MLS 064: Biochemistry

Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

Lesson title: The Respiratory Chain & Oxidative Materials:

Phosphorylation Book, Pen and Notebook
Learning Targets: References:
At the end of the module, students will be able to: Ubalde, Biochemistry for Allied Health
1. Describe the importance of mitochondria in ATP Sciences: Edric Publishing, 2019
generation.
2. Describe the process of the respiratory chain.
3. Explain how pyruvate (the final product of glycolysis)
enter the respiratory chain and the enzymes involved
in it.
4. Illustrate the steps of the respiratory chain and the
different enzymes related to them.
5. Illustrate the steps of oxidative phosphorylation.
1.

A. LESSON PREVIEW/REVIEW

Introduction
In our last activity, we have discussed about Bioenergetics and the Role of ATP. Remember that adenosine
triphosphate (ATP) transfers energy from the processes that produce it to those that use it. Bioenergetics
describes the transfer and utilization of energy in biologic systems and predicts if a process is possible to
occur. As a recall, can you answer these following questions?

a. What is bioenergetics?
b. What are the difference between enthalpy and entropy?
c. Describe the structure of ATP.

Then, the instructor will outline the new activity, “The Respiratory Chain and Oxidative Phosphorylation”

B. MAIN LESSON

The students will study and read their book about this lesson.

After a meal, generation of energy will take place in three phases. The first phase is the
breaking down of large molecules of food into smaller units by different enzymes such as amylase and lipase.
The process is called digestion. Proteins are hydrolyzed to the 20 amino acids, polysaccharides are hydrolyzed
to simple sugars such as glucose, and fats are hydrolyzed to fatty acids. The first stage does not produced
energy yet, it is just a preparatory stage for more complex processes. The second phase will include the
degradation of numerous small molecules to simpler units and these units will play a central role in
metabolism. Sugars, fatty acids, glycerol and several amino acids are converted into acetyl CoA, the activated
two-carbon unit that is the fuel for the final stages of aerobic metabolism. Some adenosine triphosphate (ATP)

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

is generated in the second phase, but the amount is small compared with that obtained in the third phase. In
the third phase, ATP is produced from the complete oxidation of acetyl CoA. The third phase consists of the
citric acid cycle and oxidative phosphorylation, which are the final common pathways in the oxidation of fuel
molecules. Acetyl CoA brings the breakdown products of proteins, sugars, and fats into the citric acid cycle
(also called the tricarboxylic acid (TCA) cycle or Krebs cycle), where they are completely oxidized to CO . The
2

processes is more precisely termed cellular respiration.

A. Mitochondria

Electron transport and oxidative phosphorylation occur

in the mitochondrion, the cell's "power plant". The citric acid
enzymes are housed there as is pyruvate dehydrogenase,
enzymes for fatty acid oxidation, and all of the enzymes and
proteins of the electron transport/oxidative phosphorylation
system.

Mitochondria have a smooth outer membrane and a

complicated inner membrane, with many folds inside the
organelle. This enfolding material is called cristae, the number
of which vary with the respiratory needs of the cell. Cells with
low respiration rates have fewer cristae; those with higher rates
have more. Proteins of electron transport and oxidative
phosphorylation are bound to the inner mitochondrial
membrane. The "matrix" of the inner mitochondrial
compartment (a gel-like aqueous material) contains high
concentrations of oxidative metabolic enzymes (citric acid
cycle, etc.) as well as the mitochondrial DNA, RNA, and
ribosomes for making mitochondrial proteins.

The outer membrane of the mitochondrion contains porin (also called VDAC), a pore-forming protein
that allows diffusion of up to 10 kD (10,000 Dalton molecular weight) molecules. The inner membrane is much
richer in proteins (up to 75% protein by mass) than the outer membrane and allows only O , CO and H 0 to
2 2 2

freely pass. The inner membrane is the anchor for electron transport and oxidative phosphorylation proteins,
and contains transport proteins for passing common metabolites, such as ATP, ADP, pyruvate, Ca , and++

phosphate. The integrity of the inner membrane is important for operation of the mitochondrion, which
harnesses energy from the chemical gradients it creates across the membrane.

B. Conversion of Pyruvate to acetyl CoA

As we have learned in the previous modules, the pyruvate produced by glycolysis can have many fates.
In the absence of oxygen (anaerobic conditions), the pyruvate is converted into lactic acid or ethanol,

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

depending on the organism. In the presence of oxygen (aerobic conditions), it is converted into a molecule,
called acetyl coenzyme A (acetyl CoA) that is able to enter the citric acid cycle. The path that pyruvate takes
depends on the energy needs of the cell and the oxygen availability. In most tissues, pyruvate is processed
aerobically because oxygen is readily available. For instance, in resting human muscle, most pyruvate is
processed aerobically by first being converted into acetyl CoA. However, in very active muscle, for instance,
the thigh muscles of a sprinter, much of the pyruvate is processed to lactate because the oxygen supply
cannot meet the oxygen demand.

Glycolysis takes place in the cytoplasm of the cell, but the citric acid cycle takes place in mitochondria.
Pyruvate must therefore be transported into mitochondria to be aerobically metabolized. In the mitochondrial
matrix, pyruvate is oxidatively decarboxylated by the pyruvate dehydrogenase complex to form acetyl CoA:

Pyruvate + CoA + NAD 🡪 acetyl CoA + CO + NADH + H

+
2
+

PYRUVATE DEHYDROGENASE COMPLEX

Enzymes Prosthetic group Reaction catalyzed
E1: Pyruvate dehydrogenase Thiamine pyrophosphate (TPP) Oxidative decarboxylation of
pyruvate
E2: Dihydrolipoyl Lipoamide and coenzyme A (coAsh) Transfer of acetyl group to CoA
transacetylase
E3: Dihydrolipoyl Flavin adenine (FAD) from flavin Regeneration of the oxidized from
dehydrogenase and NAD from niacin of lipoamide

Recall that glycolysis generates two molecules of pyruvate for each glucose molecule metabolized.
This irreversible conversion of pyruvate into acetyl CoA is the link between glycolysis and the citric acid cycle.
This reaction is a decisive reaction in metabolism: it commits the carbon atoms of carbohydrates to oxidation
by the citric acid cycle or to the synthesis of lipids

The steps:

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

a. Decarboxylation. Pyruvate combines with the ionized (carbanion) form of TPP and is then decarboxylated to
yield hydroxyethyl-TPP. This reaction, the rate-limiting step in the synthesis of acetyl CoA, is catalyzed by
the pyruvate dehydrogenase component (E1) of the multienzyme complex.

b. Oxidation. The hydroxyethyl group attached to TPP is oxidized to form an acetyl group while being
simultaneously transferred to lipoamide, a derivative of lipoic acid.
c. Formation of acetyl CoA. The acetyl group is transferred from acetyllipoamide to CoA to form acetyl CoA.
Dihydrolipoyl transacetylase (E2) catalyzes this reaction. The energy-rich thioester bond is preserved as the
acetyl group is transferred to CoA. Acetyl CoA, the fuel for the citric acid cycle, has now been generated from
pyruvate.

C. The Citric Acid Cycle

The tricarboxylic acid cycle (TCA cycle), also known as the citric acid cycle or the Krebs cycle, is a major
energy-producing pathway in living bodies. Cells obtain ATP from breakdown of glucose in the absence of
oxygen as in glycolysis. However, most organisms normally are aerobic and oxidize their organic fuels
completely to CO and water. Foodstuffs feed into the citric acid cycle as acetyl-CoA and the acetyl-CoA is
2

oxidized to carbon dioxide and water in order to generate energy. Thus, under aerobic conditions, the generation
of energy from glucose is the oxidative decarboxylation of pyruvate to form acetyl CoA. The cycle also serves in
the synthesis of fatty acids, amino acids, and glucose.

The citric acid cycle occurs in the mitochondrial matrix in the eukaryotes. All the enzymes of the TCA
cycle are in the mitochondrial matrix except succinate dehydrogenase, which is in the inner mitochondrial
membrane. However, in the prokaryotes, the reaction cycle occurs in plasma membrane.

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

The cycle starts with the 4-carbon compound oxaloacetate, adds two carbons from acetyl-CoA, loses two
carbons as CO , and regenerates the 4-carbon compound oxaloacetate. Electrons are transferred by the cycle
2

to NAD+ and FAD. As the electrons are subsequently passed to O by the electron transport chain, the process
2

of oxidative phosphorylation generates ATP. ATP is also generated from GTP, produced in one reaction of the
cycle by substrate-level phosphorylation. Oxidation of the carbons of acetyl-CoA to carbon dioxide requires
capturing eight electrons from the molecule.

Steps:
1. Acetyl-CoA and oxaloacetate condense, forming citrate.
Acetyl CoA + Oxaloacetate 🡪 citrate
Enzyme: Citrate synthase.
Cleavage of the high-energy thioester bond in acetyl-CoA provides the energy for this condensation.
Citrate (the product) is an inhibitor of this reaction.

2. Citrate is isomerized to isocitrate by a rearrangement of the molecule.

Citrate 🡪 isocitrate
Enzyme: Aconitase/Aconitase hydratase

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

3. Isocitrate is oxidized to α-ketoglutarate, in a two-step reaction in which there is first an oxidation, and then a
decarboxylation. CO is produced, and the electrons are passed to NAD+ to form NADH and H+. This step
2

captures two of the eight electrons present in the carbons of acetyl-CoA.

Isocitrate 🡪 α-ketoglutarate; (released CO )2

Enzyme: Isocitrate dehydrogenase.

This key regulatory enzyme of the TCA cycle is allosterically activated by ADP and inhibited by NADH.

4. Alpha-Ketoglutarate is converted to succinyl-CoA in an oxidative decarboxylation reaction, CO is released,

2

and succinyl-CoA, NADH, and H are produced. This step captures another two electrons from the carbons
+

of acetyl-CoA.
Alpha-ketoglutarate 🡪 succinyl CoA; (released CO ) 2

Enzyme: Alpha-ketoglutarate dehydrogenase.

This enzyme requires five cofactors: thiamine pyrophosphate, lipoic acid, CoASH, FAD, and NAD+.

5. Succinyl-CoA is cleaved to succinate.

Cleavage of the high-energy thioester bond of succinyl- CoA provides energy for the substrate level
phosphorylation of GDP to GTP.
Enzyme: succinate thiokinase (succinyl-CoA synthetase).

6. Succinate is oxidized to fumarate.

Succinate transfers two hydrogens together with their electrons to FAD, which forms FADH . After this step, six
2

of the eight electrons from the carbons in acetyl-CoA have been captured.
Succinate 🡪 Fumarate
Enzyme: Succinate dehydrogenase.

7. Fumarate is converted to malate by the addition of water across the double bond.
(H O) Fumarate 🡪 Malate
2

Enzyme: Fumarase/ Fumarase hydratase

8. Malate is oxidized, regenerating oxaloacetate and thus completing the cycle.

Two hydrogens along with their electrons are passed to NAD , producing NADH and H , and finishing the capture
+ +

of the eight electrons from the carbons of acetyl-CoA.

Malate 🡪 Oxaloacetate
Enzyme: Malate dehydrogenase.

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

B. Yield of the Citric Acid Cycle

Each molecule of acetyl CoA entering the citric acid cycle yields the following:
• Two CO 2

• Three NADH
• One FADH 2

• One GTP

Because each NADH will eventually produce 2.5 ATP and each FADH will produce 1.5 ATP
2

through the electron transport chain, the overall ATP yield from 1 acetyl CoA is 10 ATP (7.5 from NADH, 1.5
from FADH , and 1 from GTP).
2

C. Oxidative Phosphorylation

Energy from fuel oxidation is converted to the high-energy phosphate bonds of adenosine
triphosphate (ATP) by the process of oxidative phosphorylation. Most of the energy from oxidation of fuels in the
tricarboxylic acid (TCA) cycle and other pathways is conserved in the form of the reduced electron-accepting
coenzymes, nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH ). The electron-
2

transport chain (ETC) oxidizes NADH and FADH and donates the electrons to O , which is reduced to H O.
2 2 2

Because of the complexity of this topic, it is better explained by reading your book. We are only
going to touch key components of ETC in this module. You can watch this video:
https://www.youtube.com/watch?v=C8VHyezOJD4

a. Oxidative phosphorylation is the last step of cellular respiration.

b. This stage consists of a series of electron transfer from organic compounds to oxygen while simultaneously
releasing energy during the process.
c. In aerobic respiration, the final electron acceptor is the molecular oxygen.
d. This chain of reactions is important as it involves breaking down of ATP into ADP and resynthesizing it in the
process to ATP, thus utilizing the limited ATPs in the body about 300 times in a day.
e. The electron flow takes place in four large protein complexes that are embedded in the inner mitochondrial
membrane, together called the respiratory chain or the electron-transport chain.
f. This stage is crucial in energy synthesis as 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.
g. Just like the citric acid cycle, ETC occurs in the mitochondria; the difference is that the electron transport
chain enzymes is in the inner mitochondrial membrane (except for the cytochrome c, which is in the

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

intermembrane space), compared to Krebs, which is in the mitochondrial matrix.

1. Three major stages of ETC

A. Transfer of electrons from NADH to coenzyme Q
a. NADH passes electrons via NADH dehydrogenase complex (complex I) to FMN. The complex is also known
as the NADH: CoQ oxidoreductase.
 NADH is produced by the α-ketoglutarate dehydrogenase, isocitrate dehydrogenase, and malate
dehydrogenase reactions of the TCA cycle, by the pyruvate dehydrogenase reaction that converts
pyruvate to acetyl-CoA, by β-oxidation of fatty acids, and by other oxidation reactions.
 NADH produced in the mitochondrial matrix diffuses to the inner mitochondrial membrane where
it passes electrons to FMN, which is tightly bound to a protein.
b. FMN passes the electrons through a series of iron–sulfur (Fe–S) complexes to coenzyme Q, which
accepts electrons one at a time, forming first the semiquinone and then ubiquinol.
c. The energy produced by these electron transfers is used to pump protons to the cytosolic side of the inner
mitochondrial membrane.
d. As the protons flow back into the matrix through the pores in the ATP synthase complex, ATP is generated.

B. Transfer of electrons from coenzyme Q to cytochrome c

a. Coenzyme Q passes electrons through Fe–S centers to cytochromes b and c1, which transfer the electrons
to cytochrome c. The protein complex involved in these transfers is called complex III, or the cytochrome b-
c1 complex. The complex is also known as CoQ:C1 oxidoreductase.
b. The energy produced by the transfer of electrons from coenzyme Q to cytochrome c is used to pump protons
across the inner mitochondrial membrane.
c. As the protons flow back into the matrix through the pores in the ATP synthase complex, ATP is generated.

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

d. Electrons from FADH2, produced by reactions such as the oxidation of succinate to fumarate, enter the
electron transport chain at complex II, which contains succinate dehydrogenase. Complex II will transfer
electrons to coenzyme Q, without the associated proton pumping across the inner mitochondrial membrane.

C. Transfer of electrons from cytochrome c to oxygen

a. Cytochrome c transfers electrons to the cytochrome aa complex, which transfers the electrons to molecular
3

oxygen, reducing it to water. Cytochrome oxidase (complex IV) catalyzes this transfer of electrons.
b. The energy produced by the transfer of electrons from cytochrome c to oxygen is used to pump protons
across the inner mitochondrial membrane.
c. As the protons flow back into the matrix, ATP is generated.

F. Chemiosmotic Model of Adenosine Triphosphate Synthesis

The chemiosmotic model explains how energy from transport of electrons to O is transformed into the
2

high-energy phosphate bond of ATP. The ETC contains three large protein complexes (I, III, and IV) that span
the inner mitochondrial membrane. As electrons pass through these complexes in a series of oxidation–reduction
reactions, protons are transferred from the mitochondrial matrix to the cytosolic side of the inner mitochondrial
membrane. The pumping of protons generates an electrochemical gradient (Δp) across the membrane
composed of the membrane potential and the proton gradient. ATP synthase contains a proton pore that spans
the inner mitochondrial membrane and a catalytic headpiece that protrudes into the matrix. As protons are driven
into the matrix through the pore, they change the conformation of the headpiece, which releases ATP from one
site and catalyzes formation of ATP from ADP and inorganic phosphate (Pi) at another site.

Summary of the components of the ETC

Complex I (NADH Contains FMN, which accepts 2e and H from 2 NADH to become the reduced form
− +

dehydrogenase) of FMNH ; also contains iron atoms, which assist in the transfer of the e and H to
2
− +

coenzyme Q. Inhibited by amobarbital and rotenone.

Complex II (Succinate Contains iron and succinate, which oxidizes FAD to form FADH . Inhibited 2

dehydrogenase) by antimycin A.
Coenzyme Q Accepts e from FMNH (complex I) and FADH (complex II). Transfers e to complex
−
2 2
−

III.
Complex III Contains heme group, in which the Fe accepts the e from coenzyme Q to become
3+ −

(cytochrome b) Fe . Transfers e to cytochrome c.

2+ −

Cytochrome c Contains heme group, in which the Fe accepts the e from complex III to become
3+ −

Fe . Transfers e to complex IV.

2+ −

Complex IV Contains heme group, in which the Fe accepts e from cytochrome c to become
3+ −

(cytochrome a) Fe . Transfers e to O , which is combined with hydrogen to form H O. Inhibited by

2+ −
2 2

cyanide, CO, and sodium azide.

Complex V (ATP Contains a proton channel that allows for protons to cross into the matrix, using the
synthase) proton gradient energy to form ATP. Inhibited by oligomycin (blocks H channel). +

Note that each NADH yields 2.5 ATP; each FADH 2 yields 1.5 ATP.

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

CHECK FOR UNDERSTANDING

You will answer and rationalize this by yourself. This will be recorded as your quiz. One (1) point will be given to
correct answer and another one (1) point for the correct ratio. Superimpositions or erasures in you answer/ratio
is not allowed. You are given 25 minutes for this activity:

Multiple Choice

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

1. Loss of electrons can be termed as ______________.

a. Metabolism
b. Anabolism
c. Oxidation
d. Reduction

2. Gain of electrons can be termed as ___________.

a. Metabolism
b. Anabolism
c. Oxidation
d. Reduction

3. Where does oxidative phosphorylation take place?

a. Mitochondria
b. Nucleus
c. Ribosomes
d. Cell membrane

4. Dihydrolipoyl transacetylase enzyme that is one of the components of the Pyruvate dehydrogenase complex
has what cofactor?
a. Coenzyme A
b. Thiamine pyrophosphate
c. Flavin adenine
d. Nicotinamide adenine dinucleotide

5. During the Krebs cycle, which enzyme catalyzes cleaving of a high-energy thioester bond of succinyl CoA?
a. Succinate dehydrogenase
b. Isocitrate dehydrogenase
c. Succinate thiokinase
d. Succinate decarboxylase

6. Each Krebs cycle will yield what compounds?

a. Two CO , Three NADH, One FADH , One GTP
2 2

b. Two CO , Three NAD, One FAD, One GTP

2

c. Three CO , 2.5 NAD, 1.5 FADH , One ATP

2 2

d. Three CO , 2.5 NAD, 1.5 FADH , One ATP

2 2

7. If there is 6 NADH and two FADH and two GTP produced in two cycles of Krebs cycle, how many ATPs are
2

produced?
a. 25 ATP
b. 15 ATP
c. 18 ATP
d. 20 ATP

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

8. The following are CORRECTLY matched except?

a. Complex I: NADH dehydrogenase
b. Complex IV: cytochrome a
c. Complex II: Succinate dehydrogenase
d. Complex III: Coenzyme Q

9. The enzyme in the Krebs cycle that requires five cofactors.

a. Isocitrate dehydrogenase
b. Fumarase
c. Malate dehydrogenase
d. Alpha-ketoglutarate dehydrogenase

10. The enzyme in the Krebs cycle, which is for the substrate-level phosphorylation of GDP to GTP.
a. Citrate synthase
b. Succinate thiokinase
c. Aconitase
d. Succinate dehydrogenase

RATIONALIZATION ACTIVITY (DURING THE FACE TO FACE INTERACTION WITH THE STUDENTS)
The instructor will now rationalize the answers to the students and will encourage them to ask questions and to
discuss among their classmates for 20 minutes.

1. ANSWER: ________
RATIO:_______________________________________________________________________________
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2. ANSWER: ________
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3. ANSWER: ________
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4. ANSWER: ________

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

RATIO:_______________________________________________________________________________
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5. ANSWER: ________
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6. ANSWER: ________
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8. ANSWER: ________
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9. ANSWER: ________
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10. ANSWER: ________

RATIO:_______________________________________________________________________________
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C. LESSON WRAP-UP

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 MLS 064: Biochemistry
Module #9 Student Activity Sheet

Name: Class number: _______

_________________________________________________________________ Date:
Section: ____________ Schedule: ________________
________________________________________

AL: MUDDIEST POINT

In today’s session what was least clear to you? 
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You will now mark (encircle) the session you have finished today in the tracker below. This is simply a visual to
help you track how much work you have accomplished and how much work there is left to do.

You are done with the session! Let’s track your progress.

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