• Mechanochemistry is the coupling of the mechanical and the
chemical phenomena on a molecular scale.
• Molecular motors are biological molecular machines that are
the essential agents of movement in living organisms.
• A motor may be defined as a device that consumes energy in
one form and converts it into motion or mechanical work; for
example, many protein-based molecular motors harness the
chemical free energy released by the hydrolysis of ATP in
order to perform mechanical work
• Cytoskeletal motors
• Myosin is responsible for muscle contraction
• Dynein produces beating of cilia and flagella
• Polymerisation motors
• Microtubule polymerization using GTP.
• Rotary motors:
• FoF1-ATP synthase family of proteins convert the chemical energy in ATP to the
electrochemical potential energy of a proton gradient across a membrane or
the other way around.
• The bacterial flagellum responsible for the swimming and tumbling of
bacteria acts as a rigid propeller that is powered by a rotary motor.
• Nucleic acid motors:
• RNA polymerase transcribes RNA from a DNA template
The Motor of Life
• An enzyme within our body's cells called an ATP Synthase.
• Like any other motor it rotates, and surprisingly fast - in fact
at about 6,000 revs per minute!
• Further, it is the last word in ultra-miniaturisation, being
200,000 times smaller than a pinhead!
• We have some 100 trillion (1 followed by 14 zeros) cells, there
are in excess of 10 quadrillion (1 followed by 16 zeros) of
these amazing ultra-tiny little motors which drive our bodies
and upon which our very lives depend!
• The ATP Synthase motor's job is to manufacture a little
molecule called ATP - short for Adenosine triphosphate -
which is of enormous importance for the successful
functioning of our bodies.
The food we eat is ultimately converted into energy
• Process in which ATP is formed as a result of transfer of
electrons from NADH or FADH2 to O2 by a series of electron
• All oxidative steps in the degradation of carbohydrates, fats,
and amino acids converge at this final stage of cellular
respiration, in which the energy of oxidation drives the
synthesis of ATP.
• This process takes place in mitochondrion
• Major source of energy in our body.
• 36-38 molecules of ATP are produced when glucose is
completely oxidized to CO2 and H2O.
The Respiratory chain
• An electron transport chain
(ETC) couples electron transfer between an electron
donor (such as NADH) and an electron acceptor (such as O2)
with the transfer of H+
ions (protons) across a membrane. The
resulting electrochemical proton gradient is used to
generate chemical energy in the form of adenosine
• If protons flow back through the membrane, they enable
mechanical work, such as rotating bacterial flagella. ATP
synthase, an enzyme converts this mechanical energy into
chemical energy by producing ATP, which powers most
• The electron transport chain comprises an enzymatic series of
electron donors and acceptors. Each electron donor passes
electrons to a more electronegative acceptor, which in turn
donates these electrons to another acceptor, a process that
continues down the series until electrons are passed to oxygen, the
most electronegative and terminal electron acceptor in the chain.
• Passage of electrons between donor and acceptor releases energy,
which is used to generate a proton gradient across the
mitochondrial membrane by actively “pumping” protons into the
• This electrochemical proton gradient allows ATP synthase to use
the flow of H+
through the enzyme back into the matrix to generate
ATP from ADP and inorganic phosphate.
• Oxidative phosphorylation begins with the
entry of electrons into the respiratory chain
via electron carriers- nicotinamide nucleotides
(NAD or NADP) or flavin nucleotides (FMN or
NADH + H+
NADPH + H+
• FMN or FAD can accept 1 e-
+ 1 H+
semiquinone form or 2 e-
+ 2 H+
to form FMNH2
Respiratory chain consists of four complexes
• Complex I (NADH coenzyme Q reductase): accepts
electrons from the Krebs cycle electron carrier
nicotinamide adenine dinucleotide (NADH), and
passes them to coenzyme UQ (ubiquinone)
• Complex II (succinate dehydrogenase): also passes
electrons to UQ.
• Complex III (cytochrome bc1 complex): passes
electrons to cyt c
• Complex IV (cytochrome c oxidase) recieves
electrons from cyt c and uses the electrons and
hydrogen ions to reduce molecular oxygen to water.
• Two electrons are removed from NADH and
transferred to ubiquinone (Q). The reduced
product, ubiquinol (QH2) freely diffuses within
the membrane, and Complex I translocates
four protons (H+
) across the membrane, thus
producing a proton gradient.
• Additional electrons are delivered into the
quinone pool (Q) originating from succinate
and transferred (via FAD) to Q.
• Two electrons are removed from QH2 and
sequentially transferred to two molecules
of cytochrome c
• four electrons are removed from four
molecules of cytochrome c and transferred to
molecular oxygen (O2), producing two
molecules of water. At the same time, four
protons are translocated across the
membrane, contributing to the proton
Proton gradient powers synthesis
• Flow of electrons from NADH to oxygen is an
exergonic process which is coupled to ATP
synthesis, an endergonic process.
• Peter Mitchell proposed that electron transport and ATP
synthesis are coupled by a proton gradient across the inner
• The transfer of electrons through the respiratory chain leads
to the pumping of protons from the matrix to the cytosolic
side of the inner mitochondrial membrane.
• The H+ concentration becomes lower in the matrix, and an
electrical field with the matrix side negative is generated.
• Mitchell's idea, called the chemiosmotic hypothesis, was that
this proton-motive force drives the synthesis of ATP by ATP
• ATP synthase (mitochon-drial ATPase or F1-F0
ATPase or Complex V) 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.
• ATP synthase + ADP + Pi → ATP Synthase + ATP
• Is 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.
• It is a large, complex membrane-embedded enzyme that looks like
a ball on a stick.
• The 85-Å diameter ball, called the F1 subunit, protrudes into the
mitochondrial matrix and contains the catalytic activity of the
• The F1 subunit consists of five types of polypeptide chains (α3β3γδε).
• The α and β subunits, which make up the bulk of the F1, are
arranged alternately in a hexameric ring. Both bind nucleotides but
only the β subunits participate directly in catalysis.
• The central stalk consists of two proteins: γ and ε. The γ subunit
includes a long a-helical coiled coil that extends into the center of
• Each of the β subunits interacts with a different face of γ.
• The F0 subunit is a hydrophobic segment that spans the inner
• F0 contains the proton channel of the complex.
• This channel consists of a ring comprising from 10 to 14 c
subunits that are embedded in the membrane.
• A single a subunit binds to the outside of this ring.
• The proton channel depends on both the a subunit and the c
• The F0 and F1 subunits are connected in two ways, by the
central γε stalk and by an exterior column.
• The exterior column consists of one a subunit, two b subunits,
and the δ subunit.
ATP Synthase as Motor Protein:
The Binding Change Mechanism
• ATP synthesis is coupled with a conformational change in the
ATP synthase generated by rotation of the gamma subunit.
• the proton-motive force across the inner mitochondrial
membrane, generated by the electron transport chain, drives
the passage of protons through the membrane via the
FO region of ATP synthase.
• The changes in the properties of the three β subunits allow
sequential ADP and Pi binding, ATP synthesis, and ATP
• interactions with the gamma subunit make the three
b subunits inequivalent.
• The three β subunits can exist in three different
– T, or tight, conformation: binds ATP with great avidity to
convert bound ADP and Pi into ATP
– L, or loose, conformation: binds ADP and Pi but is
sufficiently constrained that it cannot release bound
– O, or open, form: exist with a bound nucleotide but it can
also convert to form a more open conformation and
release a bound nucleotide.
• The interconversion of these three forms can be driven by
rotation of the γ subunit. If the γ subunit is rotated 120
degrees in a counterclockwise direction there will be a change
in the subunit in the T conformation into the O conformation,
allowing the subunit to release the ATP that has been formed
within it. The subunit in the L conformation will be converted
into the T conformation, allowing the transition of bound ADP
+ Pi into ATP. Finally, the subunit in the O conformation will
be converted into the L conformation, trapping the bound
ADP and Pi so that they cannot escape.
The γ subunit rotates in 120-degree increments, with each step
corresponding to the hydrolysis of a single ATP molecule.
Proton Motion Across the Membrane Drives
Rotation of the C Ring
• The c subunit consists of two a helices with an aspartate at 61 position.
• The a subunit contains two proton half channels.
• A proton enters from the intermembrane space into the cytosolic half-
channel to neutralize the charge on an aspartate residue in a c subunit.
• With this charge neutralized, the c ring can rotate clockwise by one c
subunit, moving an aspartic acid residue out of the membrane into the
• This proton can move into the matrix, resetting the system to its initial
• Each proton enters the cytosolic half-channel, follows a complete
rotation of the c ring, and exits through the other half-channel into the