Lectures 1-2

MCB 310: Microbial Physiology and

Metabolism
Dr. Rashed Noor
Microbiology
School of Life Sciences (SLS)
Independent University, Bangladesh (IUB)

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REFERENCE

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 INTENDED LEARNING OUTCOME (ILO)

Students will understand the principal reactions of the energy

and biosynthetic metabolism in Escherichia coli (the model
organism).
They will be briefed on the diversity of aerobic metabolism.
The regulation of the level and the activity of enzymes in
bacteria will be taught.
The characteristic features of fermentative, chemolithotrophic
and phototrophic metabolism will be discussed.
Throughout the lectures, the metabolic pathways and enzyme
reactions will be described to elucidate the physiology
of the microorganisms required to conduct the metabolic
reactions.

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 LEARNING OBJECTIVES

Nutrition of Bacteria
I. Major and Minor Bioelements
II. The Two Basic Mechanisms of ATP Synthesis
III. Nutrients as Energy Sources
IV. Growth Factor Requirements of Bacteria

How Escherichia coli Synthesizes ATP during Aerobic Growth on

Glucose
I. Transport of D-Glucose into the E. coli Cell
II. Degradation of Glucose-6-Phosphate to Pyruvate via the
Embden-Meyerhof-Parnas (EMP) Pathway
III. Oxidative Decarboxylation of Pyruvate to Acetyl-Coenzyme A
IV. Oxidation of Acetyl-CoA via the Tricarboxylic Acid Cycle
V. The Formation of ATP in the Respiratory Chain

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Biosynthesis of Escherichia coli Cells from Glucose
I. Composition of E. coli Cells
II. Assimilation of Ammonia
Ill. Assimilatory Reduction of Sulfate
IV. Biosynthesis of Amino Acids
V. How Pentose Phosphates and NADPH are Formed
VI. Ribonucleotides and Deoxyribonucleotides
VII. Biosynthesis of Lipids
VIII. Formation of Carbohydrates
IX. Synthesis of Polymers
X. The Requirement for an Anaplerotic Sequence

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Aerobic Growth of Escherichia coli on Substrates Other
Than Glucose
I. Fructose and Lactose as Substrates
II. Pentoses as Substrates
Ill. Acetate, Pyruvate, and L-Malate as Substrates

Metabolic Diversity of Aerobic Heterotrophs

I. The Different Mechanisms for the Uptake of
Substrates
II. The Entner-Doudoroff Pathway
III. Sugar Degradation via the Pentose Phosphate Cycle
IV. The Methylglyoxal Bypass
V. Diversity in Energy Metabolism
VI. Dissimilatory Reduction of Nitrate
VII. Bacterial Bioluminescence
VIII. Alternate Anaplerotic Sequences
IX. Biosynthesis of Monomers and Polymers
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Catabolic Activities of Aerobic Heterotrophs
I. Degradation of Polymers by Exoenzymes
II. Growth with Amino Acids
Ill. Growth with Organic Acids
IV. Growth with Aliphatic Hydrocarbons
V. Growth with Aromatic Compounds
VI. Growth with C, Compounds
VII. Incomplete Oxidations
VIII. Plasmid-Encoded Catabolic Activities

Regulation of Bacterial Metabolism

I. Regulation of Enzyme Synthesis by Induction and Repression
II. Regulation of Enzyme Activity

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Bacterial Fermentations
I. Alcohol Fermentation
II. Lactate Fermentation
Ill. Butyrate and Butanol-Acetone
Fermentation
IV. Mixed Acici and Butanediol Fermentation
V. Propionate and Succinate Fermentation
VI. Acetate Fermentation
VII. Methane Fermentation
VIII. Sulfide Fermentation (Desulfurication)
IX. The Anaerobic Food Chain
X. Fermentation of Nitrogenous Compounds

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Chemolithotrophic and Phototrophic Metabolism
I. Chemolithotrophic Metabolism
II. Assimilation of CO,
Ill. Phototrophic Metabolism

Fixation of Molecular Nitrogen

I. Nitrogen-fixing Organisms
II. Biochemistry of Nitrogen Fixation
III. Regulation of Nitrogenase

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Assessment &
Marks Distribution Grading & Point System

Marks Grades Grade points

Evaluation Percent
90-100 A (4.0)
Criteria
85-89 A- (3.7)
Class test 20% 80-84 B+ (3.3)
75-79 B (3.0)
Assignment 10%
70-74 B- (2.7)
Mid term 30% 65-69 C+ (2.3)
Final exam 40% 60-64 C (2.0)
55-59 C- (1.7)
Total 100% 50-54 D+ (1.3)
45-49 D (1.0)
<45 F (0.7)
Lectures 1-2

Topic 1
Nutrition of Bacteria
I. Major and Minor Bioelements
II. The Two Basic Mechanisms of ATP Synthesis
III. Nutrients as Energy Sources
IV. Growth Factor Requirements of Bacteria

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Why do the bacteria need nutrients?

What are the basic functions of nutrients?

What are the energy conversion forms?

What types of energy?

How do the bacteria utilize those energy?

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Bacteria, like all other living organisms, require certain
nutrients for growth. These nutrients must contain
those chemical elements that are constituents of the
cellular materials and that are necessary for the activity
of enzyme and transport systems. In addition, the
nutrients must provide the organisms with materials for
the production of biologically utilizable energy.

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Only a small number of the elements of the periodic system are
required by organisms in relatively high concentrations (> 10-4 M).
These 12 major bioelements and some of their functions
are presented in the following Table:

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…………………Table continued: 12 major bioelements

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Minor bioelements

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 ATP

The principal carrier of biologically utilizable energy is adenosine-5‘

triphosphate (ATP), and all energy-requiring processes in living
cells are directly or indirectly coupled to the conversion of ATP to
adenosine-5 'diphosphate (ADP) and inorganic phosphate (Pi):

ATP contains two phosphate bonds

with a high free energy of hydrolysis.
These bonds are often symbolized by
the squiggle "-":

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What does ATP do?

Because of the high-energy phosphoryl bonds, ATP is an excellent

phosphorylating agent, and it is used as such in a large number of
reactions by all organisms.

At the expense of ATP, intermediates of cell metabolism

are activated for further reactions, such as condensations,
reductions, and cleavages.

Glutamine, for instance, can be synthesized from glutamate and

ammonia only if a phosphorylated intermediate is formed. The
reaction is, therefore, connected with the formation of ADP and
Pi from ATP:

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The high potential of group transfer of the AMP and the ADP
group is also taken advantage of in a number of reactions; amino
acids are activated by their conversion into the corresponding
AMP derivatives with ATP, and AMP is released in the formation
of aminoacyl-transfer RNA:

The enzyme adenylate kinase catalyzes the phosphorylation

of AMP to ADP with ATP; pyrophosphate (PPj ) is hydrolyzed
to inorganic phosphate by pyrophosphatase so that the end
products of this reaction series are also ADP and Pi:

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 ADP and Pi are thus the principal products of the
energy expenditure in metabolism, and the
generation of ATP from ADP and Pi is a vital process
of all living organisms.

The Two Basic Mechanisms of

ATP Synthesis

There are two basic mechanisms of ATP generation:

electron transport phosphorylation and
substrate-level phosphorylation.

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Electron Transport Phosphorylation
Electron transport phosphorylation refers to a mechanism
in which the flow of electrons from donors with a negative
redox potential to acceptors with a more positive redox
potential is coupled to the synthesis of ATP from ADP and
Pi.

Systems in which electron transport phosphorylation

occurs are the respiratory chains and the photosynthetic
apparatus, they are principally membrane-bound.

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Substrate level Phosphorylation
Substrate-level phosphorylation is the second mechanism of
ATP generation.
During the degradation of organic substrates a small number of
intermediates is formed containing high-energy phosphoryl
bonds. Intermediates of this kind are:

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The further metabolism of such organic - P compounds
is coupled to the transfer of the phosphate group to
ADP, and this kind of ATP synthesis is called substrate-
level phosphorylation:

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 Nutrients as ENERGY SOURCES

The function of the nutrients is not only to provide

the organisms with the bioelements; nutrients are
also required as energy sources-as fuel for the
production of ATP.

Various energy sources are available in nature and

are taken advantage of by microorganisms, but
they cannot be used by every bacterium, and it
has become useful to group bacteria on the basis
of their characteristic energy source.

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Organisms using light as energy source are called phototrophs
(Greek phos = light, trophe = nutrition). If ATP comes from
chemical reactions, the organisms that carry out this type of
energy metabolism are called chemotrophs.

Phototrophy
Phototrophs contain a photosynthetic apparatus that enables
them to convert light energy into the high-energy phosphate
bonds of ATP:

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TWO TYPES OF PHOTOTROPHIC METABOLISM

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 Chemotrophy
Most bacteria gain ATP by chemical reactions. These are
commonly oxidation-reduction reactions, which means
that one substrate is reduced at the expense of a second
one:

Higher organisms can only use organic substrates as electron

donors (Xred) and oxygen as electron acceptor (Aox) and it is a
specialty of the bacterial energy metabolism that, alternatively,
other donors and acceptors can be employed.

Here, Aox may stand for oxygen, nitrate, sulfate, CO2 , or an

organic compound, and Xred for an inorganic or an organic
compound.
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By analogy to the nutritional classification of the
phototrophs, bacteria that employ an organic compound as
electron donor are called chemoorganotrophs.

This group includes aerobes and anaerobes. The anaerobes

use either nitrate, sulfate, or organic substrates as electron
acceptors.

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TWO TYPES OF CHEMOTROPHIC METABOLISM

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Clearly, chemolithotrophs gain ATP without metabolizing an organic
compound. Their carbon source is usually CO2, and they are, therefore, C-
autotrophs.
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However, many chemolithotrophs are not restricted to this
kind of energy metabolism:
Hydrogen-oxidizing bacteria, for instance, can
grow as chemoorganotrophs (aerobically with carbohydrates
or organic acids) under appropriate conditions. They are,
therefore, called facultative chemolithotrophs (all hydrogen-
oxidizing bacteria, some thiobacilli).

Species (Nitrosomonas, Thiobacillus thiooxidans) , which are

unable to grow in the absence of their inorganic electron
donors, are called obligate chemolithotrophs.

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 Growth Factors requirements of bacteria
However, a number of bacteria lack the ability to synthesize
all the organic compounds needed for growth and depend on
certain growth factors. These factors can be combined to form
three groups:
1. vitamins and related compounds, required in small amounts
2. amino acids
3. purines and pyrimidines

Number and kind of growth factors, which must be present in

the growth medium, differ among bacteria.
Lactic acid bacteria require practically all amino acids, purines,
pyrimidines, and vitamins for growth. Their biosynthetic
capacity is rather limited.
Common among microorganisms are requirements for
vitamins and related compounds.
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SUMMARY

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