Chloroplasts and Photosynthesis

MM701
Dr. Muniza Shaikh
Dr. Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi
 Introduction
• Virtually all of the organic materials required by living cells have
been produced by photosynthetic organisms, including plants and
photosynthetic bacteria.
• Almost all plants are photosynthetic autotrophs, as are some
bacteria and protists
– Autotrophs generate their own organic matter through photosynthesis
– Sunlight energy is transformed to energy stored in the form of chemical
bonds
• The core machinery that drives all photosynthesis appears to have
evolved more than 3 billion years ago in the ancestors of present-
day bacteria.
 Chloroplast
• In Plants (including algae), photosynthesis occurs in a
specialized intracellular organelle—the chloroplast.
• Chloroplasts use chemiosmotic mechanisms to carry out
their energy interconversions in much the same way that
mitochondria do.
• Chloroplast are much larger than mitochondria, and
organized on the same principles.
• They have:
• A highly permeable outer membrane;
• A much less permeable inner membrane, in which
membrane transport proteins are embedded;
• A narrow intermembrane space in between.
• Together, these two membranes form the chloroplast
envelope
• The inner chloroplast membrane surrounds a
large space called the stroma, which is
analogous to the mitochondrial matrix.
• The stroma contains many metabolic enzymes
and, it is the place where ATP is made by the
head of an ATP synthase.
• Chloroplast has its own genome and genetic
system. The stroma therefore also contains a
special set of ribosomes, RNAs, and the
chloroplast DNA.
• Unlike mitochondria, chloroplast has a
separate, distinct membrane in stroma, called
thylakoid membrane, that forms a set of
flattened, disc-like sacs, the thylakoids.
• The thylakoid membrane is highly folded into
numerous local stacks of flattened vesicles
called grana, interconnected by nonstacked
thylakoids.
• The electron-transport chains, photosynthetic
light-capturing systems, and ATP synthase are
all contained in the thylakoid membrane.
A mitochondrion and
chloroplast compared

• Chloroplasts are generally larger than mitochondria.

• In addition to an outer and inner envelope membrane,
they contain the thylakoid membrane with its internal
thylakoid space.
• The chloroplast thylakoid membrane, which is the
site of solar energy conversion in plants and algae,
corresponds to the mitochondrial cristae, which are
the sites of energy conversion by cellular respiration.
• Unlike the crista membrane, which is continuous with
the inner mitochondrial membrane at cristae
junctions, the thylakoid membrane is not connected
to the inner chloroplast membrane at any point.
 Chloroplasts Capture Energy from Sunlight and Use
It to Fix Carbon
• The reactions that occur during photosynthesis
in chloroplasts are divided into two broad
categories:
• Photosynthetic electron-transfer reactions
(light reactions) (thylakoid membrane)
• Chlorophyll and other pigments of
photosynthetic cells absorb light energy and
conserve it as ATP and NADPH
simultaneously, O2 is evolved.
• Carbon-fixation reactions (stroma)
• ATP and NADPH are used to reduce CO2 to
form triose phosphates(glyceraldehyde 3-
phosphate), starch, and sucrose, and other
products derived from them.
ATP and NADPH required for carbon
fixation are generated in the chloroplast
• The thylakoid membranes contain two large membrane protein
complexes, called photosystems.
• Photosystems endow plants and other photosynthetic organisms with
the ability to capture and convert solar energy for their own use.
• Two other protein complexes in the thylakoid membrane that work
together with the photosystems in photophosphorylation are heme-
containing cytochrome b -f complex, and chloroplast ATP synthase
6
Chlorophyll–Protein Complexes Can
Transfer Either Excitation Energy or
Electrons
• The photosystems in the thylakoid membrane are
multiprotein assemblies.
• They contain large numbers of specifically bound
chlorophyll molecules, in addition to cofactors
(heme, iron–sulfur clusters, and quinones).
• Chlorophyll, the green pigment of photosynthetic
organisms, has a long hydrophobic tail that makes it
behave like a lipid, plus a porphyrin ring that has a
central Mg atom and an extensive system of
delocalized electrons in conjugated double bonds
 Continued……
• When a chlorophyll molecule absorbs a quantum of sunlight (a
photon), the energy of the photon causes one of these electrons to
move from a low-energy molecular orbital to another orbital of
higher energy.
Isol
• The excited electron in a chlorophyll molecule tends to return Chl ated
o
mo rophy
quickly to its ground state, which can occur in one of three ways: lecu
solu l e
ll
tion in
1. By converting the extra energy into heat (molecular motion) or
to some combination of heat and light of a longer wavelength
(fluorescence);
2. By transferring the energy directly to a neighboring chlorophyll Chl
o
mo rophy
molecule by a process called resonance energy transfer. com lecule ll
plex in
pro w
3. By transferring the excited electron to another nearby tein ith
s
molecule, an electron acceptor.
Continued……

• When excited by a photon, most protein-bound chlorophylls simply

transmit the absorbed energy to another nearby chlorophyll by the process
of resonance energy transfer.
• However, in a few specially positioned chlorophylls, the energy difference
between the ground state and the excited state is just right for the photon
to trigger a light-induced chemical reaction.
• The special state of such chlorophyll molecules derives from their close
interaction with a second chlorophyll molecule in the same chlorophyll–
protein complex. Together, these two chlorophylls form a special pair.
• The protein coordinates the central Mg atom in the chlorophyll porphyrin,
most often through a histidine side chain located in the hydrophobic
interior of a membrane, causing each of the chlorophylls in a protein
complex to be held at exactly defined distances and orientations.
• The photosynthetic electron transfer process starts when a photon of suitable energy ionizes a
chlorophyll molecule in such a special pair, dissociating it into an electron and a positively
charged chlorophyll ion
• The energized electron is passed rapidly to a quinone in the same protein complex, preventing its
unproductive reassociation with the chlorophyll ion
• This light-induced transfer of an electron from a chlorophyll to a mobile electron carrier is the
central charge-separation step in photosynthesis, in which a chlorophyll becomes positively
charged and an electron carrier becomes negatively charged.
• The chlorophyll ion is a very strong oxidant that is able to withdraw an electron from a low-
energy
• substrate; in the first step of oxygenic photosynthesis, this low-energy substrate is water.
A Photosystem Consists of an Antenna
Complex and a Reaction Center
• There are two distinct types of chlorophyll–
protein complexes in the photosynthetic
membrane.
• A photochemical reaction center
(transmembrane chlorophyll–protein
complex), contains the special pair of
chlorophylls
• An antenna complex engages exclusively in
light absorption and resonance energy transfer. The solar energy for photosynthesis is collected by the antenna complexes,
which account for most of the chlorophyll in a plant cell. The energy hops
randomly by resonance energy transfer from one chlorophyll molecule to
• The two types of complex make up a another, until it reaches the reaction center complex, where it ionizes a
chlorophyll in the special pair. The chlorophyll special pair holds its
photosystem electrons at a lower energy than the chlorophyll in the antenna complexes,
causing the energy transferred to it from the antenna complex to become
trapped there. Note that it is only energy that moves from one chlorophyll
molecule to another in the antenna complex, not Electrons.
 Continued…….
• The antenna complex in the photosystem collects the energy of a
sufficient number of photons for photosynthesis
• The antenna complex is also known as a light-harvesting
complex, or LHC.
• When light excites a chlorophyll molecule in the antenna
complex, the energy passes rapidly from one protein- bound
chlorophyll to another by resonance energy transfer until it
reaches the special pair in the reaction center.
• In addition to many chlorophyll molecules, an LHC contains
orange carotenoid pigments. The carotenoids collect light of a
different wavelength from that absorbed by chlorophylls,
helping to make the antenna complex more efficient.
• They also have an important protective role in preventing the
formation of harmful oxygen radicals in the photosynthetic
membrane.
The Thylakoid Membrane Contains Two
Different Photosystems Working in Series
• Chloroplasts contain two functionally
different although structurally related
photosystems,
• Photosystem I confined to the unstacked
stroma thylakoids
• Photosystem II confined to stacked grana
thylakoids
• Electrons are first activated in photosystem II
before being transferred to photosystem I. The Z scheme for photosynthesis. The thylakoids of plants and
cyanobacteria contain two different photosystems, known as photosystem
• The path of the electron through the two I and photosystem II, which work in series. Each of the photosystem I and
II reaction centers receives excitation energy from its own set of tightly
photosystems can be described as a Z-like associated antenna complexes, known as LHC-I and LHC-II, by resonance
trajectory and is known as the Z scheme. energy transfer.
Continued…….
• In the Z scheme, the reaction center of photosystem II first withdraws
an electron from water.
• The electron passes via an electron-transport chain (composed of the
electron carrier plastoquinone, the cytochrome b -f complex, and the
6

protein plastocyanin) to photosystem I.

• Photosystem I propels the electron across the membrane in a second
light-driven charge-separation reaction that leads to NADPH
production.
• The Z scheme is necessary to bridge the very large energy gap
between water and NADPH.
Changes in redox potential during photosynthesis.

The redox potential for each molecule is indicated

by its position along the vertical axis.
Photosystem II passes electrons derived from
water to photosystem I, which in turn passes them
to NADP+ through ferredoxin- NADP+
reductase.
The net electron flow through the two
photosystems is from water to NADP+, and it
produces NADPH as well as an electrochemical
proton gradient.
This proton gradient is used by the ATP synthase
to produce ATP .
Photosystem II Uses a Manganese Cluster to
Withdraw Electrons From Water
• The withdrawal of electrons from water and to
generate molecular oxygen as a waste product is a
remarkable specialization of photosystem II.
• This specialty is conferred by the unique properties of
one of the two chlorophyll molecules of its special
pair and by a manganese cluster linked to the protein.
• The chlorophyll molecules and manganese cluster
form the catalytic core of the photosystem II reaction
center.
• The chlorophyll special pair called P680 (P680/P680+
redox potential = +1270 mV) is responsible of
harvesting electrons from highly stable water • The intermediates remain firmly attached to the manganese
molecule. cluster until two water molecules have been fully oxidized to
O2.
• The reaction 2H2O + 4 photons → 4H+ + 4e– + O2 is • The protons released by the two water molecules are
catalyzed by its adjacent manganese cluster. discharged to the thylakoid space, contributing to the proton
gradient across the thylakoid membrane (pH lower in the
thylakoid space than in the stroma).
 The Cytochrome b6-f Complex Connects Photosystem II to
Photosystem I

• The cytochrome b6-f complex is the functional equivalent of cytochrome c reductase (the cytochrome b-
c1 complex) in mitochondria
• Like its mitochondrial homolog, the b6-f complex receives its electrons from a quinone and pumps two
protons across the membrane.
• It hands its electrons, one at a time, to plastocyanin (pC).
• Plastocyanin diffuses along the membrane surface to photosystem I and transfers the electrons via
ferredoxin (Fd) to the ferredoxin-NADP+ reductase (FNR), where they are utilized to produce NADPH.
• P700 is a special pair of chlorophylls that absorbs light of wavelength 700 nm.
 Photosystem I Carries Out the Second
Charge-Separation Step in the Z Scheme
• Photosystem I receives electrons from plastocyanin in the thylakoid
space and transfers them, via a second charge-separation reaction, to
the small protein ferredoxin on the opposite membrane surface.
• in a final step, ferredoxin feeds its electrons to a membrane-associated
enzyme complex, the ferredoxin-NADP+ reductase, which uses the
electrons to produce NADPH from NADP+
• The redox potential of the NADP+/NADPH pair (–320 mV) is already
very low, and reduction of NADP+ therefore requires a compound with
an even lower redox potential.
• A chlorophyll molecule near the stromal membrane surface of
photosystem I has a redox potential of –1000 mV (chlorophyll A ),0

which hand the electrons on to ferredoxin via two plastoquinones (PQ;

purple) and three iron–sulfur clusters
• The reduced NADPH is released into the chloroplast stroma, where it
is used for biosynthesis of glyceraldehyde 3-phosphate, amino acid
precursors, and fatty acids, much of it to be exported to the cytoplasm.
• The linear Z scheme for photosynthesis can switch to a circular mode of
electron flow through photosystem I and the b6-f complex.
• The reduced ferredoxin diffuses back to the b6-f complex to reduce
plastoquinone, instead of passing its electrons to the ferredoxin-NADP+
reductase enzyme complex.
• This turns photosystem I into a light-driven proton pump, thereby increasing
the proton gradient and thus the amount of ATP made by the ATP synthase.
• An elaborate set of regulatory mechanisms control this switch, which
enables the chloroplast to generate either more NADPH (linear mode) or
more ATP (circular mode), depending on the metabolic needs of the cell.
The Proton-Motive Force for ATP
Production
• The proton gradient across the thylakoid membrane depends
on:
1. The proton-pumping activity of the cytochrome b6-f
complex
2. The photosynthetic activity of the two photosystems, which
in turn depends on light intensity
• In chloroplasts exposed to light, H+ is pumped out of the
stroma (pH around 8, similar to the mitochondrial matrix)
into the thylakoid space (pH 5–6), creating a gradient of 2–3
pH units across the thylakoid membrane, representing a
proton-motive force of about 180 mV.
• In contrast to mitochondrial ATP synthase, which forms long
rows of dimers along the cristae ridges, the chloroplast ATP
synthase is monomeric and located in flat membrane regions
Carbon Fixation Uses ATP and
NADPH to Convert CO2 into Sugars
• Animal cells produce ATP by using the large amount of free energy
released when carbohydrates are oxidized to CO2 and H2O.
• The reverse reaction, in which plants make carbohydrate from CO2
and H2O, takes place in the chloroplast stroma.
• The large amounts of ATP and NADPH produced by the
photosynthetic electron-transfer reactions are required to drive this
energetically unfavorable reaction.
The initial reaction in carbon fixation.

• This carboxylation reaction allows one molecule each of carbon

dioxide and water to be incorporated into organic carbon
molecules.
• It is catalyzed in the chloroplast stroma by an abundant large
enzyme ribulose bisphosphate carboxylase, or Rubisco.
• The product is two molecules of 3-phosphoglycerate.
• The reaction catalyzed by Rubisco is so slow (each Rubisco molecule
turns over only about 3 molecules of substrate per second, compared
to 1000 molecules per second for a typical enzyme).
• An unusually large number of enzyme molecules are needed to speed
up the reaction.
• Rubisco often constitutes more than 50% of the chloroplast protein
mass, and it is thought to be the most abundant protein on Earth.
• Rubisco also keeps the amount of the greenhouse gas CO2 in the
atmosphere at a low level
• Although the production of carbohydrates from CO2 and H2O is
energetically unfavorable, the fixation of CO2 catalyzed by Rubisco is
an energetically favorable reaction.
• Carbon fixation is energetically favorable because a continuous supply
of the energy-rich ribulose 1,5-bisphosphate is fed into the process.
• This compound is consumed by the addition of CO2, and it must be
replenished.
• The energy and reducing power needed to regenerate ribulose 1,5-
bisphosphate come from the ATP and NADPH produced by the
photosynthetic light reactions
Carbon-fixation cycle, Calvin cycle

• This central metabolic pathway allows organic molecules to

be produced from CO2 and H2O.
• In the first stage of the cycle (carboxylation), CO2 is added
to ribulose 1,5-bisphosphate.
• In the second stage (reduction), ATP and NADPH are
consumed to produce glyceraldehyde 3-phosphate
molecules.
• In the final stage (regeneration), some of the glyceraldehyde
3-phosphate produced is used to regenerate ribulose 1,5-
bisphosphate.
• Other glyceraldehyde 3-phosphate molecules are either
converted to starch and fat in the chloroplast stroma, or
• transported out of the chloroplast into the cytosol.
• The number of carbon atoms in each type of molecule is
indicated in yellow.
Sugars Generated by Carbon Fixation Can Be
Stored as Starch or Consumed to Produce ATP
• The glyceraldehyde 3-phosphate generated by carbon fixation in the chloroplast
stroma can be used in a number of ways, depending on the needs of the plant.
• During periods of excess photosynthetic activity, much of it is retained in the
chloroplast stroma and converted to starch.
• Other glyceraldehyde 3-phosphate molecules are converted to fat in the stroma.
• This material, which accumulates as fat droplets, likewise serves as an energy
reserve.
• At night, this stored starch and fat can be broken down to sugars and fatty acids,
which are exported to the cytosol to help support the metabolic needs of the plant.
• Some of the exported sugar enters the glycolytic pathway where it is converted to
pyruvate.
How chloroplasts and mitochondria collaborate to supply cells with both
metabolites and ATP

• The inner chloroplast membrane is impermeable to the ATP and NADPH that are produced in the
stroma during the light reactions of photosynthesis.
• These molecules are therefore funneled into the carbon-fixation cycle, where they are used to
make sugars.
• The resulting sugars and their metabolites are either stored within the chloroplast—in the form of
starch or fat—or exported to the rest of the plant cell.
• There, they can enter the energy-generating pathway that ends in ATP synthesis linked to
oxidative phosphorylation inside the mitochondrion.
• The O2 released to the atmosphere by photosynthesis in chloroplasts is used for oxidative
phosphorylation in mitochondria; Similarly, the CO2 released by the citric acid cycle in
mitochondria is used for carbon fixation in chloroplasts.
• (B) In a leaf, mitochondria (red) tend to cluster close to the chloroplasts (green), as seen in this
light micrograph. (B, courtesy of Olivier Grandjean.)
• In some specialized fat cells, mitochondrial respiration is uncoupled from ATP
synthesis by the uncoupling protein, another member of the mitochondrial carrier
family.
• In these cells, known as brown fat cells, most of the energy of oxidation is dissipated
as heat rather than being converted into ATP.
• In the inner membranes of the large mitochondria in these cells, the uncoupling
protein allows protons to move down their electrochemical gradient without passing
through ATP synthase.
• This process is switched on when heat generation is required, causing the cells to
oxidize their fat stores at a rapid rate and produce heat rather than ATP.
• Tissues containing brown fat serve as “heating pads,” helping to revive hibernating
animals and to protect newborn human babies from the cold.
THE GENETIC SYSTEMS OF
MITOCHONDRIA AND CHLOROPLASTS

• Mitochondria and chloroplasts are thought to

have evolved from endosymbiotic bacteria.
• Both types of organelles still contain their The origin of mitochondria. An ancestral anaerobic predator cell (an archaeon) is thought to have engulfed the
bacterial ancestor of mitochondria, initiating a symbiotic relationship. Clear evidence of a dual bacterial and
archaeal inheritance can be discerned today in the genomes of all eukaryotes.

own genomes.
• They also retain their own biosynthetic
machinery for making RNA and organellar
proteins.
• Mitochondria and chloroplasts proliferate by
growth and division of an existing organelle The origin of chloroplasts. An early eukaryotic cell, already possessing mitochondria, engulfed a
Photosynthetic bacterium (a cyanobacterium) and retained it in symbiosis. Present-day chloroplasts
are thought to trace their ancestry back to a single species of cyanobacterium that was adopted as
an internal symbiont (an endosymbiont) over a billion years ago.
• Mitochondria and chloroplasts proliferate by growth and division of an existing
organelle
• Organelle growth and proliferation are carefully controlled.
• The process is complicated because mitochondrial and chloroplast proteins are
encoded in two places:
1. the nuclear genome
2. and the separate genomes harbored in the organelles themselves.
• Most organellar proteins are encoded by the nuclear DNA
• The organelle imports these proteins from the cytosol, after they have been
synthesized on cytosolic ribosomes, through the mitochondrial protein translocases
of the outer and inner mitochondrial membrane—TOM and TIM.
The Genetic Systems of Mitochondria and
Chloroplasts Resemble Those of Prokaryotes
• It is thought that eukaryotic cells originated through a symbiotic relationship between an archaeon
and an aerobic bacterium
• This endosymbiont hypothesis of organelle development receives strong support from the observation
that the genetic systems of mitochondria and chloroplasts are similar to those of present-day bacteria
• For example, chloroplast ribosomes are very similar to bacterial ribosomes, both in their structure and
in their sensitivity to various antibiotics (such as chloramphenicol, streptomycin, erythromycin, and
tetracyclin).
• Protein synthesis in chloroplasts starts with N-formylmethionine,
• Although mitochondrial genetic systems are much less similar to those of present-day bacteria than
are the genetic systems of chloroplasts, their ribosomes are also sensitive to antibacterial antibiotics,
and protein synthesis in mitochondria also starts with N-formylmethionine
• The processes of organelle DNA transcription, protein synthesis, and DNA replication take place in
the matrix of mitochondria or the stroma of chloroplasts.
One suggested pathway for the evolution of the eukaryotic
cell and its internal membranes There is evidence that the
nuclear genome of a eukaryotic cell evolved from an ancient
archeaon.
For example, clear homologs of actin, tubulin, histones, and the
nuclear DNA replication system are found in archaea, but not in
bacteria. Thus, it is now thought that the first eukaryotic cells
arose when an ancient anaerobic archaeon joined forces with an
aerobic bacterium roughly
1.6 billion years ago. As indicated, the nuclear envelope may
have originated from an invagination of the plasma membrane
of this ancient archaeon—an invagination that protected its
chromosome while still allowing access of the DNA to the
cytosol (as required for DNA to direct protein synthesis). This
envelope may have later pinched off completely from the
plasma membrane, so as to produce a separate nuclear
compartment surrounded by a double membrane. Because this
double membrane is penetrated by nuclear pore complexes, the
nuclear compartment is topologically equivalent to the cytosol.
In contrast, the lumen of the ER is continuous with the space
between the inner and outer nuclear membranes, and it is
topologically equivalent to the extracellular space.
Over Time, Mitochondria and Chloroplasts Have Exported
Most of Their Genes to the Nucleus by Gene Transfer
• The smallest and presumably most highly evolved mitochondrial genomes, for
example, encode only a few hydrophobic inner-membrane proteins of the electron-
transport chain, plus ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs).
• The most complex mitochondrial genomes include genes that encode components
of the mitochondrial genetic system, such as RNA polymerase subunits and
ribosomal proteins
• The protein traffic between the cytosol and these organelles seems to be
unidirectional: proteins are normally not exported from mitochondria or
chloroplasts to the cytosol.
• An important exception occurs when a cell is about to undergo apoptosis (during
apoptosis the mitochondrion releases proteins (most notably cytochrome c) from
the crista space through its outer mitochondrial membrane)
The Fission and Fusion of Mitochondria
Are Topologically Complex Processes
• The topologically complex processes must ensure the integrity of the
separate mitochondrial compartments defined by the inner and outer
membranes.
• These processes control the number and shape of mitochondria, which
can vary dramatically in different cell types, ranging from multiple
spherical or wormlike organelles to a highly branched, net-shaped
single organelle called a reticulum.
Mitochondrial Fission
• The mitochondrial fission machine works by
assembling dynamin-related GTPases into helical
oligomers that cause local constrictions in tubular
mitochondria.
• GTP hydrolysis then generates the mechanical force
that severs the inner and outer mitochondrial
membranes in one step

A model for mitochondrial division. Dynamin-1 (yellow) exists as

dimers in the cytosol, which form larger oligomeric structures in a
process that requires GTP hydrolysis. Dynamin assemblies interact with
the outer mitochondrial membrane through special adaptor proteins,
forming a spiral of GTP-dynamin around the mitochondrion that causes
a constriction.
A concerted GTP-hydrolysis event in the dynamin subunits is then
thought to produce the conformational changes that result in fission.
Mitochondrial fusion
• Mitochondrial fusion requires two
separate machineries, one each for
the outer and the inner membrane.
A model for mitochondrial fusion.
• The fusions of the outer and inner mitochondrial membranes are
coordinated sequential events, each of which requires a separate set of
protein factors.
• Outer membrane fusion is brought about by an outer-membrane
GTPase (purple), which forms an oligomeric complex that includes
subunits anchored in the two membranes to be fused.
• Fusion of outer membranes requires GTP and an H+ gradient across
the inner membrane.
• For fusion of the inner membrane, a dynamin-related protein forms an
oligomeric tethering complex (blue) that includes subunits anchored in
the two inner membranes to be fused.
• Fusion of the inner membranes requires GTP and the electrical
component of the potential across the inner membrane.
Animal Mitochondria Contain the Simplest
Genetic Systems Known
• Comparisons of DNA sequences in different organisms reveal that, in
vertebrates (including ourselves), the mutation rate during evolution
has been roughly 100 times greater in the mitochondrial genome than
in the nuclear genome.
• This difference is likely to be due to:
a) lower fidelity of mitochondrial DNA replication
b) inefficient DNA repair, or both,
• given that the mechanisms that perform these processes in the
organelle are relatively simple compared with those in the nucleus.
• There are 13 protein-encoding genes in human
mitochondrial DNA
• These code for hydrophobic components of the
respiratory-chain complexes and of ATP synthase.
• In contrast, roughly 1000 mitochondrial proteins are
encoded in the nucleus, produced on cytosolic
ribosomes, and imported by the protein import
machinery in the outer and inner membrane.
• cytosolic production of hydrophobic membrane proteins
and their import into the organelle may present a
problem to the cell, and that this is the reason why their The organization of the human mitochondrial genome.
genes have remained in the mitochondrion. The human mitochondrial genome of ≈16,600 nucleotide pairs
contains 2 rRNA genes, 22 tRNA genes, and 13 protein-coding
• The size range of mitochondrial DNAs is similar to that sequences.
of viral DNAs. There are two transcriptional promoters, one for each strand of the
• In animals, the mitochondrial genome is a simple DNA mitochondrial DNA (mtDNA).
The DNAs of many other animal mitochondrial genomes have been
circle of about 16,600 nucleotide pairs (less than completely sequenced.
0.001% of the nuclear genome), and it is nearly the Most of these animal mitochondrial DNAs encode precisely the
same size in organisms as different from us as same genes as humans, with the gene order being identical for
Drosophila and sea urchins animals ranging from fish to mammals.
Mitochondria Have a Relaxed Codon Usage
and Can Have a Variant Genetic Code
• The human mitochondrial genome has several surprising features that distinguish it from
nuclear, chloroplast, and bacterial genomes:
• Dense gene packing: Unlike other genomes, the human mitochondrial genome seems to
contain almost no noncoding DNA
• Relaxed codon usage: Whereas 30 or more tRNAs specify amino acids in the cytosol
and in chloroplasts, only 22 tRNAs are required for mitochondrial protein synthesis.
• The normal codon–anticodon pairing rules are relaxed in mitochondria, so that many
tRNA molecules recognize any one of the four nucleotides in the third (wobble) position.
• Such “2 out of 3” pairing allows one tRNA to pair with any one of four codons and
permits protein synthesis with fewer tRNA molecules.
• Variant genetic code: 4 of the 64 codons have different “meanings” from those of the
same codons in other genomes
Chloroplasts and Bacteria Share Many
Striking Similarities
• The chloroplast genomes of land plants range in size from 70,000 to
200,000 nucleotide pairs.
• More than 300 chloroplast genomes have now been sequenced.
• Chloroplast genes are involved in three main processes:
1. transcription,
2. translation, and
3. photosynthesis.
• Plant chloroplast genomes typically encode 80–90 proteins and around
45 RNAs, including 37 or more tRNAs.
Continued……
• Basic regulatory sequences, in genomes of chloroplasts and bacteria
such as transcription promoters and terminators, are virtually identical.
• The amino acid sequences of the proteins encoded in chloroplasts are
clearly recognizable as bacterial, and several clusters of genes with
related functions (such as those encoding ribosomal proteins) are
organized in the same way in the genomes of chloroplasts, the
bacterium E. coli, and cyanobacteria.
The Mechanisms by which Chloroplasts
and Bacteria Divide are also Similar.
• Both utilize FtsZ proteins, which are self-assembling
GTPases related to tubulins
• Bacterial FtsZ is a soluble protein that assembles into a
dynamic ring of membrane-attached protofilaments beneath
the plasma membrane in the middle of the dividing cell.
• The FtsZ ring acts as a scaffold for recruitment of other
cell-division proteins and generates a contractile force that
results in membrane constriction and eventually in cell
division The bacterial FtsZ protein, a tubulin homolog in
prokaryotes. (A) A band of FtsZ protein forms a ring
• Presumably, chloroplasts divide in very much the same in a dividing bacterial cell. This ring has been labeled
by fusing the FtsZ protein to green fluorescent protein
way. (GFP), which allows it to be observed in living E. coli
cells with a fluorescence microscope. (B) FtsZ
filaments and circles, formed in vitro, as visualized
using electron microscopy. (C) Dividing chloroplasts
(red) from a red alga also cleave using a protein ring
made from FtsZ (yellow).
Mitochondria and Chloroplasts Divide Differently
• Although both orgenelles employ membrane-interacting GTPases, the
mechanisms by which mitochondria and chloroplasts divide are
fundamentally different.
• The machinery for chloroplast division acts from the inside, as in
bacteria, while the dynamin-like GTPases divide mitochondria from
the outside
• The chloroplasts have remained closer to their bacterial origins than
have mitochondria, since the eukaryotic mechanisms of membrane
constriction and vesicle formation have been adapted for
mitochondrial fission.
Organelle Genes Are Maternally Inherited
in Animals and Plants
• Mitochondrial inheritance in yeasts is biparental: both parents contribute
equally to the mitochondrial gene pool of the progeny
• In Saccharomyces cerevisiae (baker’s yeast), when two haploid cells mate,
they are equal in size and contribute equal amounts of mitochondrial DNA to
the diploid zygote.
• During the course of the subsequent asexual, vegetative growth, the
mitochondria become distributed more or less randomly to daughter cells.
• After a few generations, the mitochondria of any given cell contain only the
DNA from one or the other parent cell, because only a small sample of the
mitochondrial DNA passes from the mother cell to the bud of the daughter
cell.
• This process is known as mitotic
segregation, and it gives rise to a
distinct form of inheritance that is
called non-Mendelian, or
cytoplasmic inheritance, in
contrast to the Mendelian
inheritance of nuclear genes.
 The inheritance of mitochondria in
animals and plants is quite different
• In plants and animals, the egg cell contributes much more cytoplasm to the
zygote than does the male gamete (sperm in animals, pollen in plants).
• A typical human oocyte contains about 100,000 copies of maternal
mitochondrial DNA, whereas a sperm cell contains only a few.
• As sperm mature, the DNA is degraded in their mitochondria. Sperm
mitochondria are also specifically recognized then eliminated from the
fertilized egg cell by autophagy in very much the same way that damaged
mitochondria are removed (by ubiquitylation followed by delivery to
lysosomes)
• Because of these two processes, the mitochondrial inheritance in both
animals and plants is uniparental. More precisely, the mitochondrial DNA
passes from one generation to the next by maternal inheritance.
Continued……

• In about two-thirds of higher plants, the chloroplast precursors

from the male parent (contained in pollen grains) fail to enter the
zygote, so that chloroplast as well as mitochondrial DNA is
maternally inherited.
• In other plants, the chloroplast precursors from the pollen grains
enter the zygote, making chloroplast inheritance biparental.
• In such plants, defective chloroplasts are a cause of variegation: a
mixture of normal and defective chloroplasts in a zygote may sort
out by mitotic segregation during plant growth and development,
thereby producing alternating green and white patches in leaves.
• Leaf cells in the green patches contain normal chloroplasts, while
those in the white patches contain defective chloroplasts
Mutations in Mitochondrial DNA Can
Cause Severe Inherited Diseases
• Mutations in mitochondrial DNA can lead to human genetic disorders.
• For example, large deletions in mitochondrial DNA cause a condition
called Kearns-Sayre syndrome.
• These deletions keep the mitochondria from doing their job of
extracting energy.
• Kearns-Sayre syndrome can cause symptoms such as weakness of the
muscles, including those that control eyelid and eye movement, as
well as degeneration of the retina and development of heart disease
Continued……
• Genetic disorders caused by mitochondrial mutations are not
transmitted from fathers to children, because mitochondria are
provided only by the mother. Instead, they are transmitted from
mothers to children in one of the following ways:
• A person with a disease caused by a mitochondrial mutation
may lack normal mitochondria (and have only abnormal,
mutation-bearing ones). In this case, an affected mother will
always pass on mutation-bearing mitochondria to her children.
• A mitochondrial disorder may occur when a person has a mix
of normal and abnormal mitochondria her body. In this case,
normal and mutation-bearing mitochondria may go randomly
into eggs during meiosis. Children who get a large proportion
of mutant mitochondria may have severe disease, while those
with few mutant mitochondria may have mild or no disease
The Accumulation of Mitochondrial DNA
Mutations Is a Contributor to Aging
• In highly developed, long-lived animals such as ourselves, the cells in
our body age and eventually die.
• A factor in this inevitable process is the accumulation of deletions and
point mutations in mitochondrial DNA.
• Oxidative damage to the cell by reactive oxygen species (ROS) such as
H2O2, superoxide, or hydroxyl radicals also increases with age.
• The mitochondrial respiratory chain is the main source of ROS in
animal cells, and animals in which mitochondrial superoxide
dismutase—the main ROS scavenger—has been knocked out, die
prematurely.
• The less complex DNA replication and repair systems in mitochondria mean that accidents are
corrected less efficiently.
• This results in a 100-fold higher occurrence of deletions and point mutations than in nuclear
DNA.
• Mathematical modeling suggests that most of these mutations and lesions are acquired in
childhood or early adult life, and then proliferate by clonal expansion in later life.
• Due to mitotic segregation, some cells will accumulate higher levels of faulty mitochondrial
DNA than others.
• Above some threshold, serious deficiencies in respiratory-chain function will develop,
producing cells that are senescent.
• In many organs of the human body, senescent cells with high levels of mitochondrial DNA
damagemare intermingled with normal cells, resulting in a mosaic of cells with and without
respiratory-chain deficiency