The document discusses bioenergetics and several key concepts: 1) Photosynthesis captures energy from sunlight and converts it to chemical energy stored in glucose, which all animals obtain directly or indirectly. 2) Cellular respiration releases energy by combining oxygen and energy-rich compounds to produce ATP, the primary energy carrier in cells. 3) Metabolism consists of catabolic reactions that break down molecules and anabolic reactions that use energy from catabolism to build molecules. Metabolic pathways involve a series of reactions to produce a product.

1. Bioenergetics
Dr.B.RENGESH | M.Tech., Ph.D.
Associate Professor, Department of Pharmaceutical Technology,
Mahendra Engineering College (Autonomous),
Namakkal District, Tamil Nadu, India

2. The Sun and Photosynthesis
• The sun is the ultimate source of energy for all biological processes. This energy results
from the fusion of hydrogen atoms to form helium atoms:
• A portion of this energy reaches the Earth’s surface as sunlight, and is captured by the
chlorophyll in plants. This energy drives the conversion of carbon dioxide and water to form
glucose, and then into starch, triglycerides, and other forms of stored energy:
• All animals obtain energy either directly or indirectly from these energy stores in plants

3. Cellular Respiration
• During cellular respiration, plants and animals combine energy-rich compounds with
oxygen from the air, producing CO2 and releasing energy.
• Cellular respiration can be represented as:
– A portion of the energy released during respiration is captured in the form of adenosine
triphosphate (ATP), which stores energy for use in other processes.
– The remainder of the energy from respiration is released as heat.
An extremely simplified carbon cycle

4. Energy Flow in the Biosphere

5. Metabolism
• Metabolism is the sum of all reactions occurring in an organism:
– catabolism — the reactions involved in the breakdown of biomolecules.
– anabolism — the reactions involved in the synthesis of biomolecules.
• In general, energy is released during catabolism and required during anabolism.
Metabolic Pathways
• A metabolic pathway is a sequence of reactions used to produce one product or accomplish
one process.
– Each pathway consists of a series of chemical reactions that convert a starting material
into an end product (e.g., the citric acid cycle and the electron transport chain).
– Fortunately, there are a great many similarities among the major metabolic pathways in
all life forms.

6. Catabolism of food
• The catabolism of food is a three stage process.
Stage I : The digestion of large, complex molecules into simpler ones.
– The most common reaction in digestion is hydrolysis:
Stage II : The small molecules from digestion are broken down into even simpler units,
usually the two-carbon acetyl portion of acetyl coenzyme A (acetyl CoA):
– Some energy is produced at this stage, but much more is produced during the oxidation of
the acetyl units in Stage III.

7. Catabolism of food
Stage III : This is referred to as the common catabolic pathway because the reactions are the
same regardless of the type of food being degraded.
– citric acid cycle
– electron transport
– oxidative phosphorylation
• Energy released in Stage III appears in
the form of energy-rich molecules of
ATP.
– The whole purpose of the catabolic
pathway is to convert the chemical
energy in foods into molecules of
ATP, which carries energy to parts
of the cell where energy is needed.

8. ATP – The primary energy carrier – Structure
• Adenosine triphosphate, ATP, consists of:
– the heterocyclic base adenine
– the sugar ribose
– a triphosphate group
• At physiological pH, the protons on the triphosphate group are removed, giving ATP a
charge of -4.
– In the cell, it is complexed with Mg2+ in a 1:1 ratio, giving it a net charge of -2.
adenine + ribose is called adenosine

9. ATP – The primary energy carrier – Hydrolysis
• The triphosphate group is the part of the molecule that is important in the transfer of
biochemical energy. The key reaction is the transfer of a phosphoryl group, —PO3
2-, from
ATP to another molecule.
– During the hydrolysis of ATP in water, a phosphoryl group is transferred from ATP to a
water molecule:
– The products are adenosine diphosphate (ADP) and a phosphate ion, often referred to as
an inorganic phosphate, Pi, or just phosphate.

10. ATP – The primary energy carrier – Hydrolysis
• The transfer of a phosphoryl group from ATP to water is accompanied by a release of
energy.
• Free energy, ΔG, is used as a measure of the energy change.
– When energy is released, ΔG is negative.
– When energy is absorbed, ΔG is positive.
– When ΔG is measured under standard conditions, it is represented by ΔG º.
– When ΔG º is measured under body conditions, it is represented by ΔG º’.
• The liberated free energy is available for use by the cell to carry out processes requiring an
input of energy:

11. ATP – The primary energy carrier – Hydrolysis
• Compounds that liberate a large amount of free energy on hydrolysis are called high-
energy compounds.
• The hydrolysis of ATP to ADP is the principal energy-releasing reaction for ATP. Some
other hydrolysis reaction occur under some conditions, such as the hydrolysis of ATP to
adenosine monophosphate, AMP, and pyrophosphate, PPi:

12. ATP – The primary energy carrier – Hydrolysis
– This is usually followed by immediate hydrolysis of the pyrophosphate, which releases even
more energy:
• The hydrolyses of ATP and related
compounds are summarized below:

13. Important Coenzymes in the Common Catabolic Pathway
Coenzyme-A
• Coenzymes are weakly-bound organic groups that participate in enzyme-catalyzed
reactions, often by acting as shuttle systems for the transfer of chemical groups (e.g.,
hydrogen transport). Many important coenzymes are formed from vitamins.
• Coenzyme A is a central compound in metabolism. It is part of acetyl coenzyme A (acetyl
CoA), the substance formed from all foods as they pass through Stage II of catabolism.

14. Important Coenzymes – Coenzyme-A – Components
• Components of coenzyme A:
– vitamin B5, pantothenic acid, in the center.
– a phosphate derivative of ADP
– β-mercaptoethylamine, which puts a reactive sulfhydryl group (—SH) at the end of the
molecule (CoA—SH).

15. Important Coenzymes – Coenzyme-A – Nomenclature
• The letter A is included in the name Coenzyme A to signify its participation in the transfer
of acetyl groups, but Coenzyme A transfers all acyl groups. This is important in fatty acid
oxidation and synthesis.
• Acyl groups are linked to coenzyme A through the sulfur atom in a thioester bond:

16. Important Coenzymes – Ubiquinone (Q)
• Also called coenzyme Q
• A membrane-soluble low molecular weight compound
• Long hydrophobic tail keeps Q anchored in the mitochondrial inner membrane
• Q is a lipid soluble molecule that diffuses within the lipid bilayer, and shuttles electrons
from
• Complexes I and II and pass them to III
• Not a part of any complex

17. Important Coenzyme – Nicotinamide Adenine Dinucleotide (NAD+)
• NAD+, is an electron transporter which is a derivative of ADP and the vitamin
nicotinamide (B3).
• The reactive site of NAD+ is in the nicotinamide
portion.
– When oxidizing a substrate, the nicotinamide
ring accepts two electrons and one proton,
forming the reduced coenzyme NADH:

18. Important Coenzyme – Nicotinamide Adenine Dinucleotide (NAD+)
• A typical cellular reaction in which NAD+ serves as an electron acceptor is the oxidation
of an alcohol:
• In this reaction, one hydrogen atom of the alcohol substrate is directly transferred to
NAD+, whereas the other appears in solution as H+. Both electrons lost by the alcohol
have been transferred to the nicotinamide ring in NADH.
• Biochemical reactions involving coenzymes are often written more concisely:
– This notation emphasizes the oxidation
reaction and the involvement of the
coenzyme.

19. Important Coenzymes – Flavin Adenine Dinucleotide (FAD)
• FAD is another major electron carrier. It is a derivative of ADP & the vitamin riboflavin.
• The active site is located within the riboflavin
ring system. Unlike NAD+, FAD accepts both of
the hydrogen atoms lost by the substrate,
forming the reduced species FADH2:

20. Important Coenzymes – Flavin Adenine Dinucleotide (FAD)
• The substrates for reactions involving FAD are often those in which a —CH2—CH2—
portion of the substrate is oxidized to a double bond:

21. Mitochandria
• The mitochondrion is the powerhouse of the cell. It is the
organelle where many of the reactions of the common
catabolic pathway occur. It consists of an outer membrane,
which surrounds a inner membrane.
– The folds of the inner membrane are called cristae.
– The space that surrounds them is the matrix.
• The enzymes for ATP synthesis (electron
transport and oxidative phosphorylation) are
located on the cristae. The enzymes for the citric
acid cycle are found within the matrix, near the
surface of the inner membrane.

22. An Animal Cell
Schematic of typical animal cell:
(1) Nucleolus (2) Nuclear membrane (3) Ribosomes
(4) Vesicle (5) Rough endoplasmic reticulum (ER) (6) Golgi body (7) Cytoskeleton
(8) Smooth ER (9) Mitochondria (10) Vacuole (11) Cytosol (12) Lysosome (13)
Centrioles within centrosome

23. ELECTRON TRANSPORT CHAIN & OXIDATIVE PHOSPHORYLATION
Mitochondrial Electron Transport How did we get here?
• Summary of glycolysis
• Summary of the citric acid cycle (including pyruvate dehydrogenase)

24. ELECTRON
TRANSPORT CHAIN &
OXIDATIVE
PHOSPHORYLATION

25. • Final stages of aerobic oxidation of biomolecules in eukaryotes occur in the mitochondrion
• Reduced coenzymes NADH and FADH2 from:
(1) Aerobic oxidation of pyruvate by the citric acid cycle
(2) Oxidation of fatty acids and amino acids
Electron Transport Chain is the process by which NADH and FADH2 are oxidized and a
proton gradient is formed.
Oxidative phosphorylation is the process of making ATP by using the proton gradient
generated by the ETC.
Respiration by mitochondria:
• Oxidation of substrates is coupled to the phosphorylation of ADP
• Respiration (consumption of oxygen) proceeds only when ADP is present
• The amount of O2 consumed depends upon the amount of ADP added
ELECTRON TRANSPORT CHAIN & OXIDATIVE PHOSPHORYLATION

26. • Respiratory electron-transport chain (ETC) Series of enzyme complexes
embedded in the inner mitochondrial membrane, which oxidize NADH and
FADH2. Oxidation energy is used to transport protons creating a proton gradient –
protons pumped from matrix to intermembrane space across IMM
• ATP synthase uses the proton gradient energy to produce ATP; It is the release of
the energy in the gradient back through the membrane through the protein ATP
Synthase that drives ATP synthesis
ELECTRON TRANSPORT CHAIN & OXIDATIVE PHOSPHORYLATION

27. • The electron transport chain is associated with the mitochondrial
inner membrane
• Complexes I-IV contain multiple cofactors, and are involved in
electron transport
• Overall transfer of 2 electrons from NADH through ETC to
molecular oxygen:
ELECTRON TRANSPORT CHAIN (ETC) – Overview

28. • Complexes I – where NADH electrons enter the chain
• Complex II – Where FADH2 electrons enter the chain
• Electrons passed from Complex I or II to Coenzyme Q
• Coenzyme Q shuttles electrons to complex III
• Complex III shuttles electrons to cytochrome C
• Cytochrome C shuttles electrons to Complex IV
• Complex IV transfers electrons to O2 which is then reduced to water
• Flow through Complexes I, III and IV release energy which is used to pump
protons across the IMM and form a “proton gradient”
• Proton gradient has lots of potential energy
• When the energy is released (protons flow back into matrix through ATP synthase),
the energy drives ATP synthesis
ELECTRON TRANSPORT CHAIN (ETC) – Overview

29. • Also called NADH-ubiquinone oxidoreductase
• Complex I includes a flavoprotein (contains FMN – related to FAD) and proteins with Fe-
S centers (iron-sulfur clusters)
• These proteins provide two centers for oxidation reduction reactions
ETC – Electron transfer and proton flow in Complex I
• Transfers electrons from NADH to
Coenzyme Q via FMN and iron-sulfur
proteins
• NADH transfers a two electrons as a
hydride ion (H:-) to FMN
• Reduction of Q to QH2 requires 2 e-
• About 4 H+ translocated per 2 e-
transferred

30. • Succinate-ubiquinone oxidoreductase
• Same as succinate dehydrogenase, a component of the TCA cycle
• Succinate dehydrogenase
- Directs transfer of electrons from succinate to CoQ via FADH2.
- Catalyzes the reduction of Q to QH2
• Acyl-CoA dehydrogenase
- From β-oxidation of fatty acids. It also transfers electrons to CoQ via FADH2.
• Complex II proteins provide two centers for oxidation reduction reactions
- FAD → FADH2
- Fe3+ → Fe2+ (iron-sulfur cluster)
• FAD of Complex II is reduced in a 2-electron transfer of a hydride ion from succinate
• Complex II does NOT contribute to proton gradient, but supplies electrons from succinate
**Note that all electrons from FADH2 and NADH must pass through CoQ.**
ETC – Electron transfer in Complex II

31. ETC – Electron transfer in Complex II

32. ETC – Electron transfer and proton flow in Complex III
• Ubiquinol-cytochrome c oxidoreductase
• Transfers electrons to cytochrome c
• Complex III contains several cytochromes (heme prosthetic group) and Fe-S center proteins which
provide several centers for oxidation reduction reactions
• Oxidation of one QH2 is
accompanied by the translocation of
4 H+ across the inner mitochondrial
membrane
- Two H+ are from the matrix,
two from QH2
- Regenerates Q for next round

33. ETC – Electron transfer and proton flow in Complex IV
• Cytochrome c oxidase - Combination of cytochromes
- A complex of 10 protein subunits that contains 2 cytochromes (a and a3) and proteins with
copper centers that provide multiple centers for oxidation-reduction
- Consists of, 2 types of prosthetic groups - 2 heme and 2 Cu.
- Fe3+ → Fe2+
- Cu2+ → Cu1+
- Source of electrons is cytochrome c (links Complexes III and IV)
- Catalyzes a four-electron reduction of molecular oxygen (O2) to water (H2O)
- Cytochromes a and a3 are the only species capable of direct transfer of electrons to
oxygen.
- Translocates H+ into the intermembrane space and contributes to the proton gradient

34. ETC –
Electron
transfer and
proton flow in
Complex IV
Net effect is transfer of four H+ for each pair of e-
Proton translocation of 2 H+ for each pair of electrons transferred (each O atom reduced)
However, for each pair of electrons (e.g. NADH), only get 2H+ transferred to intermembrane
space in complex IV

35. SUMMARY OF
ELECTRON
TRANSPORT CHAIN

36. SUMMARY OF ELECTRON TRANSPORT CHAIN

37. ATP Synthase
• F0F1 ATP Synthase uses the proton gradient
energy for the synthesis of ATP
• Large transmembrane protein complex
• Faces into the mitochondrial matrix – spans
the IMM
• Composed of a “knob-and-stalk” structure
• F0 (stalk) has a proton channel which spans
the membrane.
- Forms a proton pore.
- Membrane-spanning portion – integral
membrane protein
- Made up of 4 different subunits
- F0 subunit composition: a1b2c9-12 (c
subunits form cylindrical, membrane-
bound base)

38. ATP Synthase
• F1 (knob) contains the catalytic subunits (ATP-
synthesizing subunits)
- Where ATP synthesis takes place
- F1 knobs: inner face of the inner
mitochondrial membrane
- (subunit composition: α3β3γδε)
- α3β3 oligomer of F1 is connected to
c subunits by a multisubunit stalk of
γ and ε chains
• Passage of protons through the F0 (stalk) into
the matrix is coupled to ATP formation
• Estimated passage of 3 H+ / ATP synthesized
• F0 is sensitive to oligomycin, an antibiotic that
binds in the channel and blocks H+ passage,
thereby inhibiting ATP synthesis

39. ATP Synthase – Mechanism
• F1-F0 complex serves as the molecular apparatus for coupling H+ movement to ATP synthase.
• There are 3 active sites, one in each β subunit
• Passage of protons through the F0 channel causes the rotor to spin in one direction and the stator to
spin in the opposite direction

40. Respiratory Inhibitors & Uncouplers
Inhibitors are chemicals that can block electron transfer through
specific complexes in the ETC
- Complex I: blocked by rotenone, barbiturates
- Complex III: blocked by antimycin A
- Complex IV: blocked by cyanide, azide, carbon monoxide
Uncouplers
• In some special cases, the coupling of the two processes can be
disrupted.
• Uncouplers stimulate the oxidation of substrates in the absence of
ADP
• Large amounts of O2 are consumed but no ATP is produced.
• Uncouplers are lipid-soluble weak acids
• Both acidic and basic forms can cross the inner mitochondrial
membrane

41. Respiratory Inhibitors & Uncouplers
Uncouplers
• Uncouplers deplete any proton gradient by transporting protons across the membrane
• Do NOT affect electron transport
• Allow protons back into the matrix without making ATP
• Stimulate oxygen consumption
2,4-Dinitrophenol: an uncoupler
• Used as a diet/weight loss drug
• Hydrophobic low molecular weight substance that can diffuse through the mitochondrial inner
membrane
• Shuttles protons across the membrane and dissipates proton gradient
• ATP synthesis goes down
– ADP concentration in cells goes up and acts as a stimulator
– Signals to turn on pathways to make ATP
– Therefore, electron transport and O2 consumption turned on fully and is NOT regulated

42. Respiratory Inhibitors & Uncouplers
2,4-Dinitrophenol: an uncoupler
• Energy produced by electron transport released as HEAT rather than harnessed into ATP synthesis
• Fuels (carbs and fats) are consumed at great rates and get quick weight loss BUT
– Get heavy breathing – using lots of oxygen
– Excessive fever (heat generation)
– BIG problem – no control over uncoupling
– Brain, heart and muscles are affected as well
• 2,4-dinitrophenol is extremely toxic and pulled from the market

43. Natural Uncouplers
• In newborn and hibernating animals, brown fat oxidizes large amounts of substrate (mostly fatty
acids) to generate heat
• ‘Brown fat’- brown because of the large number of mitochondria and their associated
cytochromes
• In brown fat mitochondria oxidation of NADH and FADH2 is uncoupled from ATP synthesis
– Mitochondria contain thermogenin (uncoupling protein).
– Thermogenin allows the release of energy as heat instead of ATP.
– Thermogenin dissipates proton electrochemical gradient
• By providing another channel for return of protons - bypasses ATP synthase
• Also called uncoupling protein (UCP)
• In brown fat mitochondria, the energy that would have been used to make ATP is liberated as heat