enzymes are only active in
the light when ATP and NADPH are produced by
photosynthesis.
▪ Thioredoxin occurs in two forms:
1. Reduced → Calvin Cycle enzyme activation → synthesis
of carbohydrates in chloroplast
2. Oxidized → occurs in that dark and causes enzyme
inactivation because the flow of electrons to thioredoxin
ceases.
Fig. 6.22 Redox control of the Calvin cycle
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

▪ Photorespiration → series of reactions that

involve the uptake of O2 and release of CO2.
▪ It accounts for the loss of up to 50% of fixed
CO2.
▪ Rubisco also catalyzes the attachment of O2
to RuBP to produce 2-phosphoglycolate.
▪ Glycolate is then transferred to the
peroxisome and leads to the release of CO2.
Fig. 6.23 The reactions of photorespiration
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

Plants living in a hot, dry climate

Closed stomata: to avoid dehydration

Increase concentrations of O2
Decrease concentrations of CO2

Rubisco uses O2------2-phosphoglycolate.

Fixed CO2 release
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis on C3 Plants

Peroxisomes and Photorespiration

▪ Glycolate is shuttled out of the chloroplast into
a peroxisome.
▪ In the peroxisome:
▪ glycolate → glyoxylate → glycine

▪ In the mitochondrion:
▪ two molecules of glycine → one molecule of
serine and the release of one molecule of CO2.
Fig. 6.24 Cellular basis of photorespiration
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis

Two groups of plants, called C4 and CAM plants, have overcome the negative effects of
photorespiration by evolving metabolic mechanisms that increase the CO2 /O2 ratio to which
the Rubisco enzyme molecules are exposed.
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
C4 Plants

▪ The C4 pathway involves the production of

phosphoenolpyruvate (PEP), which then
combines with CO2 to produce 4-carbon
compounds oxaloacetate or malate.
▪ PEP carboxylase
▪ Mesophyll (CO2 fixation) and bundle-sheath
cells (CO2 splitting by Rubisco), minimize
the rate of photorespiration
▪ Plants utilizing this pathway are C4 plants,
Fig. 6.25 Structure and function in C4 plants
usually tropical grasses.
▪ Sugarcane, corn, and sorghum
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
C4 Plants

▪ Disadvantage to C4 metabolism
• It requires more ATP and NADPH to
produce carbohydrates than C3 plants.
▪ C3 plants have more efficient
photosynthesis when photorespiration is not
a problem (under cooler, well-watered
conditions).
▪ C4 plants do not do well under cooler
temperatures or higher latitudes
▪ PEP carboxylase gene from C4 plants has
Fig. 6.25 Structure and function in C4 plants
been introduced into C3 plants in hopes of
generating a CO2-concentrating mechanism
• Maize-Rice
Carbon Dioxide Fixation and the Synthesis of Carbohydrate
Carbohydrate Synthesis
▪ CAM plants carry out light reactions and CO2 fixation at different
times of the day using the enzyme PEP carboxylase.
▪ CAM plants keep their stomata closed during the day, and then open
at night.
▪ Night: they open their stomata and CO2 fix by means of PEP
carboxylase.
• The malate generated in mesophyll cells is transported into the cell’s
central vacuole.
▪ During the day (stomata close) → malic acid is moved into the
cytoplasm.
• There it can be fixed by Rubisco under conditions of low O2
concentration.
▪ Carbohydrates are then synthesized using energy from ATP and
NADPH generated by the light-dependent reactions.
What enzyme is responsible for fixing CO2 out of the
atmosphere in C4 plants?

a) PEP decarboxylase

b) ATP synthase

c) PEP carboxylase

d) Rubisco

c) PEP carboxylase
 Module 6a
Interactions Between Cells and Their Environment
Weight final grade based on assessment groups
Assessment Value of Total Grade
Exams (x4) 69%
Quizzes (x10) 10%
Analytical assignments (x5) 8%
Study case (x3) 8%
Discussion board (x3) 5%
Total: 100%
Quiz 5: Feb 15th -today
Discussion board: Feb 19th
Quiz 6 will open on Feb 20th
Extra credits=bonus points
Learning objectives

By the end of this module, you should be able to:

▪ Identify the structures and functions of the extracellular matrix in animal tissue.
Poll 1

The extracellular matrix includes all of the following EXCEPT _________.

a) laminin
b) collagen
c) proteoglycan
d) fibroblast
Poll 2

The degradation of extracellular materials is accomplished largely

by_____________.

a) protein kinases
b) ubiquitins
c) matrix metalloproteinases
d) fibronectin
Overview of Extracellular Interactions
Cell organization into tissues
Human Skin
▪ The outer layer of skin (epidermis)
has closely packed cells attached to
one another forming an epithelial
tissue
▪ The dermis is a type of connective
tissue
▪ Fibroblasts of the dermis have
receptors that mediate interactions
cell-to-cell and their environment
▪ Contain receptors with dual function
• Attachments and transit messages

An overview of how cells are organized into tissues and how they
interact with one another and with their extracellular environment.
The Extracellular Matrix
▪ Carbohydrate projections form part of the glycocalyx (cell coat) on the outer surface of
the plasma membrane.
▪ Roles of the glycocalyx
• Mediator of cell-cell and cell–substratum interactions
• Mechanical protection
• Barrier to molecular movement
• Regulatory factor binding site
Molecular model of the
glycocalyx

EM: endothelial glycocalyx in a

coronary capillary
The Extracellular Matrix
▪ Many types of animal cells produce an extracellular matrix (ECM)
• an organized network of secreted molecules
▪ Holds cells together
▪ It provides physical, biochemical, and mechanical signals that can play key
regulatory roles in determining the shape and activities of the cell.
The Extracellular Matrix
▪ One of the best-defined extracellular matrices is the basement membrane
(or basal lamina)
• Surrounds nerve fibers, muscles, and fat cells
• Underlies the basal surface of epidermis of the skin, the digestive and respiratory tract
and the lining of blood vessels.
• Provide mechanical support for the attached cells
• Generate signals that maintain cell survival
• Serve as a substratum for cell migration
• Separate adjacent tissues within an organ
• Act as a barrier to the passage of macromolecules
The Extracellular Matrix

Organized network of extracellular materials outside plasma membrane, provides

support and determines shape and activity of cell.
The Extracellular Matrix
▪ The major components of extracellular matrices
include:
• collagens, proteoglycans, and a variety of
proteins, such as fibronectin, and laminin
▪ They form an interconnected network that is bound
to the cell surface.
▪ These proteins are secreted into the extracellular
space.
▪ Each of the proteins of the extracellular matrix
contains binding sites for one another and for
receptors on the cell surface.

Organized network of extracellular materials outside

plasma membrane, provides support and determines
shape and activity of cell.
Components of the Extracellular Matrix
Collagen

▪ Collagen is the single most abundant protein in

the human body.
▪ Collagens comprise a family of fibrous
glycoproteins present only in the ECM.
▪ Produced by fibroblasts, smooth muscle and
epithelial cells.
▪ 28 fiber types, often mixed in ECM
▪ Each collagen type is restricted to particular
locations within the body Collagen I molecules become
aligned in staggered rows
Components of the Extracellular Matrix
Collagen molecule: all share at least two important structural features.
1. Consisting of three polypeptide chains (trimers),
called α helix chains.
2. They are wound around one another to form a rod-
like triple helix
▪ The α chains contain hydroxylated amino acids
(proline & lysine) and form hydrogen bonds
• Provide stability to the triple helix
• Failure to hydroxylate collagen chains has serious
consequences for the structure and function of
connective tissues.
▪ Scurvy disease: vitamin C deficiency (ascorbic acid)
• Inflamed gums and tooth loss, brittle bones
• Ascorbic acid is required as a coenzyme by the enzymes
that add hydroxyl groups to the lysine and proline amino
acids of collagen.
Components of the Extracellular Matrix
Proteoglycans

▪ Proteoglycans – protein-polysaccharide
complex, with a core protein attached to
glycosaminoglycans (GAGs).
▪ Have a repeating disaccharide structure, -A-
B-A-B-, where A and B represent two different
sugars.
▪ GAGs are highly acidic due to the presence
of both sulfate and carboxyl groups attached
to the sugar rings.
▪ Proteoglycans are assembled into gigantic
complexes by linkage of their core proteins to Schematic representations of a single proteoglycan,
a molecule of hyaluronic acid, a nonsulfated repeating disaccharide structure of GAGs, and
linkage to hyaluronic acid to form a giant complex
GAG
The Extracellular Matrix

Organized network of extracellular materials outside plasma membrane, provides

support and determines shape and activity of cell.
Components of the Extracellular Matrix
Fibronectin

▪ Fibronectin consists of a linear array of 30

Fn domains to give a modular construction
▪ Fn-type domains are found in blood
clotting factors and receptors.
▪ Binds to numerous ECM components
• such as collagens, proteoglycans, and
other fibronectin molecules.
• stable, interconnected network
▪ Binds to cell surface receptors
• forming a stable attachment between the
ECM and the cell Human fibronectin molecule consists of two similar
polypeptides joined by disulfide bonds.
Components of the Extracellular Matrix
Fibronectin

▪ Fibronectin and other extracellular

proteins have important roles during
embryonic development.
▪ Development is characterized by
waves of cell migration.

A summary of some of the cellular traffic

occurring during mammalian development
Components of the Extracellular Matrix
Fibronectin

▪ Several organs (e.g., salivary gland, kidney,

and lung) are formed by a process of
branching/cleft formation.
▪ Cell adhesion and shape determination also
fibronectin-dependent
Fibronectin in embryonic salivary
gland cleft formation

Endothelial cell spread over a

square‐shaped patch of fibronectin
Components of the Extracellular Matrix
Laminin
▪ Family of at least 15 extracellular glycoproteins.
▪ Laminin has three polypeptide chains linked by
disulfide bonds
▪ They can greatly influence a cell’s potential for
migration, growth, and differentiation.
▪ Laminins can bind tightly to cell-surface receptors,
other laminin molecules, proteoglycans, and to
other components of basement membranes
Primordial germ cells (green) migrating along a
tract of laminin (red) from the dorsal mesentery to
the developing gonad.
Dynamic Properties of the Extracellular Matrix
▪ ECM can exhibit dynamic properties both in space and time
▪ Spatially, ECM fibrils can stretch several times their normal length
▪ Temporally, ECM components are subject to continual degradation and
reconstruction.
▪ Matrix metalloproteinases (MMP) family of zinc-containing enzymes
• Secreted into the extracellular space or anchored to the plasma membrane
• MMPs degrade ECM materials and cell surface proteins
• The physiological roles of MMPs are thought to be involved in tissue
remodeling, embryonic cell migration, wound healing, and the formation of
blood vessels
• Abnormal expression of MMPs linked to a variety of diseases like arthritis
Engineering Linkage: Organoids
▪ Organoids, 3D cellular structures that resemble
organs in both development and organization
▪ Cells are typically derived from stem cells
▪ These cells are then grown in a complex mixture of
extracellular matrix proteins and other
components for cellular growth.
▪ Small clump of tissue that can often approximate a
full-sized organ
▪ The engineering of organoids has made advances
over the years.
• Intestine, Pancreas, Stomach, Optic cup & Brain
▪ Applications:
• Disease research
• Pharmaceutical research
Poll 1

The extracellular matrix includes all of the following EXCEPT _________.

a) laminin
b) collagen
c) proteoglycan
d) fibroblast

d) fibroblast
Poll 2

The degradation of extracellular materials is accomplished largely

by_____________.

a) protein kinases
b) ubiquitins
c) matrix metalloproteinases
d) fibronectin

c) matrix metalloproteinases
 Module 6b
Interactions Between Cells and Their Environment
Learning objectives

By the end of this module, you should be able to:

• Explain the functions of selectins, immunoglobulins, integrins, cadherins,
adherens junctions, and desmosomes.
Which of the following statements about integrins is true?

a) They anchor cells to the substrate.

b) They are found in both animal and plant cells.

c) Different cell types are restricted to just one type of integrin.

d) All of these statements are true.

While most IgSF members are involved in various aspects
of immune function, some of them mediate ________ cell-
cell adhesion.

a) calcium-dependent

b) calcium-independent

c) magnesium-dependent

d) manganese-dependent
The Extracellular Matrix

The major components of

extracellular matrices include
collagens, proteoglycans,
and a variety of proteins,
such as fibronectin, and
laminin
• capable of binding to
receptors situated on the
cell surface
Organized network of extracellular materials outside plasma membrane, provides
support and determines shape and activity of cell.
Interactions of Cells with Extracellular Materials
Integrins

▪ Family of membrane receptor proteins unique to

animals.
▪ Composed of two membrane-spanning
polypeptide chains, an α chain and a β chain.
▪ The bent conformation of integrin corresponds to
its inactive state, Integrins with a bound ligand
are found in an upright conformation.
▪ The transmembrane domains of the two subunits
are in close proximity.
EMs and ribbon drawings of the extracellular domains
of an integrin (avb3) in the “bent”/inactive and
“upright”/active conformation. Changes driven by
divalent metal ions.
Interactions of Cells with Extracellular Materials
Integrins
▪ Integrins have two major activities: adhesion of cells to their substratum
(or to other cells) and transmission of signals between the external
environment and the cell interior.
▪ Inside-out signals: The cytoplasmic domains of integrins bind a wide
array of proteins; like talin, causes separation of the α and β subunits
• primarily affects the binding properties of the integrins
▪ Outside-in signals: The binding of the extracellular domain of an integrin
to a ligand, such as fibronectin or collagen, can induce a
conformational change at the opposite, cytoplasmic end of the integrin,
especially its β subunit
• Can induce a conformational change in talin.
• Cytoplasmic protein kinases can be activated to phosphorylate other
proteins.
▪ Outside-in signals transmitted by integrins can influence differentiation,
motility, growth, and cell survival.
Interactions of Cells with Extracellular Materials
Focal Adhesions

▪ Cell adhesion in vitro

• knowledge of cell–matrix interactions
▪ At first, the cell has a rounded
morphology (aqueous medium)
▪ Once the cell contacts the substratum, it
sends out projections that form stable
attachments.
▪ Cell flattens and spreads itself out on the
substratum.
▪ Cultured cells are anchored to the Steps in the process of cell spreading. Mouse fibroblasts at
surface of the dish only at scattered, successive times during attachment and spreading on glass
discrete sites, called focal adhesions. coverslips.
Interactions of Cells with Extracellular Materials
Focal Adhesions

▪ Cultured cells are anchored to the surface of the dish

only at scattered, discrete sites, called focal
adhesions.
▪ The plasma membrane of a focal adhesion contains
large clusters of integrins.
▪ The cytoplasmic domains of the integrins are
connected to actin filaments of the cytoskeleton
through adaptor proteins (talin, α-actinin, and vinculin)

▪ Focal adhesions play a key role in cell locomotion.

▪ Focal adhesions are dynamic structures
(disassembled upon movement or cellular division- Cultured cell: actin filaments (gray-green),
mitosis) integrins (red); sites of focal adhesions
Interactions of Cells with Extracellular Materials
Hemidesmosomes (specialized adhesive structure; cell-substratum )
▪ Hemidesmosomes are differentiated sites at the basal surfaces of epithelial
cells where the cells are attached to the underlying basement membrane.
▪ Contains a dense cytoplasmic plaque with keratin filaments.
▪ Keratin filaments are linked to the ECM by integrins.

Hemidesmosomes: EM and schematic diagram.

Interactions of Cells with Other Cells
Four distinct families of integral membrane proteins play a major role in
mediating cell–cell adhesion:
1. Selectins
2. Certain members of the immunoglobulin superfamily (IgSF)
3. Certain members of the integrin family
4. Cadherins

***Mediates transmembrane signaling

Interactions of Cells with Other Cells
Selectins (cell-surface receptors)

▪ Selectins are a family of membrane glycoproteins that bind to

specific oligosaccharides.
▪ “Lectin,” is a term for a compound that binds to specific
carbohydrate groups.
▪ They possess a:
• small cytoplasmic segment
• single membrane-spanning domain
• large extracellular portion (structural domains, including
lectin)
▪ There are three known selectins:
• E-selectin, present on endothelial cells
• P-selectin, present on platelets and endothelial cells
• L-selectin, present on white blood cells
▪ Binding of selectins to their carbohydrate ligands requires
calcium. Schematic of the three selectins
and their CHO ligand
Interactions of Cells with Other Cells
The Immunoglobulin Superfamily (IgSF)
▪ The human genome encodes 765 distinct Ig domains.
▪ These are members of the immunoglobulin
superfamily.
▪ Involve in immune functions but some of these
proteins are cell-cell-adhesion mediators (Ca2+
independent)
▪ Ig-Ig binding between cells
▪ IgSF family members can also bind to integrins of
neighboring cells Cell–cell adhesion from homotypic
interactions of two L1 molecules
through Ig domains at the N-termini.
Interactions of Cells with Other Cells
Cadherins

▪ Glycoprotein family
▪ Mediate Ca2+-dependent cell–cell adhesion and transmit
signals from the ECM to the cytoplasm
▪ Cadherins typically join cells of similar type to one another
▪ The best-studied cadherins are E-cadherin (epithelial), N-
cadherin (neural), and P-cadherin (placental).
▪ Contain an extracellular segment consisting of five
tandem domains of similar size and structure, a single
transmembrane segment, and a small cytoplasmic
domain Schematic of two adhering cells due to
interactions between cadherins projecting
▪ Cadherin loss associated with spread of malignancy from the plasma membrane of each cell
tumors.
Interactions of Cells with Other Cells
Intercellular junctions: Adherens Junctions and Desmosomes

▪ Cadherins also participate in the formation

of specialized intercellular junctions
(adherens junctions and desmosomes)
▪ Epithelial cells often contain other types of
cell junctions: Tight junctions, Gap junctions.
▪ In an adherens junction, cells are held
together by Ca2+ -dependent linkages
formed between the extracellular domains of
cadherin molecules.

Diagram and EM showing the junctional complexes on

the lateral surfaces of a simple columnar epithelial cell
Interactions of Cells with Other Cells
Intercellular junctions: Adherens Junctions and Desmosomes

▪ The cadherin clusters of an adherens

junction
• Connect the external environment to the actin
cytoskeleton.
• Provide a pathway for signals to be
transmitted from the cell exterior to the
cytoplasm.
▪ Mice lacking an endothelial cell cadherin are
unable to transmit these survival signals

Diagram and EM showing the junctional complexes on

the lateral surfaces of a simple columnar epithelial cell
Interactions of Cells with Other Cells
Intercellular junctions: Adherens Junctions and Desmosomes

▪ Desmosomes are disk-shaped adhesive

junctions
• They are in tissues subjected to mechanical
stress, like cardiac muscle and the epithelial
layers of the skin.
▪ Like adherens junctions, desmosomes
contain cadherins that link the 2 cells across
a narrow extracellular gap.

Diagram and EM showing the junctional complexes on

the lateral surfaces of a simple columnar epithelial cell
Interactions of Cells with Other Cells
Intercellular junctions: Adherens Junctions and Desmosomes

The cadherins of desmosomes have

a different domain structure
▪ desmogleins
▪ desmocollins

In the cytoplasm, the desmosomal

cadherins bind indirectly to
intermediate filaments.
Interactions of Cells with Other Cells
Intercellular junctions: Gap & Tight Junctions; plasmodesmata (plants)

Diagram and EM showing the junctional complexes on the lateral

surfaces of a simple columnar epithelial cell
Which of the following statements about integrins is true?

a) They anchor cells to the substrate.

b) They are found in both animal and plant cells.

c) Different cell types are restricted to just one type of integrin.

d) All of these statements are true.

a) They anchor cells to the substrate.

While most IgSF members are involved in various aspects
of immune function, some of them mediate ________ cell-
cell adhesion.

a) calcium-dependent

b) calcium-independent

c) magnesium-dependent

d) manganese-dependent

b) calcium-independent
 Module 6c
Interactions Between Cells and Their Environment
Learning objectives
By the end of this module, you should be able to:
▪ Explain how the structure of a tight junction contributes to its function.
▪ Distinguish the mechanisms of intercellular communication.
▪ Describe the function of each component that makes up the plant cell wall.
You are studying an animal in the lab and inject fluorescein, a
fluorescent dye, into a single cell on the surface epithelium of the
animal. After a brief period of time, the dye spreads to cells
neighboring the injected cell. What do you conclude?

a) The cells are connected by adherens junctions.

b) The cells are connected by tight junctions.

c) The cells are connected by gap junctions.

d) The cells are connected by plasmodesmata.

What kind of cell constituent below does not pass
through a gap junction?

a) ions

b) cAMP

c) phosphates

d) ribosomes
The Extracellular Matrix

The major components of

extracellular matrices include
collagens, proteoglycans,
and a variety of proteins,
such as fibronectin,
integrin, and laminin

Surface receptors:
• Integrins
• Selectins
Organized network of extracellular materials outside plasma membrane, provides • Immunoglobulins
support and determines shape and activity of cell. • Cadherins
Interactions of Cells with Other Cells

An intercellular junctional complex

Tight Junctions: Sealing the Extracellular Space

▪ Tight junctions (TJs) are located at the most apical

end of the junctional complex between epithelial
and endothelial cells
▪ The points of cell–cell contact are sites where
integral proteins of two adjacent membranes meet
within the extracellular space.
▪ TJ are connected areas of the plasma membrane
that stitch cells together.

Tight junction model

showing intermittent
contact points between
proteins from two
apposing membranes
Tight Junctions: Sealing the Extracellular Space
▪ TJs serve as:
• A barrier to the free diffusion of water and solutes from the
extracellular compartment
• “fences” that help maintain the polarized character of
epithelial cells by blocking the diffusion of integral proteins
from the apical domain of the plasma membrane to its lateral
and basal domains.
▪ TJs help form the blood–brain barrier, which prevents
substances from passing from the bloodstream into the
brain.
Intercellular Communication

▪ Specialized sites of communication between adjoining cells in animals and plants

▪ Plasma membranes of a gap junction contain channels that connect the cytoplasm
of one cell with the cytoplasm of the adjoining cell.
▪ Animals: Gap junctions
▪ Plants: Plasmodesmata Plasmodesmata

Gap junctions
Intercellular Communication
Gap Junctions
▪ Gap junctions are molecular “pipelines” that pass through
the adjoining plasma membranes and open into the
cytoplasm of the adjoining cells.
▪ They are composed of an integral membrane protein
connexin, and organized into multisubunit complexes,
connexons, that span the membrane.

Schematic model of a gap junction

showing the arrangement of six
connexin subunits to form a connexon
Intercellular Communication
Gap Junctions
▪ Allow the diffusion of molecules of specific molecular weight
(~1000 Daltons)
• ions or low-molecular weight dyes, such as fluorescein
▪ Relatively nonselective
▪ Gap-junction ion channels are gated (open or closed
conformation)
▪ Channel closure can be triggered by several stimuli, including
phosphorylation of connexin subunits, and changes in voltage
across the junction

Schematic model of a gap junction

showing the arrangement of six
connexin subunits to form a connexon
Intercellular Communication
Plasmodesmata (singular plasmodesma)
▪ Plant cells are separated from one another Plasmodesma of a
by a cell wall, and lack the specialized fern gametophyte
junctions found in animal tissues.
▪ For cell-cell communication, most plant
cells are connected by plasmodesmata,
cytoplasmic channels that pass through the
cell walls of adjacent cells.
Schematic
drawing of a
plasmodesma
Intercellular Communication
Plasmodesmata
▪ Plasmodesmata allow larger molecules to pass
since the pore is capable of dilation (up to 50 kDa)
▪ Contain a dense central structure,
the desmotubule, derived from the smooth
endoplasmic reticulum of the two cells.
▪ Plant cells regulate the flow of proteins and RNAs
from cell to cell.

Schematic drawing of a plasmodesma

Intercellular Communication
Long-Range Intercellular Communication
▪ Cells can communicate with other cells over long
distances
▪ Tunneling nanotubes
• Cultured cells
• Consists of thin, highly elongated tubules capable of
conducting cell surface proteins, cytoplasmic
vesicles, organelles, and calcium signals
▪ Release extracellular vesicles
• cytosolic proteins, membrane proteins, and diverse
RNAs

Tunneling nanotubes
Cell Walls
▪ The cells of nearly all organisms other than animals
are enclosed in a protective outer envelope.
▪ In plants:
• Provide individual cell support
• Type of skeleton to the entire plant
▪ Cell walls also protect the cell against damage from
mechanical abrasion and pathogens and mediate
cell–cell interactions.
Cell Walls
▪ Plant cell walls contain a fibrous element embedded
in a nonfibrous, gel-like matrix.
• Cellulose provides the fibrous component of the cell
wall
• Proteins and pectins provide the matrix
▪ Cellulose molecules are organized into rod-like
microfibrils.

▪ Cellulose molecules are polymerized at the cell

surface.
▪ Cellulose molecules are made by a multisubunit
enzyme called cellulose synthase (embedded within
the plasma membrane).
▪ Matrix are synthesized within the cytoplasm and
carried to the cell surface in secretory vesicles. Schematic diagram of a model of a generalized
plant cell wall
Cell Walls
The matrix of the cell wall is composed of three types
of macromolecules:
1. Hemicelluloses: branched polysaccharides whose
backbone consists of one sugar (e.g., glucose, and
side chains of other sugar (e.g., xylose).
2. Pectins: negatively charged polysaccharides
containing galacturonic acid.
3. Proteins: mediate dynamic activities.

Schematic diagram of a model of a generalized

plant cell wall
You are studying an animal and inject fluorescein, a fluorescent dye,
into a single cell on the surface epithelium of the animal. After a brief
period of time, the dye spreads to cells neighboring the injected cell.
What do you conclude?

a) The cells are connected by adherens junctions.

b) The cells are connected by tight junctions.

c) The cells are connected by gap junctions.

d) The cells are connected by plasmodesmata.

What kind of cell constituent below does not pass
through a gap junction?

a) ions

b) cAMP

c) phosphates

d) ribosomes
 Module 7a
Cytoplasmic Membrane Systems: Structure, Function, and
Membrane Trafficking
Learning objectives
By the end of this module, you should be able to:
▪ Compare the components of the biosynthetic and endocytic pathways.
▪ Describe five approaches used to study the endomembrane system.
A protein is transported in a secretory vesicle and discharges into the extracellular space in
a continuous fashion. What type of secretion is this?

a) regulated

b) biosynthetic

c) constitutive

d) unregulated
Which technique breaks up cells for the isolation of specific organelles?

a) autoradiography

b) homogenization

c) cellular fractionation

d) None of these is correct.

An Overview of the Endomembrane System

▪ The ER, Golgi complex, endosomes,

lysosomes, and vacuoles form an
endomembrane system that act as a
coordinated unit.
▪ They are distinct compartments bounded
by membrane barriers and contain
specialized proteins for particular activities.

Fig. 8.1 Membrane-bound compartments of the

cytoplasm
An Overview of the Endomembrane System
Materials packaged in small, membrane-
bounded transport vesicles:
▪ Bud from a donor membrane compartment.
▪ Move via vesicles
▪ Fuse with the membrane of the acceptor
compartment

Fig. 8.2a An overview of the

biosynthetic/secretory pathways that
unite endomembranes into a dynamic
interconnected network
An Overview of the Endomembrane System
Pathways:
▪ Biosynthetic pathway: Proteins are synthesized in the ER,
modified at the Golgi complex, and transported to various
destinations.
▪ Secretory pathway: Proteins synthesized in the ER are
discharged (secreted or exocytosed) from the cell.

Secretion modes:
▪ Constitutive secretion: Materials are transported in secretory
vesicles and discharged in a continual manner.
• Plasma membrane, extracellular matrix
▪ Regulated secretion: Materials are stored in vesicles and
discharged in response to a stimulus.
An Overview of the Endomembrane System
▪ Regulated secretion occurs in endocrine cells
(hormones), pancreatic acinar cells (digestive enzymes),
and nerve cells (neurotransmitters).
• In some of these secreted materials can be stored in large,
densely packed, membrane-bound secretory granules.

▪ Proteins, lipids, and complex polysaccharides are

transported through the cell along the biosynthetic or
secretory pathway.
▪ The various types of cargo are routed to their appropriate
cellular destinations by sorting signals encoded in the pancreatic acinar cell
amino acid sequence of the proteins or in the attached
oligosaccharides.
An Overview of the Endomembrane
System
▪ Endocytic pathway, (opposite direction) materials move
from the outer surface of the cell to compartments, such
as endosomes and lysosomes
A Few Approaches to Study the Endomembranes
Insights Gained from Autoradiography

▪ Autoradiography visualizes biochemical processes by radioactively

labeling molecules.
▪ Pancreatic acinar cells: These cells function primarily in the synthesis
and secretion of digestive enzymes
▪ Palade and Jamieson (Rockefeller University) incorporated
radiolabeled amino acids into pancreatic enzymes and were able to
localize the cellular proteins.
pancreatic acinar cell
A Few Approaches to Study the Endomembranes
Insights Gained from the Use of Fluorescent Proteins

▪ GFP-“tagging” allows microscope viewing of

protein movement in living cells.
▪ Cells infected with a strain of vesicular stomatitis
virus (VSV) which has a viral–GFP gene fusion
▪ Viral genes take over the machinery of the cell.
▪ Production and movement of the viral proteins
monitored via fluorescent GFP.
A Few Approaches to Study the Endomembranes
Insights Gained from the Use of Fluorescent Proteins

Microscopic images of a
mammalian cell expressing
multiple fluorophores to
visualize different organelles.
A Few Approaches to Study the Endomembranes
Insights Gained from the Analysis
of Subcellular Fractions
▪ Cell homogenization fragments cytoplasmic
membranes
▪ Techniques to break up (homogenize) cells
and isolate particular types of organelles
▪ Vesicles derived from the endomembrane
system form similar sized vesicles referred to
as microsomes.
▪ Once isolated, the biochemical composition of
various lipid and protein fractions can be
determined.

Fig. 8.6 Isolation of a microsomal fraction by

differential centrifugation
A Few Approaches to Study the Endomembranes
Insights Gained from the Use of Cell-Free Systems- not contain whole cells
▪ Liposomes are vesicles whose surface consists of an artificial bilayer that is created from
purified phospholipids.
▪ Buds and vesicles can be produced when purified proteins normally on the cytosolic
surface of transport vesicles in the cell are added.
▪ Can study proteins:
• that bind to the membrane to initiate vesicle formation
• those responsible for cargo selection
• those that sever the vesicle from the donor membrane.

Fig. 8.7 Formation of coated

vesicles in a cell-free system
A Few Approaches to Study the Endomembranes
Insights Gained from the Study of Mutant Phenotypes

▪ A mutant is an organism (or cultured cell) with

chromosomes containing one or more genes
that encode abnormal proteins.
▪ Mutant is unable to carry out its normal function,
▪ Screen for mutant yeast cells that exhibit an
abnormal distribution of cytoplasmic membranes
reveals proteins that function in secretion.

Fig. 8.8 Use of genetic mutants

in the study of secretion
A Few Approaches to Study the Endomembranes
Insights Gained from the Study of Mutant Phenotypes
Fig. 8.9 Inhibition of gene expression with RNA
interference
▪ RNA interference (RNAi) is used to inhibit
mRNA translation into proteins.
▪ By using siRNAs libraries, one can find
genes involved in various steps of the
secretory pathway.

a) The fluorescent enzyme becomes localized in the Golgi

complex after its synthesis in the ER.
b) The siRNA has caused the fluorescent enzyme to remain in
the ER, which has fused with the Golgi membranes.
A protein is transported in a secretory vesicle and discharges into the extracellular space in
a continuous fashion. What type of secretion is this?

a) regulated

b) biosynthetic

c) constitutive

d) unregulated

c) constitutive
Which technique breaks up cells for the isolation of specific organelles?

a) autoradiography

b) homogenization

c) cellular fractionation

d) None of these is correct.

b) homogenization
 Module 7
Cytoplasmic Membrane Systems: Structure, Function, and
Membrane Trafficking
Learning objectives
By the end of this module, you should be able to:
▪ Compare the structures and functions of the RER and SER, and their roles in the
maintenance of cellular proteins and membranes.
▪ Distinguish the functions of the different types of vesicle transport.
The signal sequence is found at the N-terminus of:

a) secretory proteins

b) all proteins

c) housekeeping proteins

d) None of these is correct

Which of the following processes does NOT take place in the Golgi
complex?

a) glycosylation of glycoproteins and glycolipids

b) digestion of misfolded proteins

c) processing of membrane proteins

d) processing of lysosomal proteins

The Endoplasmic Reticulum
▪ Network of membranes that penetrates much of the cytoplasm and has a lumen
separated from the cytosol by the ER membrane.
▪ Highly dynamic structure, undergoing continual turnover and reorganization.
▪ 2 subcompartments: Rough ER and Smooth ER
▪ RER (Rough ER) :
1. ribosomes bound to its cytosolic surface
2. flattened sacs (cisternae) connected to neighbors by helicoidal membranes
3. is continuous with the outer membrane of the nuclear envelope.
The Endoplasmic Reticulum

Fig. 8.10a,b The rough endoplasmic reticulum (RER)

The Endoplasmic Reticulum
▪ SER (Smooth ER):
1. lacks ribosomes
2. membranes are highly curved and tubular
3. is continuous with the RER.
4. forms interconnecting system of pipelines traversing the cytoplasm
The Endoplasmic Reticulum

Fig. 8.10a,b The rough endoplasmic reticulum (RER)

The Endoplasmic Reticulum
The Smooth Endoplasmic Reticulum
The SER functions vary from cell to cell
SER functions include:
1. Synthesis of steroid hormones
2. Detoxification of a wide variety of organic
compounds via oxygenases including the
cytochrome P450 family.
3. Mobilization of glucose from glucose 6-phosphate
4. Sequestration and regulated release of calcium Fig. 8.11 The smooth ER (SER)
ions.
The Endoplasmic Reticulum
The Rough Endoplasmic Reticulum (RER)
▪ The RER is the starting point of the biosynthetic pathway for secretory proteins.
▪ Synthesis of proteins, carbohydrate chain and the synthesis of most of the lipids of a cell’s
membranes.
▪ The addition of sugars to the asparagine residues of proteins begins in the RER and
continues in the Golgi complex.
The Endoplasmic Reticulum
The Rough Endoplasmic Reticulum
Polypeptides are synthesized at two distinct locations
within the cell:
1. About one-third of the proteins are synthesized on
ribosomes attached to the cytosolic surface of the RER
membranes and released into the ER lumen in a
process called co‐translational translocation.
• secreted proteins
• integral membrane proteins
• soluble proteins that reside within compartments of the
endomembrane system (ER, Golgi complex, lysosomes,
endosomes, vesicles, and plant vacuoles).
The Endoplasmic Reticulum
The Rough Endoplasmic Reticulum
Polypeptides are synthesized at two distinct locations within the cell:
2. Remaining polypeptides are synthesized on “free” ribosomes in the cytosol.
These ribosomes that are not attached to the RER; Proteins are released into
the cytosol.
• proteins destined to remain in the cytosol
• peripheral proteins of the cytosolic surface of membranes
• proteins that are transported to the nucleus
• proteins to be incorporated into peroxisomes, chloroplasts, and mitochondria.
The Endoplasmic Reticulum
RER: Synthesis of Proteins on Membrane-Bound versus Free Ribosomes

What determines the location in a cell where a protein is synthesized?

▪ The site of protein synthesis is determined by the sequence of amino acids in the N-
terminal portion of the polypeptide.
▪ Secretory proteins contain a signal sequence at their N-terminus that directs the
emerging polypeptide and ribosome to the ER membrane.
▪ Proteins contain built-in “address codes” for protein trafficking pathways throughout the
cell. (Signal hypothesis)

N-terminal SS C-terminal
The Endoplasmic Reticulum
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins

Fig. 8.13a A schematic model of the synthesis of a secretory protein (or a lysosomal enzyme) on a
membrane-bound ribosome of the RER
The Endoplasmic Reticulum
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins
▪ Take place by co-translational translocation
▪ The nascent protein is deposited into the ER lumen by a ribosome attached to ER
membrane.
• Polypeptide signal sequence 6–15 hydrophobic amino acid residues, targeting polypeptide to
ER membrane.
▪ Signal sequence (SS) recognized by signal recognition particle (SRP).

• Fig. 8.13a A schematic model of the synthesis of a secretory protein (or a lysosomal enzyme) on a
membrane-bound ribosome of the RER
 The Endoplasmic Reticulum
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins
▪ SRP binds polypeptide and the ribosome, arresting synthesis.
▪ The SRP–ribosome–nascent polypeptide complex is recruited to ER membrane
through interactions between the SRP and the SRP receptor on the ER membrane.
▪ The ribosome is handed off to the translocon, a protein channel embedded in the ER
membrane. Upon attachment, the SS is recognized, the polypeptide is inserted into the
translocon channel.

• Fig. 8.13a A schematic

model of the synthesis
of a secretory protein
(or a lysosomal
enzyme) on a
membrane-bound
ribosome of the RER
The Endoplasmic Reticulum
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins
▪ After the nascent polypeptide passes into the lumen of the ER, the signal peptide is
cleaved by a membrane protein (signal peptidase)
▪ The new protein undergoes folding with the aid of ER chaperones, such as BiP

• Fig. 8.13a A schematic model of the synthesis of a secretory protein (or a lysosomal enzyme) on a
membrane-bound ribosome of the RER
The Endoplasmic Reticulum
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins

▪ Several of the steps involved in the synthesis and trafficking of secretory proteins are regulated
by the binding or hydrolysis of GTP.
▪ SRP and the SRP receptor are G proteins (GTP binding proteins) that interact with one another in
their GTP-bound states; GTP hydrolysis triggers the release of the signal sequence by the SRP.
The Endoplasmic Reticulum
RER: Processing of Newly Synthesized Proteins in the ER

▪ The signal peptide is removed from most nascent polypeptides by signal peptidase,
while carbohydrates are added by oligosaccharyltransferase.
• Both enzymes are integral membrane proteins associated with the translocon.
▪ The ER lumen also contains protein disulfide isomerase (PDI).
• Catalyzed the formation of disulfide bonds between cysteine residues (-SS-).
• Disulfide bonds play an important role in maintaining the stability of proteins in the extracellular
space.
▪ The ER membrane provides a large surface area for ribosomes to attach, and the lumen
gives a specialized local environment that favors protein processing (modification,
folding, and assembly)
The Endoplasmic Reticulum
RER: Synthesis of Integral Membrane Proteins on ER-Bound Ribosomes
▪ Integral membrane proteins are synthesized co-translationally, and their
hydrophobic transmembrane segments are shunted from the translocon into the
lipid bilayer.
▪ During membrane protein synthesis, the inner lining of the translocon orients the
nascent polypeptide so that the more positive end faces the cytosol.

Fig. 8.14 A schematic model for the synthesis of an integral membrane protein
The Endoplasmic Reticulum
RER: Membrane Biosynthesis in the ER
▪ Membranes arise from pre-existing membranes
▪ Membranes are enzymatically modified as they
move from ER into other cellular compartments
▪ Membranes are asymmetric with a cytosolic
face and a luminal/extracellular face established
in the ER

Fig. 8.15 Maintenance of membrane

asymmetry
The Endoplasmic Reticulum
RER: Membrane Biosynthesis in the ER
▪ Membranes of different organelles have different
lipid compositions. They can change their lipid
composition by:
• Using lipid-modifying enzymes to convert a
phospholipid to another

• Preferentially including or excluding phospholipid

vesicles

• Exchanging lipids between organellar compartments

using lipid transfer proteins

Fig. 8.16 Modifying the lipid

composition of membranes
The Endoplasmic Reticulum
RER: Glycosylation in the Rough ER

▪ Nearly all proteins produced on RER become glycoproteins.

▪ Addition of sugars to an oligosaccharide is catalyzed by glycosyltransferases, each
transfers a specific monosaccharide to the growing end of the carbohydrate chain.
▪ The sugar arrangement in the oligosaccharide chains of a glycoprotein depends on the
spatial localization of enzymes in the assembly line.
The Endoplasmic Reticulum Fig. 8.17 Steps in the synthesis
of the core portion of an N-linked
oligosaccharide in the rough ER

RER: Glycosylation in the Rough ER

Step 1,2,3
• The first sugars (five mannose and two NAG
residues) are transferred one at a time to the
dolichol phosphate (dolichol-PP) on the
cytosolic side of the ER membrane.
• dolichol-PP: lipid carrier embedded in the
ER membrane.

• The dolichol with its attached oligosaccharide

is then flipped across the membrane.
The Endoplasmic Reticulum Fig. 8.17 Steps in the synthesis of the core
portion of an N-linked oligosaccharide in the
RER: Glycosylation in the Rough ER rough ER

Step 4, 5, 6
▪ More mannose are attached to dolichol phosphate
molecule (cytosol; one sugar at a time) and then
then flips across the membrane and donates its
sugar to the growing end of the oligosaccharide
chain.

Step 7, 8, 9
▪ Same steps (like 4,5,6) for glucose molecules

Step 10, 11, 12

▪ The assembled oligosaccharide is transferred
enzymatically to an asparagine residue of the
nascent polypeptide.
▪ The dolichol-PP is flipped back across the
membrane and is ready to begin accepting sugars
again.
The Endoplasmic Reticulum
RER: Glycosylation in the Rough ER

▪ Soon after transfer to the polypeptide, the oligosaccharide is gradually modified.

• enzymatic removal of the three terminal glucose residues
▪ A glycoprotein goes through a system of quality control to determine its fitness for a
specific compartment.
• Glucosyltransferase (UGGT) recognizes misfold proteins
▪ Misfolded proteins will be glucose tagged, mannose deficient and ultimately degraded by
proteasomes (ER-associated degradation; occur in the cytosol).
The Endoplasmic Reticulum
RER: Mechanisms That Ensure the Destruction of Misfolded Proteins

▪ Accumulation of misfolded proteins triggers the unfolded protein response (UPR).

▪ Sensors in the ER are kept inactive by the chaperone BiP.
▪ When misfolded proteins accumulate, BiP is incapable of inhibiting the sensors.
▪ Activated sensors send signals to trigger proteins involved in destruction of misfolded
proteins.
The Endoplasmic Reticulum
The ER to Golgi Vesicular Transport
▪ The ER to the Golgi Complex is the first step in vesicular transport.
▪ RER have specialized exit sites where transport vesicles are formed.
▪ Transport vesicles fuse with one another to form larger vesicles and interconnected
tubules in the region between the ER and Golgi complex called ERGIC
(endoplasmic reticulum Golgi intermediate compartment)
▪ The vesicular–tubular carriers that form there are called VTCs

Fig. 8.20 Visualizing membrane traffic with the use of a fluorescent tag
The Golgi Complex
▪ The Golgi complex is a stack of flattened cisternae.
▪ Several functionally distinct compartments:
• cis face of the Golgi faces the ER
• trans face is on the opposite side of the stack.

Fig. 8.21a,b The Golgi

complex
The Golgi Complex
▪ The cis Golgi network (CGN) functions to sort proteins for the ER (shipped back) or proceed
to the next Golgi station.
▪ The bulk of the Golgi complex consists of cis, medial, trans cisternae.
▪ The trans Golgi network (TGN) functions in sorting proteins to the plasma membrane or
various intracellular destinations.
▪ The Golgi complex is not uniform in composition; there are differences in composition from the
cis to the trans face.
The Golgi Complex
▪ Assembly of carbohydrates found in glycolipids and glycoproteins takes place in the Golgi.
▪ Following the removal of the three glucose residues (ER), various mannose residues are
subsequently removed
▪ Sequence of incorporation of a variety of sugars (N-acetylglucosamine, galactose, fucose, and
sialic acid) into oligosaccharides is determined by glycosyltransferases.
▪ These enzymes are integral membrane proteins with active sites that face the lumen of the Golgi
cisternae.
▪ The synthesis of O-linkage oligosaccharides takes place in the ER and the N-linkage
oligosaccharides in the Golgi complex

Fig. 8.23 Steps in the

Glycosylation of a typical
mammalian N-linked
oligosaccharide in the Golgi
Complex
The Golgi Complex
The dynamics of transport through the
Golgi complex.
a) In the vesicular transport model, cargo is
shuttled from the CGN to the TGN in
vesicles.
b) In the cisternal maturation model, each
cisternae “matures” as it moves from the
cis face to the trans face.

Current model: similar to cisternal maturation

model but with vesicle retrograde transport.
Golgi cisternae serve a primary anterograde
carriers.

Fig. 8.24 The dynamics of transport through the Golgi complex

The signal sequence is found at the N-terminus of:

a) secretory proteins.

b) all proteins.

c) housekeeping proteins.

d) None of these is correct.

Which of the following processes does NOT take place in the Golgi
complex?

a) glycosylation of glycoproteins and glycolipids

b) digestion of misfolded proteins

c) processing of membrane proteins

d) processing of lysosomal proteins

 Module 7c
Cytoplasmic Membrane Systems: Structure, Function, and
Membrane Trafficking
Module 7: Assessments
• Quiz 6
• Due March 1st

• Analytic assignment 3
• Due by March 2nd

• Exam 2
• March 3-5th
Learning objectives
By the end of this module, you should be able to:
▪ Distinguish the functions of the different types of vesicle transport.
▪ Explain the functions of lysosomes.
▪ List the functions of plant cell vacuoles.
▪ Explain the processes involved in the bulk transport of materials into the cell
(endocytic pathway).
▪ Describe how proteins are taken up by mitochondria, chloroplasts, and
peroxisomes.
Targeting vesicles to a particular compartment
includes the following steps EXCEPT:

a) tethering of vesicles

b) movement of vesicles

c) docking of vesicles

d) coating of vesicles
In phagocytosis, the phagosome fuses with which
organelle, leading to the digestion of engulfed material?

a) Golgi complex

b) endoplasmic reticulum

c) lysosome

d) mitochondria
The Golgi Complex
▪ The cis Golgi network (CGN) functions to sort proteins for the ER (shipped back) or
proceed to the next Golgi station.
▪ The trans Golgi network (TGN) functions in sorting proteins to the plasma
membrane or various intracellular destinations.
Vesicle Transport
▪ Bud from donor membranes and fuse with
acceptor membranes.
▪ Materials are carried between compartments
using coated vesicles.
▪ Protein coats have two functions:
1. Cause the membrane to curve and form a
vesicle.
2. Select the components to be carried by the
vesicle.

Selected components include: Fig. 8.25 Coated

• secretory, lysosomal, and membrane proteins Vesicles
• the machinery required to target and dock the
vesicle to the correct acceptor membrane

Fig. 8.2 Vesicle transport

Types of Vesicle Transport
▪ COPII-coated vesicles – move materials from
the ER “forward” to the ERGIC intermediate
compartment and Golgi complex.
• ER export signals
▪ COPI-coated vesicles – move materials from
ERGIC and Golgi “backward” to ER, or from the
trans Golgi to the cis Golgi cisternae.
• Retrieval signals (C-terminal)
▪ Clathrin-coated vesicles – move materials
from:
• the TGN to endosomes, lysosomes, and
plant vacuoles.
• the plasma membrane to cytoplasmic
compartments (endocytic pathway).
• They have also been implicated in
trafficking from endosomes and lysosomes.
Fig. 8.26 Proposed transport between membrane
compartments of the biosynthetic-secretory pathway
Types of Vesicle Transport
Beyond the Golgi Complex: Sorting Proteins at the
TGN to lysosomes
▪ Sorting and transport of lysosomal enzymes utilizes
clathrin-coated vesicles.
▪ Lysosomal proteins are tagged in the cis-Golgi with
phosphorylated mannose residues.
▪ Tagged lysosomal enzymes are recognized and
captured by mannose 6-phosphate receptors
(MPRs), which are bound by coat proteins.

Fig. 8.30 Targeting lysosomal

enzymes to lysosomes
Types of Vesicle Transport
▪ Vesicle coat is composed of two distinct protein
layers:
• an outer cage or scaffolding that forms the
framework for the coat
• an inner layer of adaptors that binds both to the
outer surface of the lipid bilayer and to the
membrane’s cargo.
▪ Adaptors are able to select specific cargo
molecules by the cytosolic “tails” of the integral
proteins.

Proposed transport between membrane

compartments of the biosynthetic-secretory pathway
Types of Vesicle Transport
Beyond the Golgi Complex: Sorting Proteins at the TGN—Targeting Vesicles to
a Particular Compartment
▪ The steps that occur between vesicle budding and vesicle fusion
include:
1. Movement of the vesicle toward the specific target compartment:
mediated largely by microtubules and their associated motor proteins
(railroad system).
2. Tethering vesicles to the target compartment: mediated by a
diverse collection of “tethering” proteins. Rab proteins recruit the
tethering proteins
3. Docking vesicles to the target compartment: vesicle and target
compartment membranes come into close contact via interaction
between integral proteins of the two membranes. SNARE proteins
4. Fusion between vesicle and target membranes.
Types of Vesicle Transport
Beyond the Golgi Complex: Sorting Proteins at the TGN—Targeting Vesicles to
a Particular Compartment

▪ Rabs are a family of small G proteins that

cycle between an active GTP bound state
and an inactive GDP bounds state.
▪ GTP-bound Rabs associate with membranes
by a lipid anchor. Lipid anchor protein
▪ Over 60 different Rab genes identified in
humans
▪ Different Rabs become associated with
different membrane compartments.
Fig. 8.32a Proposed steps in the targeting
▪ Rab proteins recruit the tethering proteins of transport vesicles to target membranes
Types of Vesicle Transport
Beyond the Golgi Complex: Sorting Proteins at the TGN—Targeting Vesicles to
a Particular Compartment

Docking vesicles to the target compartment

▪ SNAREs constitute a family of proteins localized to
specific subcellular compartments.
▪ SNAREs are integral proteins that bring the vesicle
and target compartment in close contact
▪ v‐SNAREs are found in transport vesicles and
t‐SNAREs are located in the target compartments.

Fig. 8.32c Proposed steps in the targeting

of transport vesicles to target membranes
Types of Vesicle Transport
Beyond the Golgi Complex: Sorting Proteins at the TGN—Targeting Vesicles to
a Particular Compartment

Fig. 8.32c Proposed steps in the targeting of transport vesicles to target membranes
Types of Vesicle Transport
Beyond the Golgi Complex: Sorting Proteins at the TGN—Exocytosis
▪ Exocytosis – discharge of a secretory vesicle or
granule after fusion with the plasma membrane (PM).
▪ Process is triggered by an increase in [Ca2+].
▪ The luminal part of the vesicle membrane becomes the
outer surface of the PM, and the cytosolic part becomes
part of the inner surface of the PM.
Lysosomes
▪ Role of lysosomes is the breakdown of materials in the cell.
▪ Lysosomes contain at least 50 different hydrolytic enzymes produced in the
RER and can hydrolyze virtually every type of biological macromolecule.
▪ Lysosomal enzymes (acid hydrolases) have optimal activity in the acidic lumen
(pH 4.6)
Lysosomes-Autophagy
▪ Lysosomes play a role in the regulated process of
organelle turnover, known as autophagy.
(destruction and replacement of the cell’s own
organelles)
▪ A phagophore envelops an organelle to produce a
double-membrane sequestering vesicle called an
autophagosome.
▪ This fuses with a lysosome, generating an
autolysosome, both the inner membrane of the
autophagosome and the enclosed contents are
degraded.
Lysosomes-Autophagy
▪ Autophagy is a natural process in which the body's
cells clean out any damaged or unnecessary
components.
▪ Starvation response
▪ Cells acquire energy to maintain their life by
cannibalizing their own organelles.
Green Cells: Plant Cell Vacuoles
▪ Lysosomes are found in all animal cells, not in
plant cells
▪ A vacuole is a membrane-bound, fluid-filled
compartment.
▪ Plant vacuoles have several storage functions:
• Storage of solutes and macromolecules
• Storage of toxins
• Ionic concentration capability
▪ The vacuole membrane (tonoplast) contains an
active transport system to keep a high
concentration of ions so that water enters by
osmosis.
▪ Plant vacuoles contain acid hydrolases for
degradation of biomolecules.
▪ RER-Golgi complex-vacuole
Fig. 8.38 Plant cell vacuoles
The Endocytic Pathway: Moving Membrane and
Materials into the Cells Interior

Two basic processes, different mechanisms:

1. Endocytosis is primarily a process by which the cell
internalizes cell-surface receptors and bound
extracellular ligands.
2. Phagocytosis is the uptake of particulate matter
The Endocytic Pathway: Moving Membrane and Materials
into the Cells Interior
Endocytosis: The Endocytic Pathway
Two different types of receptors that are subjected to
endocytosis:
▪ housekeeping receptors: responsible for the uptake of
materials that will be used by the cell. E.g. iron & cholesterol
▪ signaling receptors: responsible for binding extracellular
ligands that carry messages that change the activities of the
cell. E.g. hormones such as insulin and growth factors
The Endocytic Pathway: Moving Membrane and Materials
into the Cells Interior
Endocytosis: The Endocytic Pathway
▪ After internalization, vesicle-bound
materials are transported in vesicles
and tubules known as endosomes.
▪ Early endosomes are located near
the periphery of the cell. It sorts
materials and sends bound ligands to
the late endosomes.
The Endocytic Pathway: Moving Membrane and
Materials into the Cells Interior
Phagocytosis “cell eating”
▪ Phagocytosis is carried out by cells specialized for
the uptake of relatively large particles.
▪ The folds fuse to produce a vacuole (phagosome)
that pinches off inwardly from the plasma membrane
and fuses with a lysosome (phagolysosome).
▪ In most animals, phagocytosis is a protective
mechanism rather than a mode of feeding.
▪ Mammals have “professional” phagocytes, e.g.,
macrophages and neutrophils, that phagocytize
invading organisms, damaged and dead cells.
Posttranslational Uptake of Proteins by Peroxisomes,
Mitochondria, and Chloroplasts
▪ Unlike RER, which generally imports its proteins cotranslationally, the proteins of
these other organelles are imported posttranslationally, following their complete
synthesis on free ribosomes in the cytosol.

▪ The nucleus, mitochondria, chloroplasts, and peroxisomes import proteins through

one or more outer boundary membranes.

▪ These proteins contain amino acid sequences that serve as addresses that are
recognized by receptors at the organelle’s outer membrane.
Posttranslational Uptake of Proteins by Peroxisomes,
Mitochondria, and Chloroplasts
Uptake of Proteins Into Peroxisomes
▪ Peroxisomes have two subcompartments in which an imported protein can be placed: the
boundary membrane and the internal matrix.
▪ Peroxisomal proteins possess a peroxisomal targeting signal
Posttranslational Uptake of Proteins by Peroxisomes,
Mitochondria, and Chloroplasts
Uptake of Proteins Into Mitochondria
▪ The outer mitochondrial membrane includes a
protein-import complex (TOM complex) which
includes a receptor and channel.
▪ Proteins destined for the inner mitochondrial
membrane engage with another protein-import
complex (TIM complex).
▪ Inner membrane: internal targeting sequences
▪ Matrix: presequence located at the N-terminus

Fig. 8.49 Importing

proteins into a
mitochondrion
Posttranslational Uptake of Proteins by Peroxisomes,
Mitochondria, and Chloroplasts
Uptake of Proteins Into Chloroplasts
▪ Outer and inner envelope membranes contain
translocation complexes (Toc and Tic) to
facilitate the import of the proteins.
▪ Chaperones unfold proteins in the cytosol and
fold them in the chloroplasts.
▪ Chloroplast translocation:
• Proteins include a transit peptide sequence.
▪ All proteins translocated through the chloroplast
envelope contain a
• stroma-targeting domain
▪ Thylakoid translocation
• thylakoid transfer domain Fig. 8.50 Importing proteins
into a chloroplast
Targeting vesicles to a particular compartment
includes the following steps EXCEPT:

a) tethering of vesicles

b) movement of vesicles

c) docking of vesicles

d) coating of vesicles

d) coating of vesicles
In phagocytosis, the phagosome fuses with which organelle,
leading to the digestion of engulfed material?

a) Golgi complex

b) endoplasmic reticulum

c) lysosome

d) mitochondria

c) lysosome