• 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 (singular: mitochondrion) are
organelles within eukaryotic cells that produce
adenosine triphosphate (ATP), the main
energy molecule used by the cell.
• For this reason, the mitochondrion is
sometimes referred to as “the powerhouse of
the cell”.
• Mitochondria are found in all eukaryotes.
• In addition to supplying cellular energy,
mitochondria are involved in cell death, as
well as the control of the cell cycle and cell
growth.
• Mitochondria mainly consists of the following:
- Outer Membrane
- Inner Membrane
- Intermembrane Space
- Cristae
- Matrix
•  INNER MEMBRANE
• Is freely permeable only to oxygen, carbon dioxide, and water.
• Contains complexes of the ETC, the ATP synthase complex,
and transport proteins.
• Presence of sophisticated ion transporters exist.
• Several antiport systems exist, allowing exchange of anions
between the cytosol and the mitochondrial matrix.
• It is devoid of cholesterol and rich in phospholipid &
cardiolipin.
• The inner membrane is folded into tubular invaginations called
cristae.
• Cristae junctions connect the cristae membranes with the
remainder of the inner membrane, which is adjacent to the
outer membrane and is called the inner boundary membrane.
•  A large protein complex of the inner membrane that plays
a crucial role in the maintenance of inner membrane
architecture. The complex was termed mitochondrial
inner membrane organizing system (MINOS),
mitochondrial contact site complex, or mitochondrial
organizing structure.
• Two core proteins, mitofilin are essential for keeping the
cristae membranes attached to the inner boundary
membrane.
• The inner mitochondrial membrane contains proteins that
perform redox reactions in oxidative phosphorylation, ATP
synthase,transport proteins, protein import machinery,
mitochondria fusion and fission protein. 
• A crista ( plural cristae) is a fold in the inner membrane of
a mitochondrion.
• The name is from the Latin for crest or plume, and it gives
the inner membrane its characteristic wrinkled shape,
providing a large amount of surface area for chemical
reactions to occur on.
• Cristae are studded with proteins, including ATP
synthase and a variety of cytochromes.
• The folded cristae membrane contains cylindrical
connections to the inner membrane called cristae junctions.
• Stalked particles or inner membrane spheres:
• Cristae is covered with inner membrane spheres called
stalked particles or knobs or heads.
• They contain protein called F1 portion & F0 portion for ATP
synthesis.
• Functions of cristae
• These folds increase surface area of the membrane,
which is important because the inner membrane
holds the proteins involved in the electron transport
chain.
• It is also where many other chemical reactions take
place to carry out the mitochondria’s many
functions.
• An increased surface area creates more space for
more reactions to occur, and increases the
mitochondria’s output.
• Outer membrane
• The outer mitochondrial membrane encloses the entire organelle.
• It 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 membrane proteins called
porins.
• These porins form channels that allow low molecular weight
molecules to freely diffuse from one side of the membrane to the
other.
• Larger proteins can enter the mitochondrion if a signaling sequence
at their N-terminus binds to a large multisubunit protein called
translocase of the outer membrane, which then actively moves
them across the membrane.
• The outer membrane also contains enzymes involved in such diverse
activities as the elongation of fatty acids, oxidation of epinephrine,
and the degradation of tryptophan.
• These enzymes include monoamine oxidase, rotenone-
insensitive NADH-cytochrome c- reductase, kynurenine
hydroxylase and fatty acid Co-A ligase.
• Disruption of the outer membrane permits proteins in the
intermembrane space to leak into the cytosol, leading to
certain cell death.
• The mitochondrial outer membrane can associate with the
endoplasmic reticulum (ER) membrane, in a structure called
MAM (mitochondria-associated ER-membrane).
• This is important in the ER- mitochondria calcium signaling
and is involved in the transfer of lipids between the ER and
mitochondria.
• Outside the outer membrane there are small particles named
sub-units of Parson.
•  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 in the cytosol.
• 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.
• Matrix
• The matrix is the space enclosed by the inner
membrane.
• It contains about 2/3 of the total protein in a
mitochondrion.
• 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 the mitochondrial DNA
genome.
• Of the enzymes, the major functions include oxidation of
pyruvate and fatty acids, and the citric acid cycle.
• Mitochondria have their own genetic material, and the
machinery to manufacture their own RNAs and proteins .
• Mitochondrial DNA is the DNA present in the
organelle mitochondrion.
• The mitochondrial DNA is genetically distinct from that in
the nucleus. The entire genetic information in mitochondria
is called the mitochondrial genome or mitogenome.
•  In mammals, the mitochondrial DNA is a double-stranded
circular DNA.
• One of the two strands is rich in guanine and is referred to as
the heavy strand (or H-strand).
• The other strand is rich in cytosine and is referred to as
the light strand (or L-strand).
• The H-strand is known to encode 9 genes whereas the L-
strand encodes 28 genes, thus, for a total of 37 genes.
• The mammalian mitogenome codes for 13 proteins, 22
tRNA, and 2 for rRNA. Since a mitochondrion has its own
genetic material and is capable of manufacturing its own
RNAs and proteins, it is said to be a semi-autonomous, self-
reproducing cytoplasmic structure.
• Mitochondrial Porins
• 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.
• Our current understanding of ATP synthesis in
mitochondria is based on the hypothesis,
introduced by Peter Mitchell in 1961,
chemiosmotic theory.
• Chemiosmotic hypothesis
• Mitchell proposed chemiosmotic hypothesis in
1961, which was further elaborated in 1966.
• According to chemiosmotic hypothesis, ATP
synthesis is coupled to electrochemical gradient
which is created across inner mitochondrial
membrane due to asymmetric distribution of
protons across the membrane with protons
accumulating in the inter membrane space.
• The electrochemical gradient results in proton
motive force (PMF).
• Proton motive force is created due to:
• i) Chemical potential gradient created across
the inner mitochondrial membrane due to
difference in concentration of protons, i.e., Δ pH.
• ii) Voltage gradient across the inner
mitochondrial membrane due to charge
separation with positively charged ions
accumulating in the intermembrane space, i.e.,
ΔE.
• Oxidative Phosphorylation
• Mitochondria are the site of oxidative
phosphorylation in eukaryotes.
• It is the process in which ATP is formed as a result of
transfer of electrons from NADH or FADH2 to O2 by a
series of electron carriers.
• This transfer of electrons through the inner
mitochondrial membrane leads to the pumping of
protons out of the mitochondrial matrix.
• ATP is synthesized when protons flow back to the
mitochondrial matrix through an enzyme complex.
• The actual synthesis of ATP is carried out by an
enzyme called ATP synthase located in the inner
mitochondrial membrane
• Oxidative phosphorylation is the last step of cellular
respiration process where ATP is synthesised from the reduced
products, NADH and FADH2, of glycolysis and TCA cycle, and
oxygen is utilised.
• Though NADH is sometimes used directly as reducing molecule
in biosynthetic pathways such as in gluconeogenesis, both
NADH and FADH2 are mostly used to reduce molecular oxygen
to water. The energy released in the process drives the
synthesis of ATP, the energy currency of the cell.
• Process occurs in the presence of oxygen.
• NADH and FADH2 get oxidised by donating two electrons each
to oxygen and reducing it to water.
• Since the energy for synthesis of ATP molecules is derived from
oxidation of NADH or FADH2, which in turn are formed by
oxidation of energy-rich molecules such as carbohydrates and
fats, this type of phosphorylation or ATP synthesis is called
oxidative phosphorylation.
• Electrons donated by NADH and FADH2 are transported
through components of electron transport chain (ETC)
sequentially from one having a more negative
electron/reduction potential to the next with less negative
potential, till they are accepted by molecular oxygen.
• As the electrons move through components of ETC with
increasing redox potentials, their free energy is reduced
and is released.
• According to the chemiosmotic theory put forth by Peter
Mitchell in 1961, energy released during the movement of
electrons through ETC is used in pumping protons across
the inner mitochondria membrane and generating a
proton concentration gradient. It is the electrochemical
energy of this gradient that drives the synthesis of ATP.
• Universal Electron Acceptors
• Oxidative phosphorylation begins with the entry of
electrons into the respiratory chain.
• Most of these electrons arise from the action of
dehydrogenases that collect electrons from catabolic
pathways and funnel them into universal electron
acceptors—nicotinamide nucleotides (NAD+ or NADP+)
or flavin nucleotides (FMN or FAD).
• NAD
• NAD-linked dehydrogenases remove two hydrogen
atoms from their substrates. One of these is transferred
as a hydride ion (H-) to NAD+; the other is released as H+
in the medium.
• NADH and NADPH are water-soluble electron carriers that
associate reversibly with dehydrogenases.
• NADH carries electrons from catabolic reactions to their point of
entry into the respiratory chain, the NADH dehydrogenase
complex described below.
• NADPH generally supplies electrons to anabolic reactions.
• Neither NADH nor NADPH can cross the inner mitochondrial
membrane, but the electrons they carry can be shuttled across
indirectly.
• Flavoproteins contain a very tightly, sometimes covalently,
bound flavin nucleotide, either FMN or FAD.
• The oxidized flavin nucleotide can accept either one electron
(yielding the semiquinone form) or two (yielding FADH2 or
FMNH2).
• Electron transfer occurs because the flavoprotein has a higher
reduction potential than the compound oxidized.
• The standard reduction potential of a flavin
nucleotide, unlike that of NAD or NADP, depends
on the protein with which it is associated.
• Local interactions with functional groups in the
protein distort the electron orbitals in the flavin
ring, changing the relative stabilities of oxidized
and reduced forms.
• Because flavoproteins can participate in either
one- or two-electron transfers, they can serve as
intermediates between reactions in which two
electrons are donated and those in which only
one electron is accepted.
• The mitochondrial respiratory chain consists of a series
of sequentially acting electron carriers, most of which are
integral proteins with prosthetic groups capable of
accepting and donating either one or two electrons.
• Three types of electron transfers occur in oxidative
phosphorylation:
(1) direct transfer of electrons, as in the reduction of Fe3+
to Fe2+
(2) transfer as a hydrogen atom (H+ + e-)
(3) transfer as a hydride ion (:H), which bears two electrons.
• In addition to NAD and flavoproteins, three other types of
electron-carrying molecules function in the respiratory chain:
a hydrophobic quinone (ubiquinone) and two different types
of iron-containing proteins (cytochromes and iron-sulfur
proteins).
• Ubiquinone (also called coenzyme Q, or simply Q) is a lipid-
soluble benzoquinone with a long isoprenoid side chain.
• Ubiquinone can accept one electron to become the
semiquinone radical (QH) or two electrons to form ubiquinol
(QH2).
• Because ubiquinone is both small and hydrophobic, it is freely
diffusible within the lipid bilayer of the inner mitochondrial
membrane and can shuttle reducing equivalents between
other, less mobile electron carriers in the membrane.
• And because it carries both electrons and protons, it plays a
central role in coupling electron flow to proton movement.
• The cytochromes are proteins with characteristic strong
absorption of visible light, due to their ironcontaining
heme prosthetic groups.
• Mitochondria contain three classes of cytochromes,
designated a, b, and c, which are distinguished by
differences in their light-absorption spectra. Each type of
cytochrome in its reduced (Fe2+) state has three
absorption bands in the visible range.
• The cytochromes of type a and b and some of type c are
integral proteins of the inner mitochondrial membrane.
• One striking exception is the cytochrome c of
mitochondria, a soluble protein that associates through
electrostatic interactions with the outer surface of the
inner membrane.
• The components of ETC are electron carriers which are single
molecules or multi-subunit protein complexes or enzymes
containing prosthetic groups capable of accepting and
donating electrons. These complexes are associated with the
inner mitochondrial membrane.
• There are five complexes/enzymes of mitochondrial ETC:
• Complex I, also known as ubiquinone oxidoreductase: is made
up of NADH dehydrogenase, flavin mononucleotide (FMN),
and eight iron-sulfur (Fe-S) clusters.
• The NADH donated from glycolysis, and the citric acid cycle is
oxidized here, transferring 2 electrons from NADH to FMN.
• Then they are transferred to the Fe-S clusters and finally from
Fe-S to coenzyme Q. During this process, 4 hydrogen ions pass
from the mitochondrial matrix to the intermembrane space,
contributing to the electrochemical gradient
• Complex II, also known as succinate dehydrogenase, accepts
electrons from succinate (an intermediate in the citric acid
cycle) and acts as a second entry point to the ETC.
• When succinate oxidizes to fumarate, 2 electrons are accepted
by FAD within complex II.
• FAD passes them to Fe-S clusters and then to coenzyme Q,
similar to complex I.
• No protons are translocated across the membrane by complex
II, therefore less ATP is produced with this pathway.
• Complex III, also known as cytochrome c reductase, is made
up of cytochrome b, Rieske subunits (containing two Fe-S
clusters), and cytochrome c proteins.
• A cytochrome is a protein involved in electron transfer that
contains a heme group.
• The heme groups alternate between ferrous (Fe2+) and ferric
(Fe3+) states during the electron transfer.
• Because cytochrome c can only accept a single electron at
a time, this process occurs in two steps (the Q cycle), in
contrast to the single-step complex I and II pathways.
• Complex III also releases 4 protons into the
intermembrane space at the end of a full Q cycle,
contributing to the gradient.
• Cytochrome c then transfers the electrons one at a time
to complex IV.
• Complex IV, also known as cytochrome c oxidase, oxidizes
cytochrome c and transfers the electrons to oxygen, the
final electron carrier in aerobic cellular respiration.
• The cytochrome proteins a and a3, in addition to heme
and copper groups in complex IV transfer the donated
electrons to the bound dioxygen species, converting it
into molecules of water.
• The free energy from the electron transfer causes 4 protons to move
into the intermembrane space contributing to the proton gradient. 
• ATP synthase, also called complex V, uses the ETC generated proton
gradient across the inner mitochondrial membrane to form ATP.
• ATP-synthase contains up of F0 and F1 subunits, which act as a
rotational motor system.
• F0 is hydrophobic and embedded in the inner mitochondrial
membrane. It contains a proton corridor that is protonated and
deprotonated repeatedly as H+ ions flow down the gradient from
intermembrane space to matrix.
• The alternating ionization of F0 causes rotation, which alters the
orientation of the F1 subunits.
• F1 is hydrophilic and faces the mitochondrial matrix. Conformational
changes in F1 subunits catalyze the formation of ATP from ADP and
Pi. For every 4 H+ ions, 1 ATP is produced.
• ATP synthase is a multi-subunit protein complex
consisting of two major components, F1 – the
headpiece which projects into the matrix and
contains the site for synthesis of ATP, and F0 – the
stalk-like integral membrane protein complex
forming a pore or channel through which protons
pass from the inter-membrane space to the matrix.
• It is very similar to ATP synthase enzyme found in
chloroplasts.