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mitochondria
A mitochondrion contains outer
and inner membranes
composed ofphospholipid
bilayers and proteins.[7]The
two membranes have different
properties. Because of this
double-membraned
organization, there are five
distinct parts to a
mitochondrion. They are:
the outer mitochondrial membrane,
the intermembrane space (the
space between the outer and
inner membranes),
the inner mitochondrial membrane,
the cristae space (formed by
infoldings of the inner
membrane), and
the matrix (space within the inner
membrane).
Mitochondria stripped out their
outer membrane are
called mitoplasts.
Outer membrane
• The outer mitochondrial membrane, which encloses the
entire organelle, has a protein-to-phospholipid ratio similar to that of
the eukaryotic plasma membrane (about 1:1 by weight). It contains
large numbers of integral proteins called porins. These porins form
channels that allow molecules 5000 Daltons or less in molecular
weight to freely diffuse from one side of the membrane to the
other.[7] Larger proteins can enter the mitochondrion if a signaling
sequence at their N-terminus binds to a large multisubunitprotein
called translocase of the outer membrane, which then actively
moves them across the membrane.[17] Disruption of the outer
membrane permits proteins in the intermembrane space to leak into
the cytosol, leading to certain cell death.[18] The mitochondrial outer
membrane can associate with the endoplasmic reticulum (ER)
membrane, in a structure called MAM (mitochondria-associated ERmembrane). This is important in the ER-mitochondria calcium
signaling and involved in the transfer of lipids between the ER and
mitochondria
Intermembrane space
• The intermembrane space is the space between the
outer membrane and the inner membrane. It is also
known as Perimitochondrial space. Because the outer
membrane is freely permeable to small molecules, the
concentrations of small molecules such as ions and
sugars in the intermembrane space is the same as
the cytosol.[7] However, large proteins must have a
specific signaling sequence to be transported across the
outer membrane, so the protein composition of this
space is different from the protein composition of
the cytosol. One protein that is localized to the
intermembrane space in this way is cytochrome c
Inner membrane
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The inner mitochondrial membrane contains proteins with five types of functions:[7]
Those that perform the redox reactions of oxidative phosphorylation
ATP synthase, which generates ATP in the matrix
Specific transport proteins that regulate metabolite passage into and out of the matrix
Protein import machinery.
Mitochondria fusion and fission protein.
It contains more than 151 different polypeptides, and has a very high protein-tophospholipid ratio (more than 3:1 by weight, which is about 1 protein for
15 phospholipids). The inner membrane is home to around 1/5 of the total protein in a
mitochondrion.[7] In addition, the inner membrane is rich in an unusual
phospholipid, cardiolipin. This phospholipid was originally discovered in cowhearts in
1942, and is usually characteristic of mitochondrial and bacterial plasma
membranes.[20] Cardiolipin contains four fatty acids rather than two, and may help to
make the inner membrane impermeable.[7] Unlike the outer membrane, the inner
membrane doesn't contain porins, and is highly impermeable to all molecules. Almost
all ions and molecules require special membrane transporters to enter or exit the
matrix. Proteins are ferried into the matrix via the translocase of the inner
membrane(TIM) complex or via Oxa1.[17] In addition, there is a membrane potential
across the inner membrane, formed by the action of the enzymes of the electron
transport chain.
Cristae
• The inner mitochondrial membrane is compartmentalized into
numerous cristae, which expand the surface area of the inner
mitochondrial membrane, enhancing its ability to produce ATP. For
typical liver mitochondria, the area of the inner membrane is about
five times as great as the outer membrane. This ratio is variable and
mitochondria from cells that have a greater demand for ATP, such as
muscle cells, contain even more cristae. These folds are studded
with small round bodies known as F1 particles or oxysomes. These
are not simple random folds but rather invaginations of the inner
membrane, which can affect overallchemiosmotic function.[21]
• One recent mathematical modeling study has suggested that the
optical properties of the cristae in filamentous mitochondria may
affect the generation and propagation of light within the tissue
F0-F1 complex
subunit composition of ATP
synthetase
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ATP synthase is a large mushroom-shaped asymmetric protein complex.
The simplest bacterial enzyme (see the cartoon below) is composed of 8
subunit types, of which 5 form the catalytic hydrophilic F1-portion (the "cap"
of the mushroom). These subunits are named by Greek letters (Alpha, Beta,
Gamma, Delta and Epsilon) in accordance with their molecular weight. The
proton translocating FO portion is composed of subunits of 3 types
named a, b and c. <="" a="" style="color: rgb(0, 0, 0); font-family: 'Times
New Roman'; font-size: medium; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height: normal; orphans:
auto; text-align: -webkit-left; text-indent: 0px; text-transform: none; whitespace: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width:
0px;">The catalytic portion of ATP synthase (F1) is formed by
Alpha 3 Beta 3 hexamer with Gamma subunit inside it and Epsilon attached
to the Gamma. Subunit Delta is bound to the "top" of the hexamer and to
subunits b. The hydrophobic transmembrane segment of subunit b is in
contact with subunit a. Subunits Gamma and Epsilon of the catalytic domain
are bound to the ring-shaped oligomer of c-subunits. Proton translocation
take place at the interface of subunits a and c.
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ATP synthase (EC 3.6.3.14) is an important enzyme that provides energy for the cell
to use through the synthesis of adenosine triphosphate (ATP). ATP is the most
commonly used "energy currency" of cells from most organisms. It is formed
from adenosine diphosphate(ADP) and inorganic phosphate (Pi), and needs energy.
The overall reaction sequence is: ADP + Pi → ATP, where ADP and Piare joined
together by ATP synthase
Energy is often released in the form of protium, or H+
, moving down anelectrochemical gradient, such as from the lumen into the stroma
ofchloroplasts or from the inter-membrane space into the matrix inmitochondria. ATP
synthase (EC 3.6.3.14) is an important enzyme that provides energy for the cell to
use through the synthesis of adenosine triphosphate (ATP). ATP is the most
commonly used "energy currency" of cells from most organisms. It is formed
from adenosine diphosphate(ADP) and inorganic phosphate (Pi), and needs energy.
The overall reaction sequence is: ADP + Pi → ATP, where ADP and Piare joined
together by ATP synthase
Energy is often released in the form of protium, or H+
, moving down anelectrochemical gradient, such as from the lumen into the stroma
ofchloroplasts or from the inter-membrane space into the matrix inmitochondria.
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Located within the mitochondria, ATP synthase consists of 2 regions
the FO portion is within the membrane.
The F1 portion of the ATP synthase is above the membrane, inside the matrix of the mitochondria.
Mitochondria structure: (1) inner membrane, (2) outer membrane, (3) cristae, (4) matrix
The nomenclature of the enzyme has from a long history. The F1 fraction derives its name from
the term "Fraction 1" and FO (written as a subscript letter "o", not "zero") derives its name from
being the oligomycin binding fraction.[1] Oligomycin, an antibiotic, is able to inhibit the FO unit of
ATP synthase.
These functional regions consist of different protein subunitsLocated within the mitochondria, ATP
synthase consists of 2 regions
the FO portion is within the membrane.
The F1 portion of the ATP synthase is above the membrane, inside the matrix of the mitochondria.
Mitochondria structure: (1) inner membrane, (2) outer membrane, (3) cristae, (4) matrix
The nomenclature of the enzyme has from a long history. The F1 fraction derives its name from
the term "Fraction 1" and FO (written as a subscript letter "o", not "zero") derives its name from
being the oligomycin binding fraction.[1] Oligomycin, an antibiotic, is able to inhibit the FO unit of
ATP synthase.
These functional regions consist of different protein subunits
F1-ATP Synthase structure
• The F1 particle is large and can be seen in the transmission electron
microscope by negative staining.[2] These are particles of 9 nm
diameter that pepper the inner mitochondrial membrane. They were
originally called elementary particles and were thought to contain
the entire respiratory apparatus of the mitochondrion, but, through a
long series of experiments, Ephraim Racker and his colleagues
(who first isolated the F1 particle in 1961) were able to show that
this particle is correlated with ATPase activity in uncoupled
mitochondria and with the ATPase activity in submitochondrial
particles created by exposing mitochondria to ultrasound. This
ATPase activity was further associated with the creation of ATP by a
long series of experiments in many laboratorie
• FO-ATP Synthase Structure[edit source | editbeta]
• The FO region of ATP synthase is a proton pore that is
embedded in the mitochondrial membrane. It consists of
three main subunits A, B, and C, and (in humans) six
additional subunits, d, e, f, g, F6, and 8 (or A6L). FO-ATP
Synthase Structure[edit source | editbeta]
• The FO region of ATP synthase is a proton pore that is
embedded in the mitochondrial membrane. It consists of
three main subunits A, B, and C, and (in humans) six
additional subunits, d, e, f, g, F6, and 8 (or A6L).
• Subunits of ATP synthase[edit
source | editbeta]
• ATP synthase alpha/beta subunits
• ATP synthase delta subunit
• ATP synthase gamma subunit
• ATP synthase subunit C
Matrix
• The matrix is the space enclosed by the inner membrane. It contains
about 2/3 of the total protein in a mitochondrion.[7] The matrix is
important in the production of ATP with the aid of the ATP synthase
contained in the inner membrane. The matrix contains a highly
concentrated mixture of hundreds of enzymes, special
mitochondrial ribosomes, tRNA, and several copies of
themitochondrial DNA genome. Of the enzymes, the major functions
include oxidation of pyruvate and fatty acids, and the citric acid
cycle.[7]
• Mitochondria have their own genetic material, and the machinery to
manufacture their own RNAs and proteins (see: protein
biosynthesis). A published human mitochondrial DNA sequence
revealed 16,569 base pairs encoding 37 total genes: 22 tRNA,
2rRNA, and 13 peptide genes.[23] The 13 mitochondrial peptides in
humans are integrated into the inner mitochondrial membrane, along
with proteins encoded by genes that reside in the host
cell's nucleus.
What Is the Purpose of a
Mitochondrial Membranes?
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mitochondria contain two major membranes. The outer mitochondrial
membrane fully surrounds the inner membrane, with a
small intermembrane space in between. The outer membrane has many
protein-based pores that are big enough to allow the passage of ions and
molecules as large as a small protein. In contrast, the inner membrane has
much more restricted permeability, much like the plasma membrane of a
cell. The inner membrane is also loaded with proteins involved in electron
transport and ATP synthesis. This membrane surrounds the mitochondrial
matrix, where the citric acid cycle produces the electrons that travel from
one protein complex to the next in the inner membrane. At the end of this
electron transport chain, the final electron acceptor is oxygen, and this
ultimately forms water (H20). At the same time, the electron transport chain
produces ATP. (This is why the the process is called oxidative
phosphorylation.)
During electron transport, the participating protein complexes push protons
from the matrix out to the intermembrane space. This creates a
concentration gradient of protons that another protein complex, called ATP
synthase, uses to power synthesis of the energy carrier molecule ATP
(Figure 2).
Figure 2: The electrochemical proton gradient and ATP
synthase
At the inner mitochondrial membrane, a high energy electron is
passed along an electron transport chain. The energy released
pumps hydrogen out to the matrix space between the
mitochondrial membranes. The gradient created by this high
concentration of hydrogen outside of the inner membrane drives
hydrogen back through the inner membrane, through ATP
synthase. As this happens, the enzymatic activity of ATP synthase
synthesizes ATP from ADP.
Metabolism in the matrix of
mitochondria.
Pyruvate and fatty acids are imported from the cytosol and converted to
acetyl CoA in the mitochondrial matrix. Acetyl CoA is then oxidized to
CO2 via the citric acid cycle, the central pathway of oxidative metabolism.
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The oxidation of acetyl CoA to CO2 is coupled to the reduction of NAD+ and FAD to
NADH and FADH2, respectively. Most of the energy derived from oxidative
metabolism is then produced by the process ofoxidative phosphorylation (discussed
in detail in the next section), which takes place in the inner mitochondrial membrane.
The high-energy electrons from NADH and FADH2 are transferred through a series of
carriers in the membrane to molecular oxygen. The energy derived from these
electron transfer reactions is converted to potential energy stored in a proton gradient
across the membrane, which is then used to drive ATP synthesis. The inner
mitochondrial membrane thus represents the principal site of ATP generation, and
this critical role is reflected in its structure. First, its surface area is substantially
increased by its folding into cristae. In addition, the inner mitochondrial membrane
contains an unusually high percentage (greater than 70%) of proteins, which are
involved in oxidative phosphorylation as well as in the transport of metabolites (e.g.,
pyruvate and fatty acids) between the cytosol and mitochondria. Otherwise, the inner
membrane is impermeable to most ions and small molecules—a property critical to
maintaining the proton gradient that drives oxidative phosphorylation.
In contrast to the inner membrane, the outer mitochondrial membrane is freely
permeable to small molecules. This is because it contains proteins called porins,
which form channels that allow the free diffusion of molecules smaller than about
6000 daltons. The composition of the intermembrane space is therefore similar to the
cytosol with respect to ions and small molecules. Consequently, the inner
mitochondrial membrane is the functional barrier to the passage of small molecules
between the cytosol and the matrix and maintains the proton gradient that
drives oxidative phosphorylation.
Function
• The most prominent roles of mitochondria
are to produce the energy currency of the
cell, ATP (i.e., phosphorylation of ADP),
through respiration, and to regulate
cellular metabolism.[8] The central set of
reactions involved in ATP production are
collectively known as the citric acid cycle,
or the Krebs Cycle. However, the
mitochondrion has many other functions in
addition to the production of ATP.
Energy conversion
• A dominant role for the mitochondria is the production
of ATP, as reflected by the large number of proteins in
the inner membrane for this task. This is done by
oxidizing the major products of glucose, pyruvate,
and NADH, which are produced in the cytosol.[8]This
process of cellular respiration, also known as aerobic
respiration, is dependent on the presence of oxygen.
When oxygen is limited, the glycolytic products will be
metabolized by anaerobic fermentation, a process that is
independent of the mitochondria.[8] The production of
ATP from glucose has an approximately 13-times higher
yield during aerobic respiration compared to
fermentation.[44] Recently it has been shown that plant
mitochondria can produce a limited amount of ATP
without oxygen by using the alternate substrate nitrite
Pyruvate and the citric acid cycle
• Each pyruvate molecule produced by glycolysis is actively
transported across the inner mitochondrial membrane, and into the
matrix where it is oxidized and combined with coenzyme A to form
CO2, acetyl-CoA, and NADH.[8]
• The acetyl-CoA is the primary substrate to enter the citric acid cycle,
also known as the tricarboxylic acid (TCA) cycle or Krebs cycle. The
enzymes of the citric acid cycle are located in the mitochondrial
matrix, with the exception of succinate dehydrogenase, which is
bound to the inner mitochondrial membrane as part of Complex
II.[46] The citric acid cycle oxidizes the acetyl-CoA to carbon dioxide,
and, in the process, produces reduced cofactors (three molecules
of NADH and one molecule ofFADH2) that are a source of electrons
for the electron transport chain, and a molecule of GTP (that is
readily converted to an ATP)
NADH and FADH2: the electron
transport chain
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The redox energy from NADH and FADH2 is transferred to oxygen (O2) in
several steps via the electron transport chain. These energy-rich molecules
are produced within the matrix via the citric acid cycle but are also produced
in the cytoplasm by glycolysis. Reducing equivalents from the cytoplasm
can be imported via the malate-aspartate shuttle system
of antiporter proteins or feed into the electron transport chain using
aglycerol phosphate shuttle.[8] Protein complexes in the inner membrane
(NADH dehydrogenase (ubiquinone), cytochrome c reductase,
andcytochrome c oxidase) perform the transfer and the incremental release
of energy is used to pump protons (H+) into the intermembrane space. This
process is efficient, but a small percentage of electrons may prematurely
reduce oxygen, forming reactive oxygen species such assuperoxide.[8] This
can cause oxidative stress in the mitochondria and may contribute to the
decline in mitochondrial function associated with the aging process.[47]
As the proton concentration increases in the intermembrane space, a
strong electrochemical gradient is established across the inner membrane.
The protons can return to the matrix through the ATP synthase complex,
and their potential energy is used to synthesize ATP from ADP and
inorganic phosphate (Pi).[8] This process is called chemiosmosis, and was
first described by Peter Mitchell[48][49] who was awarded the 1978 Nobel
Prize in Chemistry for his work. Later, part of the 1997 Nobel Prize in
Chemistry was awarded to Paul D. Boyer and John E. Walker for their
clarification of the working mechanism of ATP synthase
Heat production
• Under certain conditions, protons can re-enter the mitochondrial
matrix without contributing to ATP synthesis. This process is known
as proton leak or mitochondrial uncoupling and is due to
the facilitated diffusion of protons into the matrix. The process
results in the unharnessed potential energy of the proton
electrochemical gradient being released as heat.[8] The process is
mediated by a proton channel called thermogenin,
or UCP1.[51] Thermogenin is a 33kDa protein first discovered in
1973.[52]Thermogenin is primarily found in brown adipose tissue, or
brown fat, and is responsible for non-shivering thermogenesis.
Brown adipose tissue is found in mammals, and is at its highest
levels in early life and in hibernating animals. In humans, brown
adipose tissue is present at birth and decreases with age.
Storage of calcium ions
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The concentrations of free calcium in the cell can regulate an array of reactions and
is important for signal transduction in the cell. Mitochondria can transiently store
calcium, a contributing process for the cell's homeostasis of calcium.[53] In fact, their
ability to rapidly take in calcium for later release makes them very good "cytosolic
buffers" for calcium.[54][55][56] The endoplasmic reticulum (ER) is the most
significant storage site of calcium, and there is a significant interplay between the
mitochondrion and ER with regard to calcium.[57] The calcium is taken up into
the matrix by a calcium uniporter on the inner mitochondrial membrane.[58] It is
primarily driven by the mitochondrialmembrane potential.[53] Release of this calcium
back into the cell's interior can occur via a sodium-calcium exchange protein or via
"calcium-induced-calcium-release" pathways.[58] This can initiate calcium spikes or
calcium waves with large changes in the membrane potential. These can activate a
series of second messenger system proteins that can coordinate processes such
asneurotransmitter release in nerve cells and release of hormones in endocrine cells.
Ca2+ influx to the mitochondrial matrix has recently been implicated as a mechanism
to regulate respiratory bioenergetics by allowing the electrochemical potential across
the membrane to transiently "pulse" from ΔΨ-dominated to pH-dominated, facilitating
a reduction of oxidative stress.[59]In neurons, concominant increases in cytosolic and
mitochondrial calcium act to synchronize neuronal activity with mitochondrial energy
metabolism. Mitochondrial matrix calcium levels can reach the tens of micromolar
levels, which is necessary for the activation of isocitrate dehydrogenase, one of the
key regulatory enzymes of the Kreb's cycle.
Additional functions
• Mitochondria play a central role in many other metabolic tasks, such
as:
• Signaling through mitochondrial reactive oxygen species[61]
• Regulation of the membrane potential[8]
• Apoptosis-programmed cell death[62]
• Calcium signaling (including calcium-evoked apoptosis)[63]
• Regulation of cellular metabolism[64]
• Certain heme synthesis reactions[65] (see also: porphyrin)
• Steroid synthesis.[54]
• Some mitochondrial functions are performed only in specific types of
cells. For example, mitochondria in liver cells contain enzymes that
allow them to detoxify ammonia, a waste product of protein
metabolism. A mutation in the genes regulating any of these
functions can result in mitochondrial diseases.
Mitochondrial DNA
• The human mitochondrial genome is a circular DNA molecule of
about 16 kilobases.[83]It encodes 37 genes: 13 for subunits of
respiratory complexes I, III, IV and V, 22 for mitochondrial tRNA (for
the 20 standard amino acids, plus an extra gene for leucine and
serine), and 2 for rRNA.[83] One mitochondrion can contain two to
ten copies of its DNA.[84]
• As in prokaryotes, there is a very high proportion of coding DNA and
an absence of repeats. Mitochondrial genes are transcribed as
multigenic transcripts, which are cleaved and polyadenylated to
yield mature mRNAs. Not all proteins necessary for mitochondrial
function are encoded by the mitochondrial genome; most are coded
by genes in the cell nucleus and the corresponding proteins are
imported into the mitochondrion.[23] The exact number of genes
encoded by the nucleus and themitochondrial genome differs
between species. Most mitochondrial genomes are circular,
although exceptions have been reported.[85] In general,
mitochondrial DNA lacks introns, as is the case in the human
mitochondrial genome;[23] however, introns have been observed in
some eukaryotic mitochondrial DNA,[86] such as that
of yeast[87] and protists,[88] including Dictyosteliumdiscoideum
• In animals the mitochondrial genome is typically a single circular
chromosome that is approximately 16 kb long and has 37 genes.
The genes, while highly conserved, may vary in location. Curiously,
this pattern is not found in the human body louse (Pediculus
humanus). Instead this mitochondrial genome is arranged in 18
minicircular chromosomes, each of which is 3–4 kb long and has
one to three genes.[90] This pattern is also found in other sucking
lice, but not in chewing lice. Recombination has been shown to
occur between the minichromosomes. The reason for this difference
is not known.
• While slight variations on the standard code had been predicted
earlier,[91] none was discovered until 1979, when researchers
studying human mitochondrial genes determined that they used an
alternative code.[92] Although, the mitochondria of many other
eukaryotes, including most plants, use the standard code.[93] Many
slight variants have been discovered since,[94] including various
alternative mitochondrial codes.[95] Further, the AUA, AUC, and
AUU codons are all allowable start codons.
Replication and inheritance
•
Mitochondria divide by binary fission, similar to bacterial cell
division.[99] The regulation of this division differs between eukaryotes. In
many single-celled eukaryotes, their growth and division is linked to the cell
cycle. For example, a single mitochondrion may divide synchronously with
the nucleus. This division and segregation process must be tightly
controlled so that each daughter cell receives at least one mitochondrion. In
other eukaryotes (in mammals for example), mitochondria may replicate
their DNA and divide mainly in response to the energy needs of the cell,
rather than in phase with the cell cycle. When the energy needs of a cell are
high, mitochondria grow and divide. When the energy use is low,
mitochondria are destroyed or become inactive. In such examples, and in
contrast to the situation in many single celled eukaryotes, mitochondria are
apparently randomly distributed to the daughter cells during the division of
the cytoplasm. Understanding of mitochondrial dynamics, which is
described as the balance between mitochondrial fusion and fission, has
revealed that functional and structural alterations in mitochondrial
morphology are important factors in pathologies associated with several
disease conditions
•
An individual's mitochondrial genes are not inherited by the same
mechanism as nuclear genes. Typically, the mitochondria are inherited from
one parent only. In humans, when an egg cell is fertilized by a sperm, the
egg nucleus and sperm nucleus each contribute equally to the genetic
makeup of the zygote nucleus. In contrast, the mitochondria, and therefore
the mitochondrial DNA, usually come from the egg only. The sperm's
mitochondria enter the egg but do not contribute genetic information to the
embryo.[101] Instead, paternal mitochondria are marked with ubiquitin to
select them for later destruction inside the embryo.[102]The egg cell
contains relatively few mitochondria, but it is these mitochondria that survive
and divide to populate the cells of the adult organism. Mitochondria are,
therefore, in most cases inherited only from mothers, a pattern known
as maternal inheritance. This mode is seen in most organisms including the
majority of animals. However, mitochondria in some species can sometimes
be inherited paternally. This is the norm among certain coniferous plants,
although not in pine trees and yew trees.[103] ForMytilidae mussels
paternal inheritance only occurs within males of the
species.[104][105][106] It has been suggested that it occurs at a very low
level in humans.[107] There is a recent suggestion mitochondria that
shorten male lifespan stay in the system because mitochondria are inherited
only through the mother. By contrast natural selection weeds out
mitochondria that reduce female survival as such mitochondria are less
likely to be passed on to the next generation. Therefore it is suggested
human females and female animals tend to live longer than males. The
authors claim this is a partial explanation
• Uniparental inheritance leads to little opportunity for genetic
recombination between different lineages of mitochondria, although
a single mitochondrion can contain 2–10 copies of its DNA.[84] For
this reason, mitochondrial DNA usually is thought to reproduce
by binary fission. What recombination does take place maintains
genetic integrity rather than maintaining diversity. However, there
are studies showing evidence of recombination in mitochondrial
DNA. It is clear that the enzymes necessary for recombination are
present in mammalian cells.[109] Further, evidence suggests that
animal mitochondria can undergo recombination.[110] The data are
a bit more controversial in humans, although indirect evidence of
recombination exists.[111][112] If recombination does not occur, the
whole mitochondrial DNA sequence represents a single haplotype,
which makes it useful for studying the evolutionary history of
populations
Is the Mitochondrial Genome Still
Functional?
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Mitochondrial genomes are very small and show a great deal of variation as
a result of divergent evolution. Mitochondrial genes that have been
conserved across evolution include rRNA genes, tRNA genes, and a small
number of genes that encode proteins involved in electron transport and
ATP synthesis. The mitochondrial genome retains similarity to its prokaryotic
ancestor, as does some of the machinery mitochondria use to synthesize
proteins. In fact, mitochondrial rRNAs more closely resemble bacterial
rRNAs than the eukaryotic rRNAs found in cell cytoplasm. In addition, some
of the codons that mitochondria use to specify amino acids differ from the
standard eukaryotic codons.
Still, the vast majority of mitochondrial proteins are synthesized from
nuclear genes and transported into the mitochondria. These include the
enzymes required for the citric acid cycle, the proteins involved in DNA
replication and transcription, and ribosomal proteins. The protein complexes
of the respiratory chain are a mixture of proteins encoded by mitochondrial
genes and proteins encoded by nuclear genes. Proteins in both the outer
and inner mitochondrial membranes help transport newly synthesized,
unfolded proteins from the cytoplasm into the matrix, where folding ensues
Figure 3: Protein import into a mitochondrion
A signal sequence at the tip of a protein (blue) recognizes a receptor protein (pink) on the
outer mitochondrial membrane and sticks to it. This causes diffusion of the tethered protein
and its receptor through the membrane to a contact site, where translocator proteins line up
(green). When at this contact site, the receptor protein hands off the tethered protein to the
translocator protein, which then channels the unfolded protein past both the inner and outer
mitochondrial membranes.
The Genetic System of
Mitochondria
• Mitochondria contain their own genetic system, which is separate
and distinct from the nuclear genome of the cell. As reviewed in
Chapter 1, mitochondria are thought to have evolved from bacteria
that developed a symbiotic relationship in which they lived within
larger cells (endosymbiosis). This hypothesis has recently been
substantiated by the results of DNA sequence analysis, which
revealed striking similarities between the genomes of mitochondria
and of the bacterium Rickettsia prowazekii. Rickettsia are
intracellular parasites which, like mitochondria, are only able to
reproduce within eukaryotic cells. Consistent with their similar
symbiotic lifestyles, the genomic DNA sequences of Rickettsia and
mitochondria suggest that they share a common ancestor, from
which the genetic system of present-day mitochondria evolved.
•
Mitochondrial genomes are usually circular DNA molecules, like those of
bacteria, which are present in multiple copies per organelle. They vary
considerably in size between different species. The genomes of human and
most other animal mitochondria are only about 16 kb, but substantially
larger mitochondrial genomes are found in yeasts (approximately 80 kb)
and plants (more than 200 kb). However, these larger mitochondrial
genomes are composed predominantly of noncoding sequences and do not
appear to contain significantly more genetic information. For example, the
largest sequenced mitochondrial genome is that of the plant Arabidopsis
thaliana. Although Arabidopsis mitochondrial DNA is approximately 367 kb,
it encodes only 32 proteins: just more than twice the number encoded by
human mitochondrial DNA. The largest number of mitochondrial genes has
been found in mitochondrial DNA of the protozoanReclinomonas americana,
which is 69 kb and contains 97 genes. The mitochondrial genome
ofReclinomonas appears to more closely resemble the bacterial genome
from which mitochondria evolved than most present-day mitochondrial
genomes, which encode only a small number of proteins that are essential
components of the oxidative phosphorylation system. In addition,
mitochondrial genomes encode all of the ribosomal RNAs and most of the
transfer RNAs needed for translation of these protein-coding sequences
within mitochondria. Other mitochondrial proteins are encoded by nuclear
genes, which are thought to have been transferred to the nucleus from the
ancestral mitochondrial genome.
• The human mitochondrial genome encodes
13 proteins involved in electron transport and oxidative
phosphorylation (Figure 10.3). In addition, human
mitochondrial DNA encodes 16S and 12S rRNAs and 22
tRNAs, which are required for translation of the proteins
encoded by the organelle genome. The two rRNAs are
the only RNA components of animal and yeast
mitochondrial ribosomes, in contrast to the three rRNAs
of bacterial ribosomes (23S, 16S, and 5S). Plant
mitochondrial DNAs, however, also encode a third rRNA
of 5S. The mitochondria of plants and protozoans also
differ in importing and utilizing tRNAs encoded by the
nuclear as well as the mitochondrial genome, whereas in
animal mitochondria, all the tRNAs are encoded by the
organelle
The human mitochondrial
genome
The genome contains 13 proteincoding sequences, which are
designated as components of respiratory complexes I, III, IV, or V.
In addition, the genome contains genes for 12S and 16S rRNAs
and for 22 tRNAs, which are designated by the one-letter code for
the corresponding amino acid. The region of the genome
designated “D loop” contains an origin of DNA replication and
transcriptional promoter sequences.
• 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 (Table 10.1). As discussed in Chapter 3, there
are 64 possible triplet codons, of which 61 encode the 20 different
amino acids incorporated into proteins (see Table 3.1). Many tRNAs
in both prokaryotic and eukaryotic cells are able to recognize more
than a single codon in mRNA because of “wobble,” which allows
some mispairing between the tRNA anticodon and the third position
of certain complementary codons (see Figure 7.3). However, at least
30 different tRNAs are required to translate the universal code
according to the wobble rules. Yet human
mitochondrial DNA encodes only 22 tRNA species, and these are
the only tRNAs used fortranslation of mitochondrial mRNAs. This is
accomplished by an extreme form of wobble in which U in the
anticodon of the tRNA can pair with any of the four bases in the third
codon position of mRNA, allowing four codons to be recognized by a
single tRNA. In addition, some codons specify different amino acids
inmitochondria than in the universal code.
• Like the DNA of nuclear genomes, mitochondrial DNA
can be altered by mutations, which are frequently
deleterious to the organelle. Since almost all
the mitochondria of fertilized eggs are contributed by the
oocyte rather than by the sperm, germ-line mutations in
mitochondrial DNA are transmitted to the next generation
by the mother. Such mutations have been associated
with a number of diseases. For example, Leber's
hereditary optic neuropathy, a disease that leads to
blindness, can be caused by mutations in mitochondrial
genes that encode components of the electron transport
chain. In addition, the progressive accumulation of
mutations in mitochondrial DNA during the lifetime of
individuals has been suggested to contribute to the
process of aging.
Protein Import and Mitochondrial
Assembly
•
In contrast to the RNA components of the
mitochondrial translation apparatus (rRNAs and tRNAs), most mitochondrial
genomes do not encode the proteins required
for DNA replication, transcription, or translation. Instead, the genes that
encode proteins required for the replication and expression of mitochondrial
DNA are contained in the nucleus. In addition, the nucleus contains the
genes that encode most of the mitochondrial proteins required for oxidative
phosphorylation and all of the enzymes involved in mitochondrial
metabolism (e.g., enzymes of the citric acid cycle). The proteins encoded by
these genes (more than 95% of mitochondrial proteins) are synthesized on
free cytosolic ribosomes and imported intomitochondria as
completed polypeptide chains. Because of the double-membrane structure
of mitochondria, the import of proteins is considerably more complicated
than the transfer of a polypeptide across a single phospholipid bilayer.
Proteins targeted to the matrix have to cross both the inner and outer
mitochondrial membranes, while other proteins need to be sorted to distinct
compartments within the organelle (e.g., the intermembrane space).
•
The import of proteins to the matrix is the best-understood aspect of mitochondrial
protein sorting (Figure 10.4). Most proteins are targeted to mitochondria by aminoterminal sequences of 20 to 35 amino acids (called presequences) that are removed
by proteolytic cleavage following their import into the organelle. The presequences of
mitochondrial proteins, first characterized by Gottfried Schatz, contain multiple
positively charged amino acid residues, usually in an amphipathic α helix. The first
step in protein import is the binding of these presequences to receptors on the
surface of mitochondria. The polypeptide chains are then inserted into a protein
complex that directs translocation across the outer membrane (the translocase of the
outer membrane or Tom complex). The proteins are then transferred to a second
protein complex in the inner membrane (the translocase of the inner membrane or
Tim complex). Continuing protein translocation requires the electrochemical potential
established across the inner mitochondrial membrane during electron transport. As
discussed in the next section of this chapter, the transfer of high-energy electrons
from NADH and FADH2 to molecular oxygen is coupled to the transfer of protons
from the mitochondrial matrix to the intermembrane space. Since protons are
charged particles, this transfer establishes an electric potential across the inner
membrane, with the matrix being negative. During protein import, this electric
potential drives translocation of the positively charged presequence.
Import of proteins into mitochondria
Proteins are targeted for mitochondria by
an amino-terminal presequence
containing positively charged amino
acids. Proteins are maintained in a
partially unfolded state by association
with a cytosolic Hsp70 and are
recognized by a receptor on the surface
of mitochondria. The
unfolded polypeptide chains are then
translocated through the Tom complex in
the outer membrane and transferred to
the Tim complex in the inner membrane.
The voltage component of
the electrochemical gradient is required
for translocation across the inner
membrane. The presequence is cleaved
by a matrix protease, and a mitochondrial
Hsp70 binds the polypeptide chain as it
crosses the inner membrane, driving
further protein translocation. A
mitochondrial Hsp60 then facilitates
folding of the imported polypeptide within
the matrix.
• To be translocated across the mitochondrial
membrane, proteins must be at least partially unfolded.
Consequently, protein import into mitochondria requires molecular
chaperones in addition to the membrane proteins involved in
translocation (see Figure 10.4). On the cytosolic side, members of
the Hsp70 family of chaperones maintain proteins in a partially
unfolded state so that they can be inserted into the mitochondrial
membrane. As they cross the inner membrane, the
unfolded polypeptide chains bind to another member of the Hsp70
family, which is associated with the Tim complex and acts as a
motor that drives protein import. The polypeptide is then transferred
to a chaperone of the Hsp60 family (a chaperonin), within which
protein folding takes place. Since these interactions of polypeptide
chains with molecular chaperones depend on ATP, protein import
requires ATP both outside and inside the mitochondria, in addition to
the electric potential across the inner membrane.
•
As noted above, 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 are targeted to
their destinations by a second sorting signal following the positively charged
presequence that directs mitochondrial import. The targeting of proteins to
the mitochondrial membranes appears to be mediated by hydrophobic stoptransfer sequences that halt translocation of the polypeptide chains through
the Tim or Tom complexes, leading to their insertion into the inner or outer
mitochondrial membranes, respectively (Figure 10.5). Proteins may be
targeted to the intermembrane space by several different mechanisms
(Figure 10.6). Some proteins are transferred across the outer membrane
through the Tom complex but are then released within the intermembrane
space instead of being transferred to the Tim complex. Other proteins are
transferred to the Tim complex but are then released into the
intermembrane space as a result of cleavage of hydrophobic stop-transfer
sequences. Still other proteins may be completely imported into the
mitochondrial matrix and then exported back across the inner membrane to
the intermembrane space.
Insertion of mitochondrial membrane
proteins
Proteins targeted for the mitochondrial
membranes contain hydrophobic stop-transfer
sequences that halt their translocation through
the Tom or Tim complexes and lead to their
incorporation into the outer or inner
membranes, respectively.
Sorting proteins to the intermembrane space
Proteins can be targeted to the intermembrane space by several mechanisms.
Some proteins (I) are translocated through the Tom complex and released into the
intermembrane space. Other proteins (II) are transferred from the Tom complex to
the Tim complex, but they contain hydrophobic stop-transfer sequences that halt
translocation through the Tim complex. These stop-transfer sequences are then
cleaved to release the proteins into the intermembrane space. Still other proteins
(III) are imported to the matrix, as depicted in Figure 10.4. Removal of the
presequence within the matrix then exposes a hydrophobic signal sequence, which
targets the protein back across the inner membrane to the intermembrane space
• Not only the proteins, but also the phospholipids of
mitochondrial membranes are imported from the cytosol.
In animal cells, phosphatidylcholine and
phosphatidylethanolamine 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, buried
in a hydrophobic binding site of the protein, and released
when the complex reaches a new membrane, such as
that of mitochondria. The mitochondria then synthesize
phosphatidylserine from phosphatidylethanolamine, in
addition to catalyzing the synthesis of the unusual
phospholipid cardiolipin, which contains four fatty acid
chains