SCI104 MICROBIOLOGY

INTRODUCTION TO
MICROBIAL METABOLISM

Prepared by:
Naval, Rameses L.
Quimbo, Jasper C.
Raquel, Leo
Abayon, Myra A.
1
 Republic of the Philippines
Leyte Normal University
College of Arts and Sciences
Science Unit
Tacloban City

Module 3: Introduction to Microbial Metabolism

Key Terms: Kreb’s Cycle, metabolism, electron transport chain, glycolysis, enzymes

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INTRODUCTION
Introduction

Metabolism, from the Greek term metaballein, meaning change, pertains to all chemical
workings of cells. It is a shorthand term for encapsulating almost any activity or behavior of an
organism, from the general to the specific, including growth, synthesis, transport, digestion, energy
release and consumption, and movement. Although metabolism entails thousands of different
reactions, most of them can be placed into one of two general categories. In the case of catabolism,
larger molecules are degraded or broken down into smaller molecules, usually with the release of
energy. In the case of anabolism, also called biosynthesis, larger molecules are built from smaller
ones, which results in the formation of cell structures. It is usually driven by energy derived from
catabolism. Even though they have somewhat opposite effects, these two forms of metabolism are
tightly linked and highly complementary. The result of them working together is that all
metabolism is coordinated for the cell to carry out essential life functions.
Throughout earth’s history, microbial metabolism has been a driving force behind the
development and maintenance of the planet’s biosphere. Eukaryotic organisms such as plants and
animals typically depend on organic molecules for energy, growth, and reproduction. Prokaryotes,
on the other hand, can metabolize a wide range of organic as well as inorganic matter, from
complex organic molecules like cellulose to inorganic molecules and ions such as atmospheric
nitrogen (N2), molecular hydrogen (H2), sulfide (S2−), manganese (II) ions (Mn2+), ferrous iron
(Fe2+), and ferric iron (Fe3+), to name a few. By metabolizing such substances, microbes
chemically convert them to other forms. In some cases, microbial metabolism produces chemicals
that can be harmful to other organisms; in others, it produces substances that are essential to the
metabolism and survival of other life forms.

LEARNING
Learning Outcomes OUTCOMES
When you have mastered the information in this module, you should be able to:
1. Define metabolism and differentiate its two types.
2. Describe the basic functions of enzymes in cells.
3. Outline the prominent characteristics of enzymes.
4. Explain how enzymes lower the energy required for a reaction to occur.
5. Discuss enzyme structure, and interactions between enzymes and substrates.
6. Describe the types of enzyme functions and methods of naming them.
7. Summarize key features of enzyme regulation.

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8. Describe the importance of oxidation-reduction reactions in metabolism.
9. Describe why glycolysis is not oxygen dependent
10. Define and describe the net yield of three-carbon molecules, ATP, and NADH from
glycolysis
11. Explain how three-carbon pyruvate molecules are converted into two-carbon acetyl
groups that can be funneled into the Krebs cycle.
12. Define and describe the net yield of CO2, GTP/ATP, FADH2, and NADH from the Krebs
cycle
13. Explain how intermediate carbon molecules of the Krebs cycle can be used in a cell.
14. Compare and contrast the electron transport system location and function in a
prokaryotic cell and a eukaryotic cell
15. Compare and contrast the differences between substrate-level and oxidative
phosphorylation
16. Explain the relationship between chemiosmosis and proton motive force
17. Describe the function and location of ATP synthase in a prokaryotic versus eukaryotic
cell
18. Compare and contrast aerobic and anaerobic respiration.
19. Describe the function and locations of photosynthetic pigments in eukaryotes and
prokaryotes
20. Describe the major products of the light-dependent and light-independent reactions
21. Describe the reactions that produce glucose in a photosynthetic cell
22. Compare and contrast cyclic and noncyclic photophosphorylation

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LET’S GET STARTED
Move the terms into the correct empty boxes to complete this
concept map comparing cellular metabolism in bacteria and
eukaryotes.

bacteria, eukaryotes, glycolysis, electron transport system, Krebs cycle, cell

membrane, mitochondrial matrix, inner mitochondrial membrane, periplasmic
space, intermembrane space

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A. Metabolism and Enzymes
ENZYMES According to the figure, the amount of
energy required when an enzyme is
Metabolism require biological catalyst in present is substantially lower than in the
the form of enzymes. absence of an enzyme. As a result, an
• Enzyme speeds up the rate of a enzyme present in metabolism
metabolic reaction. contributes to the process by speeding
• Enzymes are proteins that enable up and requiring less energy to complete
our bodies' metabolism, or the processes
chemical reactions, go more
quickly.
• They construct some substances
and deconstruct others.
• Enzymes are found in all living
organisms.
• Enzymes are produced naturally in
our bodies. However, enzymes can
be found in both synthetic and
natural foods.

How Do Enzymes Work?

During a chemical reaction,

reactants are converted to products by
bond formation or breakage. A certain
amount of energy is required to initiate
every such reaction, which limits its rate.

This resistance to a reaction, which

must be overcome for a reaction to
proceed, is measurable and is called the
energy of activation or activation energy.

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 At the molecular level, an enzyme
promotes a reaction by serving as a
physical site upon which the reactant
molecules, called substrates, can be
positioned for various interactions.

The enzyme is much larger in size

than its substrate, and it presents a
uniquely shaped pocket that fits only that
particular substrate. Although an enzyme
binds to the substrate and participates
directly in changes to the substrate, it
does not become a part of the products,
is not used up by the reaction, and it can
function over and over again.

that maintains the metabolic balance inside cells.

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A Different Kind of Catalyst

Originally proteins were A conjugated enzyme, sometimes

considered the only biological molecules
that act as catalysts. Then biologists
found a novel type of RNA they termed
ribozymes.
Ribozymes appear to be rather
common, with around 500 having been
identified in all types of cells and some
viruses. They display some of the
properties of protein catalysts, such as
having a specific active site and
interacting with a substrate. But these
molecules are remarkable because their
substrates are other molecules of RNA.
referred to as a holoenzyme, is a
combination of a protein, now called the
apoenzyme, and one or more cofactors.
Cofactors are either organic
molecules, called coenzymes, or
inorganic elements (metal ions) that
many enzymes require to become
functional.
In some enzymes, the cofactor is
loosely associated with the apoenzyme
by noncovalent bonds; in others, it is
linked by covalent bonds.

In natural systems, ribozymes are

involved in self-splicing or cutting of RNA
molecules during processing of the
genetic code, and even ribosomes
function as ribozymes during protein
synthesis .

Enzyme Structure

Enzymes are composed largely of

protein molecules, although certain types
of RNA can function as nonenzyme
catalysts.

Enzymes can be classified as

simple or conjugated.
• Simple enzymes consist of protein
alone.
• Conjugated enzymes contain
protein and nonprotein molecules.

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Location and Regularity of Enzyme
Action

Enzymes perform their tasks either Most enzymes of the metabolic pathways
inside or outside of the cell in which they are of this variety.
were produced. After initial synthesis in
the cell, exoenzymes are transported
extracellularly, where they break down
large food molecules or harmful
chemicals.

Examples of exoenzymes are

cellulase, amylase, and penicillinase. By
contrast, endoenzymes are retained
intracellularly and function there.

Regulation of Enzymatic Activity and Condensation Reaction

Metabolic Pathways
It involves the removing of water
The usage of available nutrients molecule from an enzymatic activity in
and energy is maximized by following order to create a glycosidic bon and fuse
metabolic pathways in a stepwise, highly the two molecules.
regulated manner. The cell adapts to its
surroundings by changing its metabolic
state.

The cell's environment has a big

impact on an enzyme's activity. Enzymes
can only function in the natural
temperature, pH, and osmotic pressure of
an organism's environment.
Large substrates, for example, must
be broken down or digested by enzymes
into smaller molecules before being
utilized. Digestion is also referred to as a
hydrolysis since the breaking of bonds
usually necessitates the use of water.

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Hydrolysis Reaction

It involves the adding of water

molecule in an enzymatic activity in order
to break the peptide bond holding the
two fused molecules.

microbes

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B. CELL ENERGETICS
It refers to the processes that is involved in
ATP synthesis which forms energy that is used for
the organisms’ body to function.
Cells manage energy in the form of
chemical reactions that change molecules. This
often involves activities such as the making or
breaking of bonds and the transfer of electrons.
Not all cellular reactions have the same
relation to energy. Some release energy and
others require it to proceed.
The basis for cell energetics lies in the
chemical bonds, electron transfers, and special
pathways along with their enzymes.
ENDERGONIC
A process driven forward with the utilization of
energy.
EXERGONIC
A process that releases energy as it goes
forward.
During exergonic reactions, electrons are
pulled out of atoms, thereby releasing their
inherent energy. These electrons are picked up
by special carriers and transferred through a
series of reactions until they reach a final
electron acceptor. As ATP is formed, it is used to
support endergonic reactions such as synthesis.
What is the importance of Cell
Energetics to Microbes?
Cell energetics supplies a
significant amount of energy for
their bodies to function. Microbes
with high cellular energy levels
move faster because their bodies
can efficiently complete various
biological processes, allowing
them to reproduce, move, and
adapt to their surroundings.
Respiration in microbes can occur
either in aerobic or anaerobic
process
There are three main pathways
of respiration namely: glycolysis,
Krebs cycle, and the Electron
Transport Chain (ETC).
Aerobic Respiration:
The breakdown of glucose in
the presence of oxygen to
produce energy. It relies on
molecular oxygen (O2) as the
final acceptor for electrons and
hydrogens, and releases a
relatively large amount of ATP.
Anaerobic Respiration:
The breakdown of glucose in
the absence of oxygen to
produce energy. This system may
involve the same three pathways
as aerobic respiration, but it does
not use molecular oxygen as the
final electron acceptor
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Adenosine Triphosphate (ATP)

The principal carrier of energy in cells is

adenosine triphosphate (ATP). Adenosine
triphosphate (ATP) is an energy-carrying
molecule found in all living creatures' cells.

ATP is a molecule that absorbs chemical

energy from the breakdown of food molecules
and then releases it to power other cellular
operations in the microbes’ body.

ATP has been described as metabolic

currency because it can be earned, spent, and
exchanged.

Redox: Reduction and Oxidation Phosphorylation

Many chemical substances readily The process that regenerates the

donate or receive electrons and
participate in oxidation (the loss of
electrons) or reduction (the gain of
electrons).
The compound that loses the
electrons is oxidized, and the compound
that receives the electrons is reduced.
adenosine tri-phosphate (ATP) from
adenosine di-phosphate (ADP).
For energy to be biologically useful,
it must ultimately be captured through
phosphorylation, a process that adds an
inorganic phosphate Pi to adenosine
diphosphate, converting it to ATP

Na + Cl = Na+Cl-
Na and Cl both Na Oxidized Cl
neutral reduced

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Cellular Respiration

For photosynthetic microbes, cellular respiration occurs through the byproducts of

photosynthesis (sugar and oxygen). Cellular respiration breaks down these by products in
order to produce chemical energy, carbon dioxide, and water. These byproducts will
then be used by photosynthesis for the cycle to continue. In heterotrophic microbes, in
order to have enough sugar and oxygen for cellular respiration to happen, they need to
consume other forms of organism and turn it into energy they can use.

Do you
oxidation can occur in an
organism incapable of

or why not?

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 C. Pathways of Energetics
Bioenergetics is a study of the mechanisms of cellular energy release, including
catabolic and anabolic routes. Although these pathways are interconnected and
interdependent, anabolic pathways are not simply reversals of catabolic ones.
Overview
For most chemoheterotrophs, the
primary catabolism of fuels (such as
glucose) that release energy proceeds
through a series of three coupled
pathways:
1. glycolysis, * also called the Embden-
Meyerhof-Parnas (EMP) pathway
* glycolysis (gly-kol′-ih-sis) Gr. glykys,
sweet, and lysis, to split.
2. the Krebs cycle, also known as the
citric acid or tricarboxylic acid cycle
I. The EMP pathway is named for the
biochemists who first outlined its steps.
Krebs is in honor of Sir Hans Krebs who,
with F. A. Lipmann, delineated this
pathway, an achievement for which
they won the Nobel Prize in Physiology
or Medicine in 1953. TCA refers to the
involvement of several organic acids
containing three carboxylic acid
groups, citric acid being the first
tricarboxylic acid formed.
II. The respiratory chain (electron
transport and oxidative
phosphorylation). Each segment of
the pathway is responsible for a
specific set of actions on various
products of glucose.
Energy Strategies in Microorganisms
As we shall see, aerobic respiration is
a series of reactions (glycolysis, Krebs
cycle, and the respiratory chain) that
converts glucose to CO2, produces H2O,
and generates energy.
It relies on molecular oxygen (O2) as
the final acceptor for electrons and
hydrogens, and releases a relatively large
amount of ATP.
Aerobic respiration is characteristic of
fungi, protozoa, animals, plants, and
many bacteria.
Some facultative and aerotolerant
anaerobes may use only glycolysis or
similar pathways to ferment glucose.
In this case, oxygen is not required,
organic compounds are the final
electron acceptors, and a relatively small
amount of ATP is synthesized.
Some anaerobic microorganisms
metabolize by means of anaerobic
respiration. This system may involve the
same three pathways as aerobic
respiration, but it does not use molecular
oxygen as the final electron acceptor.
Instead, it uses other oxidized ions
such as NO3 −, SO4 2−, or CO2 for the final
electron acceptor.
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Figure 8.16 Side-by-side comparison of the stages, reactions, and major products of pathways for
aerobic respiration, anaerobic respiration, and fermentation. Note that all begin with glycolysis but
vary in use of other pathways, electron acceptors, and ATP yield.

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Aerobic Respiration

As a final electron acceptor. This

pathway is the principal energy-yielding
scheme for aerobic heterotrophs, and it
provides both ATP and metabolic
intermediates for many other pathways in
the cell, including those of protein, lipid,
and carbohydrate synthesis (see figure 2).

Aerobic respiration in microorganisms

can be summarized by this equation:

Glucose (C6H12O6) + 6O2 + 38 ADP + 38Pi

→ 6CO2 + 6H2O + 38 ATP

Aerobic respiration is a series of Figure 2. An amphibolic view of metabolism.

enzyme-controlled reactions that release
the energy stored up in carbohydrates
and lipids during photosynthesis and
make it available to living organisms.
Important concepts concerning its
reactants and products, as follows:
1. The steps in the oxidation of glucose,
2. The involvement of coenzyme carriers
and the final electron acceptor,
3. Where and how ATP originates
4. Where carbon dioxide originates, and
5. Where oxygen is required.
Glucose: The Starting Compound
Carbohydrates such as glucose are
good fuels because these compounds
are readily oxidized. The electrons they
donate can be used in energy transfers.
The end products of the oxidation of
such organic compounds are energy-rich
ATP and energy-poor carbon dioxideand
water.
Intermediate compounds such as pyruvic acid
and acetyl coenzyme A serve multiple
functions. With comparatively small
modifications, these compounds can be
converted into other compounds and enter a
different pathway. Note that catabolism of
glucose (center) furnishes numerous
intermediates for anabolic pathways that
synthesize amino acids, fats, nucleic acids, and
carbohydrates. These building blocks can serve
in further synthesis of larger molecules to
construct a wide array of cell components.
Polysaccharides (starch,
glycogen) and disaccharides (maltose,
sucrose) are stored sources of glucose
also available for the respiratory
pathways.
Although we use glucose as the
main starting compound, other hexoses
(fructose, galactose) and fatty acid
subunits can enter the pathways of
aerobic respiration as well.

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Glycolysis: The Starting Lineup

The process called glycolysis (EMP) is a pathway that converts glucose through
several steps into pyruvic acid. Depending on the organism and the conditions, it may be
only the first phase of respiration, or it may serve as the primary metabolic pathway for
fermentative microbes.

Glycolysis provides a way to synthesize a small amount of ATP, to release

another potential source of energy—NADH, and to generate pyruvic acid, an essential
intermediary metabolite. None of these reactions involve the direct input of oxygen.

Steps in the Glycolytic Pathway 3. Another ATP is spent in

Glycolysis proceeds along nine
linear steps. The first portion of glycolysis
involves activation of glucose, which is
followed by oxidation reactions of the
glucose fragments, the synthesis of ATP,
and the formation of pyruvic acid.
The following outline lists the
principal steps of glycolysis.
1. First, glucose is phosphorylated
at the number six carbon by an
ATP to produce glucose-6-
phosphate. This is a way of
“priming” the system and
preventing the glucose from
being transported out of the cell.
2. Glucose-6-phosphate is
converted to its isomer,
fructose- 6-phosphate.
phosphorylating the first carbon
of fructose-6-phosphate, which
yields a molecule with two
phosphates called fructose-1,6-
diphosphate.
Up to this point, no energy has been
released, no oxidation-reduction has
occurred, and, in fact, 2 ATPs have been
used and the molecules remain in the 6-
carbon state.
4. Fructose-1,6-diphosphate is split
into two 3-carbon fragments:
• glyceraldehyde-3-phosphate
(G-3-P)
• dihydroxyacetone phosphate
(DHAP).
These molecules are isomers, and DHAP is
converted to G-3-P, which is the more
reactive form for the following reactions.

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18
 The effect of the splitting of fructose
diphosphate is to double every
subsequent reaction, because where
there was once a single molecule, there
are now two to be fed into the remainder
of glycolysis and other pathways.
5. Each molecule of glyceraldehyde-3-
phosphate becomes involved in the
single oxidation-reduction reaction of
glycolysis. This sets the scene for ATP
synthesis.
The NAD+ coenzyme complex picks
up hydrogens from G-3-P, forming NADH.
This step is accompanied by the addition
of an inorganic phosphate (PO4 3−) to
form an unstable bond on the third
carbon of the G-3-P substrate. The
product of these reactions is
diphosphoglyceric acid (DPGA).
6. One of the high-energy phosphates of
diphosphoglyceric acid is donated to
ADP via substrate-level phosphorylation
resulting in a molecule of ATP. The other
product of this reaction is 3-
phosphoglyceric acid (3-PGA).
7, 8. During this phase, the 3-
phosphoglyceric acid is converted to 2-
phosphoglyceric acid (2-PGA) through
the shift of a phosphate from the third to
the second carbon.
Then, the removal of a water
molecule from 2-phosphoglyceric acid
converts it to phosphoenolpyruvic acid
(PEPA). The result gives rise to a high-
energy phosphate bond.
9. In the final reaction of glycolysis,
phosphoenolpyruvic acid gives up its
high-energy phosphate to form a second
ATP, again via substrate-level
phosphorylation. This reaction also
produces pyruvic acid (pyruvate), a
compound with many roles in
metabolism.

Pyruvic Acid—A Central Metabolite

Pyruvic acid occupies an

important position in several pathways,
and different organisms handle it in
different ways (figure 4).

In strictly aerobic organisms and

some anaerobes, pyruvic acid is
channeled into the Krebs cycle for
processing and energy release.
Facultative anaerobes can adopt a
fermentative metabolism, in which
pyruvic acid is further reduced into acids
or other products. Figure 4. The fates of pyruvic acid (pyruvate). This metabolite is an
important hub in the processing of nutrients by microbes. It may be
fermented anaerobically to several products or oxidized completely to
CO2 and H2O through the Krebs cycle and the electron transport system.

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The Preparation of Pyruvic Acid for the As we take a single spin around the
Krebs cycle Krebs cycle, it will be helpful to keep track
of
1. the numbers of carbons (#C) of
The oxidation of glucose by
each substrate and product,
glycolysis yields a comparatively small
2. reactions where CO2 is generated,
amount of energy. Pyruvic acid is still
3. reductions of the electron carriers
energy-rich, containing a number of
NAD+ and FAD, and
extractable electrons to power ATP
4. the site of ATP synthesis.
synthesis, and this will be achieved
through the work of the second and third
The eight reactions in the Krebs cycle are:
phases of respiration, during which
pyruvic acid is converted to CO2 and
1. Oxaloacetate (4C) reacts with the
H2O.
acetyl group (2C) on acetyl CoA,
thereby forming citrate (6C) and
In the following section, we examine
releasing coenzyme, making it
the second phase—the Krebs cycle—
which takes place in the mitochondrial immediately available for another
matrix in eukaryotes and in the cytoplasm acetyl group.
of bacteria.
2. Citrate is converted to its isomer,
isocitrate (6C), to prepare this
The Krebs Cycle—A Carbon and
substrate for the decarboxylation and
Energy Wheel redox reaction of the next step.
A cyclic pathway is one in which the
3. Isocitrate is acted upon by an enzyme
starting compound is regenerated at the
complex including NAD+ or NADP
end of the cycle so it will be ready to go
(depending on the organism) in a
around again.
reaction that generates NADH or
NADPH, splits off a carbon dioxide,
The Krebs cycle has eight steps,
and leaves α-ketoglutarate (5C).
beginning with citrate formation and
ending with oxaloacetate (figure 5). The
4. Alpha-ketoglutarate serves as a
2-carbon acetyl groups from coenzyme.
substrate for the final decarboxylation
reaction and yet another redox
A combine with a 4-carbon
reaction, involving coenzyme A and
oxaloacetate molecule to form citrate, a
yielding NADH. The product is the high-
6-carbon molecule. Although this seems
energy compound succinyl CoA (4C).
a cumbersome way to dismantle such a
small molecule, it is necessary in
biological systems for extracting the
remaining energy from the acetyl
fragment.

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Figure 5. The reactions of a single turn of the Krebs cycle. Each glucose will produce two turns of this
pathway. The top portion (a) depicts the conversion of pyruvic acid to acetyl Co enzyme A, a necessary
reaction that sets up the first step of Krebs

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 At this point, the cycle has
completed the formation of 3 CO2
molecules that balance out each original
3-carbon pyruvic acid released by
glycolysis. The remaining steps serve not
only to regenerate the oxaloacetate to
start the cycle again but also to extract
more energy from the intermediate
compounds leading to oxaloacetate.
5. Succinyl CoA is the source of the one
substrate level phosphorylation in the
Krebs cycle. In most bacteria, it
proceeds with the formation of ATP,
although eukaryotes produce
guanosine triphosphate (GTP), an
equivalent source of energy. The other
product at this step is succinate (4C).
6. Succinate undergoes a redox
reaction, but in this case, the electron
and H+ acceptor is flavin adenine
dinucleotide (FAD). The enzyme that
catalyzes this reaction, succinyl
dehydrogenase, is found in the
bacterial cell membrane and
mitochondrial crista of eukaryotic cells.
The Respiratory Chain: Electron
Transport and Oxidative
Phosphorylation
Overall, the electron transport
system (ETS) consists of a chain of special
carriers that receive electrons from
reduced carriers (NADH, FADH2)
generated by glycolysis and the Krebs
cycle.
The ETS shuttles the electrons
through a series of redox transfers. The
flow of electrons down this chain is highly
energetic and ultimately drives the
synthesis of ATP.
The FADH2 generated directly enters
the electron transport system but at a
different carrier site than NADH.
Fumarate (4C) is the product of this
reaction.
7. The addition of H2O to fumarate results
in malate (4C). This is one of the few
reactions in respiration that directly
incorporates a water molecule.
8. Malate is dehydrogenated (with
formation of a final NADH), and
oxaloacetate is formed. This step
brings the cycle back to its original
starting position, where the
oxaloacetate molecule is available to
react with acetyl coenzyme A.
The full Krebs cycle is not present
in all cells, and it may not function under
all metabolic conditions. But even in cells
with alternate metabolic schemes, it is
essential for generating small organic
molecules that microbes require for
synthesis.
The step that finalizes the transport
process is the acceptance of electrons
and hydrogen ions by oxygen, with the
production of water.
The Carriers of Electron Transport: The
Energy Cascade in the Mitochondria
The principal questions about the
electron transport system are these:
• How are the electrons passed from
one carrier to another in the series?
• How is this progression coupled to
ATP synthesis?
• Where and how is oxygen utilized?
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 In general, the carrier compounds
and their associated enzymes are
arranged in linear sequence and are
reduced and oxidized while shuttling the
electrons along to their final acceptor.
The electron carrier complexes
and associated molecules present in
aerobic organisms are as follows:
1. Complex I consist of a huge
multienzyme cluster termed NADH
dehydrogenase (reductase), which
receives the NADH from glycolysis
and the Krebs cycle.
2. Complex II is made up of a series of
iron-sulfur (FeS) proteins that receive
electrons from FADH2 produced in
the sixth step of the Krebs cycle.
3. Coenzyme Q, or ubiquinone, is a
mobile carrier not embedded in the
membrane that can pick up
electrons from both complexes I and
II and donate them to complex III.
4. Complex III is comprised of
cytochromes b and c1, which deliver
electrons to cytochrome c.
5. Cytochrome c is another mobile
carrier that shuttles electrons
between complexes III and IV.
6. Complex IV catalyzes the reaction
between electrons, H+, and oxygen,
yielding H2O and completing the
electron transfer process.
23
Figure 6. Electron transport, oxidative phosphorylation, the proton motive force, chemiosmosis, and ATP
synthesis in the mitochondrion.
Summary of Aerobic Respiration
Now, we estimate the theoretical
total of ATP molecules arising from a
single glucose molecule through a
combination of substrate level
phosphorylation and oxidation of NADH
and FADH2:
• There are 3 substrate-level reactions
that give rise directly to ATP—2 in
glycolysis and 1 in the Krebs cycle.
Because these are happening twice
for each event, they provide 6 ATPs
overall.
• There are 5 NADHs—1 from glycolysis,
1 from pyruvic acid oxidation, and 3
from the Krebs cycle.
Each NADH could potentially power
the synthesis of 3 ATPs, yielding 5 × 3 =
15 ATPs. Again, this happens twice for
each glucose and could potentially
generate 30 ATPs.
• There is a single reaction in the Krebs
cycle that yields FADH2, which can
power synthesis of 2 ATPs, and
multiplied by 2 provides 4 ATPs.
• The theoretical total for ATP synthesis
could be 6 + 30 + 4 = 40; however,
because the first and second
reactions of glycolysis use up 2 ATPs,
the final net number is 38 ATPs.
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25
Fermentation
Some living systems use an organic molecule (commonly pyruvate) as a final
electron acceptor through a process called fermentation. It does not involve an electron
transport system and does not directly produce any additional ATP beyond that
produced during glycolysis by substrate-level phosphorylation. Organisms carrying out
fermentation, called fermenters, produce a maximum of two ATP molecules per glucose
during glycolysis.

Products of Fermentation in Microorganisms

Alcoholic beverages (wine, beer,

whiskey) are perhaps the most prominent
among fermentation products; others are
solvents (acetone, butanol), organic
acids (lactic, acetic), dairy products.

Derivatives of proteins, nucleic acids,

and other organic compounds are
fermented to produce vitamins,
antibiotics, and even hormones such as
hydrocortisone.

Fermentation products can be grouped

into two general categories:
• alcoholic fermentation products and
• acidic fermentation products

Alcoholic fermentation occurs in yeast

or bacterial species that have metabolic
pathways for converting pyruvic acid to
ethanol. This process involves a
decarboxylation of pyruvic acid to
acetaldehyde, followed by a reduction
of the acetaldehyde to ethanol.

In oxidizing the NADH formed during

glycolysis, NAD+ is regenerated, thereby
feeding back to and maintaining the
glycolytic pathway. These processes are
crucial in the production of beer and
wine.

26
 Alcohols other than ethanol can be
produced during bacterial fermentation
pathways. Certain clostridia produce
butanol and isopropanol through a
complex series of reactions.
The pathways of acidic fermentation are
extremely varied.
When glucose is fermented to a
mixture of lactic acid, acetic acid, and
carbon dioxide, as is the case with
Leuconostoc and other species of
Lactobacillus, the process is termed
heterolactic fermentation.

Lactic acid bacteria ferment

pyruvate in the same way that humans
do—by reducing it to lactic acid. If the
product of this fermentation is mainly
lactic acid, as in certain species of
Streptococcus and Lactobacillus, it is
termed homolactic.
The souring of milk is due largely to
the production of this acid by bacteria.

D. PHOTOSYNTHESIS
The ultimate source of most of the On land, green plants are the primary
chemical energy in cells is the sun. photo synthesizers; and in aquatic
Because this source is directly available ecosystems, where 80% to 90% of all
only to the cells of photo synthesizers, photosynthesis occurs, this role is filled by
most organisms on earth are either algae, cyanobacteria, and green sulfur,
directly or indirectly dependent on purple sulfur, and purple nonsulfur
photosynthesis, except for a few bacteria.
chemoautotrophs that derive their
energy and nutrients solely from inorganic The summary equation for the main
substrates. reactants and products of photosynthesis
in aerobic organisms is
The other major products of
photosynthesis are organic carbon
compounds, which are produced from
carbon dioxide through a process called
carbon fixation.

27
 The anatomy of photosynthetic cells
is adapted to trapping sunlight, and their
physiology effectively uses this solar
energy to produce high-energy glucose
from low-energy CO2 and water.

Photosynthetic organisms achieve

this remarkable feat through a series of
reactions involving light, pigment, CO2,
and water, which is used as a source for
electrons.

Photosynthesis proceeds in two phases:

• Light-dependent reactions, which
proceed only in the presence of light
waves, and the
• Light-independent reactions, which
can operate without direct exposure
to light, but are still reliant on the
energy molecules made in the light-
dependent reactions.

Solar energy is delivered in discrete

energy packets called photons (also
called quanta) that travel as waves.
The wavelengths of light operating in
photosynthesis occur in the visible
spectrum between 400 nanometers
(violet) and 700 nanometers (red) and
above.
As this light strikes photosynthetic
pigments, some wavelengths are
absorbed, some pass through, and some
are reflected. The activity that has the
greatest impact on photosynthesis is the
absorbance of light by photosynthetic
pigments.
These include the chlorophylls, which
are green; carotenoids, which are yellow,
orange, or red; and phycobilin, which are
red or blue-green.

28
 By far the most important of these
pigments are the chlorophylls, which
contain a photocenter that consists of a
magnesium atom held in the center of a
complex ringed molecule called a
porphyrin (figure 8.28, part 3).
As we will see, the chlorophyll
molecule harvests the energy of photons
and converts it to electron (chemical)
energy.
Accessory photosynthetic pigments
such as carotenes trap light energy and
Light-Dependent Reactions
The systems that carry the
photosynthetic pigments are also the
sites for the light-dependent reactions.
They occur in the thylakoid membranes
of compartments called grana (singular,
granum) in chloroplasts (figure 8.28, part
1) and in thylakoid layers of the cell
membranes of cyanobacteria.
These systems exist as two separate
complexes called photosystem I (PS700)
and photosystem II (PS680)4 (figure 8.28,
part 4).
Both systems contain chlorophyll, but
their chlorophylls are sensitive to different
wavelengths:
• PS I absorb longer wavelengths
(above 680 nm) and PS II absorbs
shorter wavelengths (680 nm and
below), which efficiently covers the
range of light to which phototrophs
are exposed.
• Both photosystems are stationed in
antennae— clusters of about 300
molecules of chlorophyll located in
the thylakoid membranes.
shuttle it to chlorophyll, thereby
functioning like antennae.
These light-dependent reactions are
responsible for photophosphorylation,
the channeling of energy extracted from
light to make high-energy bonds of ATP.
This sets the scene for the light-
independent reactions, which use both
ATP and NADPH for synthesis. During this
phase, carbon atoms from CO2 are fixed
to the carbon backbones of organic
molecules.
• Antennae absorb light and convey it
to reaction centers, where the light-
dependent reactions take place
(figure 8.28, part 4).
• The chloroplast is composed of
separate compartments similar to
mitochondria.
One compartment—the stroma—is the
region surrounding the grana and
thylakoids, and the other one is the space
inside the thylakoids called the lumen
(figure 8.28, part 4).
Overview of the Light-Dependent
Reactions and Photophosphorylation
Most of these components are
embedded in the thylakoid membranes
and are accessible from both the lumen
and the stroma. They include
• Chlorophyll molecules and their
photosystems (PS II and PS I)5;
• Oxygen evolving complex;
• Electron transport systems—consisting
of a mobile electron carrier
plastoquinone (PQ);
29
• Cytochrome bf complex;
• Plastocyanin (PC), a second mobile
electron carrier;
• Ferredoxin (Fd) with nicotinamide
adenine dinucleotide phosphate
• (NADP+) reductase (FNR);
• ATP synthase.
The light-dependent pathway proceeds
as follows:
PS II Reactions
1. When light strikes the magnesium in PS
II, an electron becomes excited (is
raised to a higher energy level) and is
released by PS II to the first electron
transport system.
2. An oxygen-evolving complex
associated with PS II splits two water
molecules into 4 electrons, 4 protons
(H+), and oxygen. Because it occurs in
the presence of light, this step is
termed photolysis, and it results in the
first major product of the light-
dependent reactions—the O2 gas
required by all aerobic organisms,
including even most photo
synthesizers.
In addition, the electrons released
by photolysis return the PS II complex
to a ground state so it is again ready
to respond to light. Another important
effect of photolysis is the release of
protons into the lumen, which
contributes to the chemiosmotic
proton gradient so essential to ATP
synthesis.
30
Electron Transport
1. An electron given off by PS II is picked
up by the first compound of the
electron transport chain—PQ—which
moves it to the cytochrome bf
complex. From here, it is transported to
plastocyanin and to the PS I complex.
2. An event coupled to electron
transport is the delivery of protons (H+)
from the stroma side to the lumen side
by the actions of the cytochrome bf
complex, which helps maintain the
electrochemical gradient betweenthe
stroma and lumen.
PS I Reactions
1. When PS I is excited by light, it also
releases an electron that will be
transported through a different
series of carriers. In addition, it
picks up the electrons from PS II
delivered by plastocyanin.
2. These electrons are shuttled to the
final electron acceptors—
ferredoxin and the FNR complex.
The function of the FNR is to
transfer 2 electrons (and 2 protons)
to NADP+, converting it to NADPH.
This is the second major
product of the light dependent
reactions, one which provides
reducing power for the light-
independent reactions.
31
ATP Synthase and Photophosphorylation

ATP synthase complexes are distributed throughout the thylakoid membranes. They
have the same structure as those of mitochondria and they, too, capture the free energy
inherent in the proton motive force to synthesize ATP. As protons flow through the F0
portion of the synthase from the lumen to the stroma, the F1 component pulls in ADP and
Pi, releasing ATP, the third major product of the light reactions.

Light-Independent Reactions
The anabolic reactions of photosynthesis occur in the stroma of a chloroplast or the
cytoplasm of cyanobacteria. These reactions use energy produced by the light phase to
synthesize glucose by means of the Calvin cycle (figure 8.29).

The cycle begins at the point where CO2 is combined with a 5-carbon acceptor
molecule with two terminal phosphates called ribulose-1,5-bisphosphate (RuBP). This first
critical step in carbon fixation generates a 6-carbon intermediate compound that
immediately splits into two 3-carbon molecules of 3-phosphoglyceric acid (PGA).

The subsequent steps use ATP and NADPH generated by the photosystems to form
high-energy intermediates.
First, 2 ATPs are expended to add a second phosphate to 3-PGA, producing two
molecules of 1,3-bisphosphoglyceric acid (BPG).

This is followed by NADPH contributing its electrons to BPG with the removal of one
high-energy phosphate. These events give rise to two glyceraldehyde-3-phosphate (G3P).

This molecule and its isomer dihydroxyacetone phosphate (DHAP) are key
compounds in hexose synthesis leading to fructose and glucose. Some of the G3P is
conveyed to the remainder of the cycle, where it participates in the regeneration of RuBP.

32
 Other Mechanisms of Photosynthesis
The oxygenic, or oxygen-releasing, photosynthesis occurs in plants, algae,
and cyanobacteria and is the dominant type on the earth. Other photo
synthesizers such as green and purple sulfur bacteria possess bacteriochlorophyll,
which is more versatile in capturing light. They have only a cyclic photosystem I,
which routes the electrons from the photocenter to the electron carriers and
back to the photosystem again. This pathway generates a relatively small
amount of ATP, and it may not produce NADPH. As photolithotrophs, these
bacteria use H2, H2S, or elemental sulfur rather than H2O as a source of electrons
and reducing power. As a consequence, they are anoxygenic (non-oxygen-
producing), and many are strict anaerobes.

33
 E. ACTIVITIES AND ASSESSMENT

Activity 1
A. Multiple Choice. Encircle the letter of the correct answer.

1. What is the sum of all biochemical activities in the cell?

a. Chemical Synthesis c. Glycolysis
b. Metabolism d. Cellular Respiration

2. What is the biological catalyst that drives metabolism?

a. Adenosine triphosphate (ATP) c. Lipids
b. Carbohydrates d. Enzymes

3. The three pathways of respiration are:

a. Glycolysis, Krebs Cycle, and Electron Transport Chain
b. Glycolysis, Fermentation, Krebs Cycle
c. Krebs Cycle, Fermentation, Electron Transport Chain
d. Krebs Cycle, Glycolysis, Fermentation

4. Krebs Cycle is also known as.

a. Embden-Meyerhof-Parnas (EMP) pathway
b. Tricarboxylic Acid Cycle
c. Citrus Cycle
d. Pyruvate Cycle

5. Glycolysis is also known as.

a. Embden-Meyerhof-Parnas (EMP) pathway

b. Tricarboxylic Acid Cycle
c. Citrus Cycle
d. Pyruvate Cycle

6. What is the process that produces pyruvate and lactate as a product?

a. Fermentation c. Glycolysis
b. Electron Transport Chain d. Krebs Cycle

34
7. What are the two types of Metabolism?
a. Metabolic and Catabolic c. Aerobic and Anaerobic
b. Catabolic and Aerobic d. Catabolic and Anabolic

8. Is another term for biosynthesis.

a. Catabolism c. Metabolism
b. Anabolism d. Catalyst

9. Catabolism is a form of metabolism in which molecules are transformed into

molecules.
a. larger, smaller c. amino acid, protein
b. smaller, larger d. glucose, starch

10. An enzyme the activation energy required for a chemical reaction.

a. increases c. lowers
b. converts d. catalyzes

11. An enzyme
a. becomes part of the final products
b. is nonspecific for substrate
c. is consumed by the reaction
d. is heat and pH labile

12. An apoenzyme is where the is located.

a. cofactor c. redox reaction
b. coenzyme d. active site

13. Many coenzymes contain

a. metals c. proteins
b. vitamins d. substrates

14. To digest cellulose in its environment, a fungus produces a/an

a. endoenzyme c. catalase
b. exoenzyme d. polymerase

15. Energy in biological systems is primarily

a. electrical c. radiant
b. chemical d. mechanical

35
 B. Multiple Matching. Match the process a, b, or c with the metabolic events in the
list.

A. glycolysis
B. Krebs cycle
C. electron transport/oxidative phosphorylation

H+ and e− are delivered to O2 as the final acceptor.

Pyruvic acid is formed.
ATP is formed.
H2O is produced.
CO2 is formed.
Fructose diphosphate is split into two 3-carbon fragments.
NADH is oxidized.
ATP synthase is active.

C. Label and discuss. How does Krebs cycle works? Label and discuss comprehensively the
whole process of Krebs cycle. (20 pts.)

36
 Activity 2 Cellular Respiration and Photosynthesis

Directions: Venn Diagram. On a poster create a Venn diagram comparing photosynthesis and
cellular respiration. All of the words and phrases listed below should be included in your
diagram. Utilize notes, bell work, class work and text books to complete your work.

37
Activity 3. Copy and fill in the blanks with the correct words using the terms
listed below.

All organisms use to carry out their life functions. Some organisms
obtain this energy from . The process by which this energy transfer takes place is called
. Photosynthesis involves a pathway in which the of
one reaction is(are) consumed in the reaction. are organisms that carry
on photosynthesis and includes and other organisms containing the
pigment . Autotrophs use and water to make and the simple
sugar . The pigment chlorophyll absorbs _ energy from the sun during the
light . pigments also in the absorb other of light that
chlorophyll does not absorb. These accessory are responsible for other colors we
see in plants such as , orange, and . Chloroplasts are surrounded by a
membrane. Inside chloroplasts is a system of membranes arranged as stacks of
sacs called . Each sac in the stack is called a . The thylakoids are
surrounded by a solution called the . The reactions of photosynthesis takeplace
in the stroma. Most chloroplasts are found in the of plants. The of a
leaf contains openings called where such as oxygen and carbon dioxide
enter and leave. These openings or stomata are during the hottest times of the day
by cells called cells.

38
 Word Bank:
sunlight autotrophs carbon dioxide
biochemical chlorophyll light
photosynthesis next wavelengths
energy plants glucose
Yellow accessory stroma
plastids pigments reactions
Leaves oxygen dark
stomata underside gases
closed red thylakoids
flattened guard double
product granum green

Activity 4.
Find and download a copy of the article entitled “Sludge
reduction based on microbial metabolism for sustainable
wastewater treatment” by Jin-Song Guo, et al. Make an insight
paper/reflection paper about the article. The same rubric from
previous readings will be used in grading the insight paper.

Link below:
Sci-Hub | Sludge reduction based on microbial metabolism for sustainable wastewater
treatment. Bioresource Technology, 122506 | 10.1016/j.biortech.2019.122506

39
 References

Britannica. (2021). Adenosine Triphosphate. Retrieved from: https://www.britannica.

com/science/adenosine-triphosphate

Britannica. (2021). Fermentation. Retrieved from: https://www.britannica.com/science/

fermentation

Healthline. (2021). Catabolism vs. Anabolism: What’s the Difference? Retrieved from:
https:// www.healthline.com/health/fitness-exercise/hip-flexor-exercises
#stretches

Helmenstine, A.M. (2020). Anabolism and Catabolism Definition and Examples. Retrieved
from: https://www.thoughtco.com/anabolism-catabolism-definition-
examples-4178390

Jurtshuk, P. (n.d.). Medical Microbiology. 4th edition. Retrieved from: https://www.ncbi.

nlm.nih.gov/books/NBK7919/

Kumari, A. (2018). Glycolysis. Retrieved from: https://www.sciencedirect.com/topics/

neuroscience/glycolysis

Location & Importance (n.d). Retrieved from: https://sciencing.com/electron-transport-

chain-etc-definition-location-importance-13717928.html

MitoQ. (2021). The Importance of Cellular Energy7. Retrieved from: https://www.mitoq.

com/blog/blog/the-importance-of-cellular-energy

Science Clarified. (2021). Metabolism. Retrieved from: http://www.scienceclarified.com

/Ma-Mu/Metabolism.html

Study.com. (2021). Process of Cellular Respiration in Bacteria. Retrieved from: https://study.

com/academy/lesson/process-of-cellular-respiration-in-bacteria.html

40