Chapter 13

Mitochondria, Chloroplasts,
and Peroxisomes
• The generation of metabolic energy is a major activity of all cells, and
two cytoplasmic organelles are specifically devoted to energy
metabolism and the production of ATP.

• Mitochondria are responsible for generating most of the useful energy

derived from the breakdown of lipids and carbohydrates.

• Chloroplasts use energy captured from sunlight to generate both ATP and
the reducing power needed to synthesize carbohydrates from CO2 and
H2O.

• Mitochondria, chloroplasts, and peroxisomes differ from other

organelles in their functions and in their mechanism of assembly.
 Mitochondria

• Mitochondria play a critical role in the generation of metabolic

energy in eukaryotic cells.
…
• Most mitochondrial proteins are translated on free cytosolic
ribosomes and imported into the organelle by specific targeting
signals.

• Mitochondria are unique among other cytoplasmic organelles in that

they contain their own DNA, which encodes tRNAs, rRNAs, and
some mitochondrial proteins.
 Organization and Function of Mitochondria
• Mitochondria are surrounded by a double-membrane system, consisting of
inner and outer mitochondrial membranes separated by an intermembrane
space.

• The cristae are the numerous folds that form the inner membrane of the
mitochondria.
• The matrix is the interior of the mitochondria organelle and contains
the mitochondrial genetic system as well as the enzymes responsible
for the central reactions of oxidative metabolism.

…
• The inner mitochondrial membrane represents the principal site of
ATP generation, and this critical role is reflected in its structure.

• Porins are proteins that form channels that allow the free diffusion of
molecules smaller than about 1000 daltons into the highly permeable
outer mitochondrial membrane.
Figure 13.2 Oxidative metabolism in mitochondria
• As the major sources of cellular energy, the effective functioning of
mitochondria is critical for viability.

• In many cells this requires selectively positioning mitochondria to

locations of high-energy use, such as synapses in nerve cells.

• In addition, mitochondria are not static organelles but are constantly

fusing with one another and dividing.
Figure 13.3 A mitochondrial network

• In most cells mitochondria exist as part of a large interconnected

network.

• Continual fusion and fission events remodel this network of mitochondria

within the cell, and modify mitochondrial morphology and function.
 The Genetic System of Mitochondria

• Mitochondria contain their own genetic system, which is separate and

distinct from the nuclear genome of the cell.

• Mitochondria are thought to have evolved from bacteria that developed a

symbiotic relationship in which they lived within larger cells
(endosymbiosis).

• Mitochondrial genomes are usually circular DNA molecules like those of

bacteria, which are present in multiple copies per organelle.

• Most present-day mitochondrial genomes encode only a small number of

proteins that are essential components of the oxidative phosphorylation
system.
• The human mitochondrial genome encodes 13 proteins involved in
electron transport and oxidative phosphorylation.

• The mitochondrial genes encoding these proteins are transcribed and

translated within mitochondria, which contain their own ribosomes and
tRNAs.
Table 13.1 Differences between the Universal and Mitochondrial Genetic Codes

• The small number of tRNAs encoded by the mitochondrial genome

highlights an important feature of the mitochondrial genetic system—the
use of a slightly different genetic code, which is distinct from the
“universal” genetic code used by both prokaryotic and eukaryotic cells.
• In contrast to the mitochondrial genome, the proteins present in
mitochondria are much less-well understood.

…
 Protein Import and Mitochondrial Assembly

• Most mitochondrial genomes do not encode the proteins required for

DNA replication, transcription, or translation.

• The proteins encoded by nuclear genes (~99% of mitochondrial proteins)

are synthesized on free cytosolic ribosomes and imported into
mitochondria as completed polypeptide chains.

• Because of the double-membrane structure of mitochondria, the import of

proteins is complicated.

• Proteins targeted to the matrix have to cross both the outer and inner
mitochondrial membranes, while other proteins need to be sorted to
distinct compartments within the organelle, including the inner
membrane, the outer membrane, and the intermembrane space.
• Several classes of targeting signals direct proteins to these different
mitochondrial compartments.
• The most thoroughly studied targeting sequences are amino-terminal
presequences of 15-55 amino acids that direct the import of proteins to
the mitochondrial matrix as well as target some proteins to the inner
membrane.

• The presequences of mitochondrial proteins contain multiple positively

charged amino acid residues, usually in an helix, and are removed by
proteolytic cleavage following their import into the organelle.

• The first step in protein import is the binding of theses presequences to a

protein complex on the surface of mitochondria that directs translocation
across the outer membrane (the translocase of the outer membrane, or
Tom complex).

• After that, these proteins are transferred to a second protein complex,

called Tim23, in the inner membrane (one of two different translocases
of the inner membrane, or Tim complexes).
Figure 13.5 Import of mitochondrial proteins with presequences
• To be translocated across the mitochondrial membrane, proteins must be
at least partially unfolded.

• Consequently, protein import into mitochondria requires molecular

chaperons in addition to the membrane proteins involved in
translocation.

• The matrix processing peptidase, or MPP, cleaves presequences from

proteins imported to the matrix of the mitochondria.

• Some mitochondrial proteins are targeted to the outer membrane, inner

membrane, or intermembrane space rather than to the matrix, so
additional mechanisms are needed to direct these proteins to the correct
submitochondrial compartment.

• These proteins do not contain presequences but instead have multiple

internal mitochondrial import signals.
Figure 13.6 Protein targeting to the mitochondrial inner membrane

Many proteins in the inner

membrane are multiple-pass
transmembrane protein that
serve as transporters to exchange
nucleotides and ions between the
mitochondria and the cytosol.
These proteins have multiple
internal mitochondrial import
signals.
They are recognized by mobile
chaperones (Tim9-Tim10) in the
intermembrane space.
The Tim9-Tim10 chaperones
then escort these protein to the
second translocase of the inner
membrane (Tim22).
Figure 13.7 Sorting of proteins to the outer membrane and intermembrane space

• Proteins destined for the outer membrane or the intermembrane space are
also imported through the Tom complex.
• They are then recognized and carried to a second tranlocon complex, which
mediates their insertion into the outer membrane.
 Mitochondrial lipids

• In animal cells, phosphatidylcholine and phsphatidylethanolamine are

synthesized in the ER and carried to mitochondria by phospholipid
transfer proteins, which extract single phospholipid molecules from the
membrane of the ER.

• The lipid can then be transported through the aqueous environment of the
cytosol and released when the complex reaches a new membrane, such as
that of mitochondira.
• The mitochondria then
synthesize phosphatidylserine
from
phosphatidylethanolamine, in
addition to catalyzing the
synthesis of the unusual
phospholipid cardiolipin.
Figure 13.9 Phospholipid transfer proteins
 Transport of metabolites across the inner membrane

• The potential energy stored in the electrochemical gradient drives the

transport of small molecules into and out of mitochondria.

• Energy from the electrochemical gradient is similarly used to drive the

transport of other metabolites into mitochondria.
 Chloroplasts and Other Plastids

• Chloroplasts are the organelles responsible for photosynthesis and, in

many respects, are similar to mitochondria.

• Chloroplasts synthesize amino acids, fatty acids, and the lipid

components of their own membranes.
 The structure and function of chloroplasts

• Plant chloroplasts are large

organelles that, like
mitochondria, are bounded by
a double membrane called the
chloroplast envelope.

• The thylakoid membrane

forms a network of flattened
discs called thylakoids, which
are frequently arranged in
stacks called grana.
• The stroma is the compartment of chloroplast that lies between the envelope
and the thylakoid membrane.

• The major difference between chloroplasts and mitochondria, in terms of both

structure and function, is that chloroplasts contain a thylakoid membrane.
 The Chloroplast Genome

• Like mitochondria, chloroplasts contain their own genetic system,

reflecting their evolutionary origins from photosynthetic bacteria.

• The chloroplast genomes of several plants have been completely

sequenced, leading to the identification of many of the genes contained
in the organelle DNA.

• The chloroplast genome also encodes approximately 30 proteins that are

involved in photosynthesis.
 Import and Sorting of Chloroplast Proteins

• Although chloroplasts encode more of their own proteins than

mitochondria, about 3500 or 95% of chloroplast proteins are still
encoded by nuclear genes.

• As with mitochondria, these proteins are synthesized on cytosolic

ribosomes and then imported into chloroplasts as completed polypeptide
chains.
• They must then be sorted to their appropriate location within
chloroplasts.
• Most proteins are targeted for import into chloroplasts by N-terminal
sequences, usually from 30-100 amino acids, called transit peptides,
which direct protein translocation across the two membranes of the
chloroplast envelope and are then removed by proteolytic cleavage.

• Transit peptides direct proteins to the translocase of the chloroplast outer

membrane (the Toc complex).
• After proteins are transported through the Toc complex, they are
transferred to the translocase of the chloroplast inner membrane (the Tic
complex) and transported into the stroma.

• In the stroma, the transit peptide is cleaved by a stromal processing

peptidase (SPP), and the protein associates with stromal Hsp70
chaperones.
Figure 13.13 Import of proteins into the chloroplast stroma
• Proteins to be incorporated into the thylakoid membrane or lumen are
transported to their destination in two steps.
• They are first imported into the stroma, and then most are targeted for
translocation across the thylakoid membrane by a second signal sequence,
…
which is exposed following cleavage of the transit peptide.
Figure 13.14 Import of proteins into the thylakoid lumen and membrane
 Other Plastids

• Plastids are a family of plant organelles including chloroplasts,

chromoplasts, leucoplasts, amyloplasts, and elaioplasts.

• Chromoplasts lack chlorophyll but contain carotenoids and are responsible

for the yellow, orange, and red colors of some flowers and fruits.
• Leucoplasts are nonpigmented plastids, which store a variety of energy
sources in nonphotosynthetic tissues.

• Amyloplasts are plastids that store starch.

• Elaioplasts are plastids that store lipids.

• Proplastids are small undifferentiated organelles present in the rapidly

dividing cells of plant roots and shoots.

• Proplastids then develop into the various types of mature plastids

according to the needs of differentiated cells.

• Mature plastids are able to change from one type to another. Ex)
Chromoplast develop from chloroplasts during the ripening of fruit.
Figure 13.16 Interconversions of plastids

• Several types of mature plastids are able to change rom one type to
another.
 Peroxisomes

• Peroxisomes are small, single membrane-

enclosed organelles that contain enzymes
involved in a variety of metabolic
reactions.

• Peroxins are proteins present in

peroxisomes.
 Functions of Peroxisomes
• Peroxisomes contain at least 50 different enzymes, which are involved in a
variety of biochemical pathways in different types of cells.

• Catalase is an enzyme found in peroxisomes, which decomposes hydrogen

peroxide either by converting it to water or by using it to oxidize another
organic compound.

• A variety of substrates are broken down by oxidative reactions in

peroxisomes, including uric acid, amino acids, purines, methanol, and fatty
acids.
• Peroxisomes are also involved in biosynthesis of lipids and the amino acid
lysine.

• In animal cells, cholesterol and dolichol are synthesized in peroxisomes as

well as in the ER. In the liver, peroxisomes are also involved in the
synthesis of bile acids from cholesterol.

• Peroxisomes contain enzymes required for the synthesis of plasmalogens -

a family of phospholipids in which one of the hydrocarbon chains is joined
to glycerol by an ether bond rather than an ester bond.

• Plasmalogens are important membrane

components in some tissues, particularly
heart and brain.
• Peroxisomes play two particularly important roles in plants.

• First, peroxisomes in seeds are responsible for the conversion of stored fatty
acids to carbohydrates, which is critical to providing energy and raw
materials for growth of the germinating plant. This occurs via glyoxylate
cycle.

• Second, peroxisomes in leaves are involved in photorespiration, which

serves to metabolize a side product formed during photosynthesis.
 Peroxisome Assembly

• The assembly of peroxisomes is mediated by an intersection of proteins

synthesized on free cytosolic ribosomes and proteins transported to
peroxisomes from the ER.

• Internal peroxisomal proteins are synthesized on free cytosolic ribosomes

and then imported to peroxisomes, but many peroxisomal
transmembrane proteins are transported to peroxisomes from the ER.

• These transmembrane proteins include proteins involved in the transport

of metabolites as well as proteins called peroxins or Pex proteins, which
are involved in peroxisome assembly.

• Most peroxisome transmembrane proteins are first tranlocated into the

ER and inserted into the ER membrane.

• These proteins then bud in vesicles from the peroxisomal ER.

Figure 13.20 Assembly of peroxisomes
• Mutations in peroxins have been identified in yeast as well as in association
with a variety of diseases in humans (peroxisome biogenesis disorders)
that result from defective peroxisome assembly.

• Some of the peroxins form membrane channels through which the internal
(matrix) proteins of peroxisomes are imported.

• Zellweger spectrum disorders can result from mutation in the genes

affecting peroxisomal protein import.
• Vesicles budding from the peroxisomal ER do not have a COPII coat and
their formation may be driven by peroxins.

• Vesicles from the peroxisomal ER fuse to form peroxisomes into which

matrix proteins can be imported.

• Formation of a functional peroxisome requires the fusion of two different

types of vesicles containing different classes of peroxins, both of which are
needed for the import of matrix proteins.

• Most peroxins are targeted to the interior of peroxisomes by the simple

amino acid sequence Ser-Lys-Leu at their carboxy terminus (peroxisome
targeting signal 1, or PTS1).

• A small number of proteins are targeted by a sequence of nine amino acids

at their amino terminus (PTS2).

• PTS1 and PTS2 are recognized by distinct cytosolic receptors, the peroxins
Pex5 and Pex7, respectively.

• Peroxisomes can be formed by two distinct mechanisms.

Figure 13.21 Import of peroxisomal matrix proteins

• New peroxisomes can be formed by

vesicle budding from the ER,
followed by the import of matrix
proteins.
Figure 13.22 Formation of new peroxisomes

• In addition, new peroxisomes can be

formed by the growth and division
of old ones.