1. Mitochondria: Structure
and Role in Respiration
Stefan Krauss, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
Mitochondria fulfill various important roles in cellular metabolism. Of note they play a
central role in cellular energy metabolism.
Introduction
Mitochondria have captured the interest of biochemists for
more than 50 years. They have been studied intensively in
the past decades, not least because they are abundant and
can be isolated easily from different tissues. Mitochondria
have lately moved into the spotlight of other exciting areas,
namely the study of apoptosis, evolutionary biology and
molecular medicine. Originally, it was the realization that
mitochondria play a central role in cellular energy
metabolism that attracted the attention of cell physiolo-
gists and physiological chemists, and led to Nobel Prize-
winning work such as Peter Mitchell’s chemiosmotic
theory. Since the days of classical physiological chemistry,
bioenergetics research has gone a long way. Contributions
from structural biology, biophysics and mathematical
biology increase our still incomplete understanding of
mitochondrial metabolism and its regulation in ever more
detail.
Mitochondrial Architecture
Mitochondria are about 0.5–1 mm in diameter and up to
7 mm long. Their shape and number per cell depends on the
particular tissue. They may appear as spheres, rods or
filamentous bodies, but the general architecture is the same
(Figure 1). The number of mitochondria per cells varies
depending on the energy requirements: tissues with a high
capacity to perform aerobic metabolic functions such as
skeletal muscle or kidney will have a larger number of
mitochondria.
Mitochondria have two membranes, each composed of a
phospholipid bilayer. The two membranes are quite
distinct in appearance and in physico-chemical properties,
thus determining the biochemical function of each
membrane.
The inner membrane encloses and convolutes into the
mitochondrial matrix, forming cristae. This serves to
increase the surface of the inner membrane, which carries
the main enzymatic machinery of oxidative phosphoryla-
tion.
The inner and outer membranes are characterized by
different phospholipid compositions and protein-to-lipid
ratios. For the outer membrane, this ratio is about 50:50,
and it is thought that the protein has very little enzymatic
or transport function. In the inner membrane, the protein-
to-lipid ratio is 80:20.
The outer membrane is widely permeable to ions and
larger molecules. The inner mitochondrial membrane is
much less permeable to ions and small molecules than the
outer membrane, therefore providing compartmentaliza-
tion through separation of the matrix from the cytosolic
environment. This compartmentalization is a central
feature of the conversion of free energy derived from
oxidizable substrates. The inner mitochondrial membrane
is, in fact, an electrical insulator and chemical barrier.
Sophisticated ion transporters exist to allow specific
molecules to cross this barrier. There are several antiport
systems embedded in the inner membrane, allowing
exchange of anions between the cytosol and the mitochon-
drial matrix. Examples of these are a phosphate-OH2
exchanger, the adenine nucleotide translocase (which
specifically exchanges adenosine diphosphate (ADP) for
adenosine triphosphate (ATP), mono-, di- and tricarbox-
ylate carriers and the aspartate–glutamate shuttle.
Article Contents
Introductory article
. Introduction
. Mitochondrial Architecture
. Physical Organization of Mitochondrial Enzymes in
Metabolism
. H1
Gradients
. The ATP Synthase
. Major Transport Systems
. Integration of Mitochondrial Functions with
Cytoplasmic Metabolic Pathways
. Summary
Outer membrane Inner membrane
Matrix Cristae
Figure 1 Mitochondrial architecture.
1ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

2. Physical Organization of Mitochondrial
Enzymes in Metabolism
The mitochondrial matrix contains a range of enzymes,
which form parts of major metabolic pathways such as
carbohydrate, lipid and amino acid oxidation and urea and
haem biosynthesis. The enzymatic machinery of oxidative
phosphorylation, leading to ATP production, is mainly
located in the inner mitochondrial membrane.
Citric acid cycle
The citric acid cycle (also termed the tricarboxylic acid
cycle or Krebs cycle) achieves the complete oxidation of
acetyl–CoA, which is a central intermediate produced by
various catabolic pathways such as glycolysis and fatty
acid oxidation. The enzymes of this cycle are primarily
located in the mitochondrial matrix, with the exception of
succinate dehydrogenase, which is bound to the inner
membrane, forming part of complex II of the electron
transport chain. The physical closeness of the citric acid
cycle and the reactions of oxidative phosphorylation in the
mitochondrial matrix makes sense: The main function of
the citric acid cycle is to oxidize the acetyl component of
acetyl–CoA to two molecules of carbon dioxide and
concomitantly to conserve the liberated free energy in the
form of NADH (reduced form of nicotinamide–adenine
dinucleotide) and FADH2 (reduced form of flavin–
adenine dinucleotide). Most of the cell’s needs for the
cellular energy carrier ATP (adenosine 5’-triphosphate) are
then met by mitochondrial oxidative phosphorylation, for
which NADH and FADH2 are the ‘substrates’.
Oxidative phosphorylation
Oxidative phosphorylation relies on a series of respiratory
complexes (called the electron transport chain) which are
embedded in the inner mitochondrial membrane. Figure 2
gives a schematic representation of the electron transport
chain. Note that this representation is conceptual, the
complexes are thought to be laterally mobile within the
membrane. Recent work suggests that some or all of the
complexes may form large aggregates or supercomplexes.
H1
Gradients
Electrons ‘arrive’ at the electron transport chain in the
form of NADH and FADH2 (Figure 2; note that complex II
is not shown for simplicity). The electron-transporting
complexes pass electrons derived from these ‘reducing
equivalents’, NADH and FADH2, via protein-bound
redox centres onto a final recipient, oxygen, thus forming
water.
Thermodynamic calculations show that oxidation of
NADH2 by O2 is sufficient to drive the synthesis of several
moles of ATP. The mitochondrialelectron transport chain,
which features components of successively increasing
reduction potentials (i.e. reducing power), is designed to
split this large change in free energy into smaller
components. So how is the free energy derived from
oxidation of NADH and FADH2 used by the mitochon-
drion to produce ATP?
The chemiosmotic theory – the general
mechanistic principle of oxidative
phosphorylation
During the past 50 years, a number of concepts have
emerged to explain how free energy derived from the
oxidation of substrates may be conserved by the cell to
drive cellular processes, in particular how electron trans-
port and oxidative phosphorylation are coupled. Of these
hypotheses, Edward Slater’s chemical coupling hypothesis
and Paul Boyer’s conformational coupling hypothesis
have received considerable attention, although it is Peter
Mitchell’s chemiosmotic theory that has become widely
accepted.
The chemiosmotic theory seems to be consistent with
experimental evidence. It postulates the coupling of
respiration and ATP synthesis in mitochondria. The free
energy of electron transport is conserved by the proton
gradient, which is built up by the enzymatic complexes of
the electron transport chain. These complexes pump
protons from the matrix to the intermembrane space and
create an electrochemical gradient across the inner
membrane. This gradient then enables the ATPase to
synthesize ATP.
Complex I (or NADH–coenzyme Q reductase) passes
electrons from NADH to CoQ. Several iron–sulfur
clusters are involved in the electron transport process.
The two coenzymes of complex I, flavin mononucleotide
(FMN) and CoQ are able to accommodate up to two
electrons each in stable conformations and donate one or
two electrons to the cytochromes of complex III. It is
thought that fourprotonsarepumpedper pair of electrons.
Complex II (succinate–coenzyme Q reductase) contains
succinate dehydrogenase and three small hydrophobic
subunits. It is anchored in the membrane, facing the
mitochondrial matrix. It directly passes electrons from
succinate, an intermediate of the citric acid cycle, using
FAD as coenzyme, three iron–sulfur clusters and cyto-
chrome b560. It has no proton-pumping activity.
Complex III (coenzyme Q–cytochrome c reductase)
transfers electrons from reduced CoQ to cytochrome c. It
contains two b-cytochromes, one cytochrome c1, and an
iron–sulfur cluster. Two protons are pumped per pair of
electrons.
Mitochondria: Structure and Role in Respiration
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3. Complex IV (cytochrome c oxidase) catalyses the last
step of electron transfer: the reduction of oxygen to water.
Complex IVtranslocates fourprotonsper pair of electrons.
Proton translocation is an endergonic process (i.e. it
requires energy) because it occurs against an electroche-
mical gradient. The precise protein translocation mechan-
ism is still subject to research. In what has been known as
the proton pump mechanism, the transfer of electrons
results in conformational changes to the involved com-
plexes. In complex III, the Q cycle facilitates electron
transport and proton translocation. Here, CoQ is reduced
in two steps. Ubisemiquinone, carrying one electron, is
reduced by complex I and accepts a proton from the
matrix. QH2 then diffuses to the intermembrane space,
where two protons are subsequently released to the
intermembrane space. One electron is recycled to facilitate
proton uptake, thus forming ubisemiquinone at the matrix
side of the membrane, whereas another electron is passed
onto cytochrome c1. The electrochemical gradient (Dp, also
termed ‘proton motive force’) resulting from the proton-
translocating activities of complexes I, III and IV has two
components: the electrical potential (DCm) and a pH
component:
Dp 5 DCm 2 DpH
Dp is usually given in millivolts. Mitochondria isolated
from hepatocytes usually have membrane potentials of
around 170 mV.
Proton leak
Mitochondrial proton leak, also known as the proton
conductance pathway, is an established phenomenon,
which is not fully understood. Some protons which are
pumped by the electron transport chain ‘leak’ back into the
matrix, bypassing the ATP synthase (see Figure 2). This
means that some of the free energy conserved in the proton
gradient is dissipated and lost to the cell.
Mitochondria in brown adipose tissue feature an
uncoupling protein (UCP1) which catalyses proton leak
and exploits the energy dissipation for (regulated) heat
generation. However, proteins with high sequence homol-
ogy to UCP1 have been identified in other tissues such as
skeletal muscle, andalthoughtheir roleasuncouplers is not
generally established, this has led some researchers to
believe that at least part of the proton conductance
pathway may be enzymatically catalysed and regulated.
The physiological importance of proton leak is not
entirely clear, but it is thought that it may act as a ‘valve’ in
situations where Dp becomes unnaturally high, and reduce
the number of reactive oxygen species (free radicals)
generated by certain processes in the electron transport
chain. A very active area of research is the exploration of
the potential of proton leak in the regulation of body
weight.
Inner
mitochondrial
membrane
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
cyt c
QH2
NADH
ATPADP + Pi
F11/2 O2
+2H+
H2O
F0
CYTOSOL
Complex I (complex II
not shown)
Complex III Complex IV ATP synthase
MATRIX
Proton leak
Figure2 Oxidativephosphorylation – physical organizationof thecomponentsofthe electrontransportchainandthe chemiosmotic protoncircuit. As
electrons (derived from NADH or FADH2) are transported down the chain (green line), protons are being pumped from the matrix to the cytosolic side of
the inner mitochondrial membrane, thusestablishing a protongradient.This gradient maybe used by the ATP synthaseto formATP, or it may be dissipated
via the proton leak pathway, thus generating heat.
Mitochondria: Structure and Role in Respiration
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4. The ATP Synthase
The ATP synthase, or F1F0-ATPase, utilizes the proton
motive force, Dp, to convert ADP and phosphate to ATP,
thereby coupling electron transport and proton pumping
to ATP synthesis (Figure 2). This multisubunit transmem-
brane protein, which is the most complex structure in the
inner mitochondrial membrane, has attracted considerable
experimental attention in recent years. In 1997 Paul Boyer
and John Walker were awarded the Nobel Prize for their
elucidation of the enzymatic mechanism underlying the
synthesis of ATP.
The chemiosmotic theory requires that the ATPase is
located in the inner membrane in such a way that the
protons pumped by complexes I, III and IV of the electron
transport chain are allowed to return to the matrix
(chemiosmotic proton circuit). It has been shown that
purified ATPase molecules, when inserted into artificial
membrane vesicles, will synthesize ATP when an electro-
chemical gradient is established across the membrane.
The bovine enzyme contains 16 different proteins and is
over 500 kDa in size. The membrane sector (F0) contains
the proton channel and is connected to the catalytic F1
component via a stalk consisting of two parallel structures,
the ‘rotor’ and the ‘stator’. The F1 component points into
the matrix side of the membrane. It has five subunits (a–e)
in a stoichiometry 3:3:1:1:1.
The ‘head’ of the F1 subunit, which is visible on electron
micrographs as a bulb-like structure pointing into the
matrix, is a hexamer of alternating a and b subunits. It is
now generally thought that the ATPase operates by
rotational catalysis. Subunits a and b are homologous,
they both bind nucleotides but only b has catalytic activity.
Within the catalytic component F1, there are therefore
three active sites. Paul Boyer suggested a binding exchange
mechanism, according to which each site would pass
through a cycle of three different states: ‘open’ (the empty
state), ‘loose’ (where ADP and phosphate are bound), and
‘tight’ (tightly bound ATP), each site being in a different
state at any given moment. During ATP synthesis, protons
are being translocated into the matrix. It is not yet known
how the molecular mechanism works. The synthesized
ATP molecules are released into the matrix and can be
transported to the cytosol by the adenine nucleotide
translocase.
Major Transport Systems
Mitochondrial transport
Because of its composition, the inner mitochondrial
membrane is impermeable to most solutes and ions. While
the design of the inner membrane is geared to maintain a
high Dp, it is also essential that exchange of certain
metabolites and ions between the matrix and the cytosol is
possible. This is facilitated by a number of transport
systems. These systems can be electroneutral or electro-
genic (typically used to translocate polyanionic species, e.g.
the adenine nucleotide translocase), or they may be driven
by DCm (e.g. during electrical uniport of cations), or by
DpH (e.g. the Pi
2
/OH2
exchanger).
Metabolites carried across the inner mitochondrial
membrane are predominantly in anionic form. The range
of anion transporters in the inner mitochondrial mem-
brane depends on the tissue and its particular function.
Common to all mitochondria are the adenine nucleotide
carrier, which exchanges cytoplasmic ADP for ATP
generated during oxidative phosphorylation, the phos-
phate transporter and the pyruvate carrier.
Other carriers transport or exchange intermediates of
the citric acid cycle, the urea cycle (di- and tricarboxylate
carrier, 2-oxoglutarate carrier, glutamate–aspartate car-
rier), and fatty acyl esters of carnitine.
The transport of monovalent cations is tightly con-
trolled. The mitochondrial membrane potential would
drive accumulation of ions such as K1
if these could
accidentally leak into the matrix, with the result that the
mitochondria would swell (due to concomitant uptake of
water). To prevent this, mitochondria use a transporter
that exchanges matrix K1
or Na1
for H1
, maintaining a
concentration of these ions that is much lower than in the
cytosol.
The mono-, di- and tricarboxylate carriers
Citric acid cycle intermediates are used by cells for fatty
acid synthesis and gluconeogenesis, which are largely
cytosolic pathways. The di- and tricarboxylate carriers
mediate the electroneutral (net) export of citric acid cycle
intermediates for this purpose. The dicarboxylate carrier
exchanges malate or succinate for HPO4
2 2
, the tricarbox-
ylate carrier exchanges citrate and isocitrate (plus one
proton) for malate. The monocarboxylate transporter
exchanges cytosolic pyruvate for OH2
.
Ca2 1
and Pi transport
Pi (H2PO4
2
) is produced when ATP is used to drive
cytosolic processes, and must be returned to the mitochon-
drial matrix to allow ATP generation. The phosphate
transporter is ubiquitous in mitochondria of all cell types,
and exchanges H2PO4
2
either in exchange for OH2
ions or
by symport with a proton, which in either case is
electroneutral. This carrier is highly active, and the
concomitant proton translocation explains the influence
of DpH on the distribution of Pi across the membrane.
Ca2 1
acts as intracellular second messenger in cell
signalling, affecting a wide range of metabolic reactions
including intramitochondrial ones. Also, mitochondria
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5. have an important function to buffer cytosolic Ca2 1
concentrations (when Ca2 1
concentrations are in excess of
1 mmol L2 1
, mitochondria readily accumulate the cation).
Consequently, intracellular Ca2 1
concentrations must be
tightly controlled. Influx and efflux of Ca2 1
are mediated
independently by different transport systems. Ca2 1
enters
mitochondria via a uniporter. The efflux is mediated by
electroneutral antiport with H1
in liver, and with Na1
in
mitochondria from heart, brain and brown adipose tissue
(the latter is itself coupled to a Na1
/H1
exchanger).
Under steady-state conditions, the uniporter and the
antiporter work together at relatively low activity to give
symmetrical cycling of calcium which is driven by the
chemiosmotic proton circuit.
Whenthe cytosolic Ca2 1
concentration rises, theuptake
exceeds expulsion from the matrix and net uptake occurs.
The uptake of Ca2 1
lowers DCm, which results in a
transient stimulation of the proton pumping respiratory
chain (uncoupling effect), thus increasing DpH.
Ca2 1
acts as a regulator of mitochondrial function. It
causes isocitrate dehydrogenase and 2-oxoglutarate dehy-
drogenase to lower the Km for their substrates (and,
therefore, increase their affinity for them). Also affected by
Ca2 1
is pyruvate dehydrogenase phosphatase, the enzyme
that dephosphorylates the pyruvate dehydrogenase com-
plex, thus increasing its Vmax. Recent work has shown that
mitochondria are not only responding to simple increases
in Ca2 1
, but are able to decode rather complex (frequency
modulated) cytosolic Ca2 1
signals which regulate the rate
of oxidative phosphorylation.
The carnitine palmitoyltransferase system
Fatty acids are oxidized in the mitochondrion. Long-chain
fatty acyl–CoA cannot readily cross the inner mitochon-
drial membrane, but mitochondria feature a shuttle system
called the carnitine palmitoyl transferase system. Overt
carnitine palmitoyltransferase (or CPT I) transfers the acyl
portion to carnitine. A special carnitine carrier protein
then translocates acyl–carnitine to the matrix side of the
membrane in exchange for carnitine. Finally, CPT II then
transfers the acyl group to CoA from the mitochondrial
pool.
Substrate transport shuttles: transfer of
electrons from cytoplasmic NADH to the
respiratory chain
The mitochondrial inner membrane contains a number of
substrate transport shuttles. These shuttles function to
transport reducing equivalents across the inner mitochon-
drial membrane, as none of the nucleotides involved in
cellular redox reactions (NAD(P)1
, NAD(P)H, FAD,
FADH2, CoA) are permeable to the inner mitochondrial
membrane. Most of the NADH derived from glucose
oxidation is formed in the matrix, but NADH produced in
glycolysis is cytosolic. Examples of such substrate trans-
port shuttles are the a-glycerol phosphate shuttle of insect
flight muscle and the mammalian malate–aspartate
shuttle. These shuttles have in common that they involve
reciprocal transfer of oxidized and reduced species of
various redox couples, thus accomplishing the net transfer
of reducing equivalents across the membrane.
Integration of Mitochondrial Functions
with Cytoplasmic Metabolic Pathways
The citric acid cycle is a pathway central not only to
mitochondrial metabolism, but in many ways also to
cellular metabolism as a whole. In the light of mitochon-
drial oxidative phosphorylation, its major function is
catabolic as it completely oxidizes the carbon atoms in
acetyl–CoA and conserves free energy. Cycle intermedi-
ates are, however, precursors and substrates of anabolic
pathways such as gluconeogenesis as well as cholesterol,
fatty acid, porphyrin and protein biosynthesis.
Figure 3 summarizes some of the interrelationships
between major mitochondrial and cytosolic metabolic
Oxaloacetate
Malate Citrate
2-OxoglutarateFumarate
Succinyl-CoA
Amino acids
Amino acids
Glucose
Pyruvate
Acetyl-CoA HMGCoA
Fatty acid
oxidation
Ketone bodies
Glucose
Asparate
tyrosine
phenylalanine
Amino acids
CO2
GTP
NADH/
FADH2
Oxidative
phosphorylation
Carbon source
for biosynthetic
pathways
(fatty acids,
sterols)
ATP
Odd chain fatty acid
and branched chain
2-oxoacid metabolism
Porphyrin
biosynthesis
(δ-aminolevulinate)
Isoleucine
methionine
valine
Catabolic pathways
Anabolic (biosynthetic) pathways
Figure 3 Integration of cytosolic and mitochondrial pathways. The citric
acid cycle has integrative functions in a complex network of cellular
biosynthetic and degradative processes. A cell may derive energy (in the
form of ATP) from different carbon sources including carbohydrates, amino
acids (proteins) and lipids. Conversely, breakdown products and
intermediates of oxidative metabolism may be used for biosynthetic
pathways.
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6. pathways. This representationis far fromcomplete andcan
only give an indication of the complexity of such
interrelationships.
The cellular concentrations of citric acid cycle inter-
mediates exceed the catalytic amounts that would be
needed to drive the cycle. This is because the citric acid
cycle has important functions in the integration of different
pathways, providing intermediates for a range of biosyn-
thetic pathways and a sink for degradation products.
Succinyl–CoA is a breakdown product of odd chain fatty
acid oxidation and branched chain 2-oxoacid metabolism,
and also of a few amino acids (Figure 3). It serves as a
precursor for porphyrin (i.e. haem) biosynthesis. This
pathway is partially located in the mitochondrial matrix.
Citrate is used as precursor for fatty acid and cholesterol
synthesis. It also has regulatory properties: it is known to
allosterically inhibit phosphofructokinase, and to stimu-
late acetyl–CoA carboxylase. It is a source of cytosolic
reducing equivalents for reductive biosyntheses.
The particular relationships between different pathways
are dictated by the requirements of the cell, and are subject
to hormonal regulation. The fate of carbohydrates in the
well-fed stage is usually complete oxidation via glycolysis
(cytosolic) to the stage of pyruvate, conversion into acetyl–
CoA and subsequent oxidation in the citric acid cycle, thus
providing reducing equivalents which are the ‘substrates’
for oxidative phosphorylation. Amino acids are used for
protein biosynthesis or are oxidized in peripheral tissues.
Excess amino acids can be oxidized entirely to carbon
dioxide and water; alternatively the intermediates can be
used as substrates for fatty acid biosynthesis whereby the
nitrogen is converted to urea. During fasting, glycogen
stores in muscle and liver are depleted, which also yields
glucose that can be oxidized. Prolonged starvation causes
increased breakdown of fats and proteins, and the free
amino acids are then used as carbon sources for the citric
acid cycle which they enter either as acetyl–CoA or cycle
intermediates. Glucose, which is a major fuel for the brain,
can be synthesized in gluconeogenesis from malate or
oxaloacetate (using the malate–aspartate shuttle) to
provide energy for peripheral tissues.
Summary
Mitochondria play a central role in energy metabolism of
cells. They usually provide most of the ATP by oxidative
phosphorylation. A major consequence of the architecture
of mitochondria is the impermeability of the inner
membrane that facilitates the generation of a proton
gradient, called the proton motive force. The oxidative
processes cells use to degrade fuel molecules yield NADH
and FADH2 which are used as electron donors for the
electron transport chain. The components of the chain are
located in the inner mitochondrial membrane and include
four complexes and some electron carriers. While electrons
are transported along the chain, three of the four
complexes act as proton pumps, expel protons from the
matrix and build up the proton motive force. Another
enzyme, the ATPase, utilizes the proton gradient to form
ATP from ADP and Pi, thus allowing the protons to return
to the matrix. The coupling of electron transport (i.e.
oxidative processes) and ATP synthesis via the proton
gradient is the main postulate of the chemiosmotic theory.
Due to the impermeability of the inner mitochondrial
membrane to most solutes, a range of transporters exists
which allow exchange of ions and metabolites (mostly in
anionic form) between matrix and cytosol. These trans-
porters also help to integrate mitochondrial and cytosolic
metabolic pathways. The citric acid cycle can be seen as the
centre of a range of metabolic processes. It is amphibolic,
i.e. it serves both catabolic and anabolic purposes
depending on the particular requirements of a cell as
defined by function and physiological state.
Further Reading
Boyer PD (1997) The ATP synthase – a splendid molecular machine.
Annual Review of Biochemistry 66: 717–749.
Nicholls DG and FergusonSJ (1992)Bioenergetics 2. London: Academic
Press.
Saraste M (1999) Oxidative phosphorylation at the fin de sie`cle. Science
283: 1488–1493.
Abrahams JP, Leslie AG, Lutter R and Walker JE (1994) Structure at 2.8
A˚ resolution of F1-ATPase from bovine heart mitochondria. Nature
370: 621–628.
For further information on the structure and function of the ATP
synthase, see also http://www.nobel.se and follow the links to the 1997
Nobel Prize for Chemistry.
Mitochondria: Structure and Role in Respiration
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