Unit 2 Handouts BSc106

2/16/2021
BSci106:
MICROBIOLOGY and
PARASITOLOGY
UNIT 2
Chapter 6 and 7
Microbial Physiology and Genetics
Copyright © 2015 Wolters Kluwer • All Rights Reserved
Chapter 6 Outline
• Microbial Physiology • Metabolism

– Introduction – Catabolism
– Microbial Nutritional – Anabolism
Requirements
• Bacterial Genetics
– Categorizing
Microorganisms – Mutations
According to Their
Energy and Carbon – Ways in Which
Sources Bacteria Acquire New
Genetic Information
• Metabolic Enzymes
• Genetic Engineering
– Biologic Catalysts
• Gene Therapy
– Factors That Affect the
Efficiency of Enzymes
Microbial Physiology
Introduction
• Physiology is the study of the vital life processes of

organisms.
– Microbial physiology concerns the vital life
processes of microorganisms.
• Scientists can learn about human cells by studying
the nutritional needs of bacteria, their metabolic
pathways, and why they live, grow, multiply, or die
under certain conditions.
• Bacteria, fungi, and viruses are used extensively in
genetic studies because they produce generation after
generation so rapidly.
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Microbial Nutritional Requirements
• All living protoplasm contains six major chemical

elements: carbon, hydrogen, oxygen, nitrogen,
phosphorus, and sulfur.
– Combinations of these and other elements make
up vital macromolecules of life, including
carbohydrates, lipids, proteins, and nucleic acids.
• Materials that organisms are unable to synthesize,
but are required for building macromolecules and
sustaining life, are termed essential nutrients (e.g.,
certain essential amino acids and essential fatty
acids).
Categorizing Microorganisms According to
Their Energy and Carbon Sources
• Terms relating to an organism’s energy source:

– Phototrophs use light as an energy source.
– Chemotrophs use either inorganic or organic
chemicals as an energy source.
•Chemolithotrophs use inorganic chemicals as
an energy source.
•Chemoorganotrophs use organic chemicals
as an energy source.
Their Energy and Carbon Sources (cont.)
• Terms relating to an organism’s carbon source:
– Autotrophs use carbon dioxide (CO2) as their sole source
of carbon.
– Heterotrophs use organic compounds other than CO2 as
carbon sources.
• Terms that combine both energy and carbon source:
– Photoautotrophs use light as an energy source and CO2
as a carbon source.
– Photoheterotrophs use light as an energy source and
organic compounds other than CO2 as a carbon source.
– Chemoautotrophs use chemicals as an energy source and
CO2 as a carbon source.
– Chemoheterotrophs use chemicals as an energy source
and organic compounds other than CO2 as a carbon
source.
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Their Energy and Carbon Sources (cont.)
• Ecology is the study of the interactions between

living organisms and the world around them.
• Ecosystem refers to the interactions between living
organisms and their nonliving environment.
• Interrelationships among the different nutritional
types are of prime importance in the functioning of
the ecosystem.
– Example: Phototrophs, such as algae and
plants, are the producers of food and oxygen for
chemoheterotrophs, such as animals.
Decomposition of a Fallen Tree
Metabolic Enzymes
• Metabolism refers to all of the chemical reactions

that occur in a cell. The chemical reactions are
referred to as metabolic reactions.
– Metabolic reactions are enhanced and regulated
by enzymes known as metabolic enzymes.
• Biologic Catalysts
– Enzymes are biologic catalysts; they are
proteins that either cause a particular chemical
reaction to occur or accelerate it.
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Metabolic Enzymes
Biologic Catalysts (cont.)
• Enzymes are specific, in that they catalyze only one

particular chemical reaction.
• A particular enzyme can exert its effect on only one
particular substance, known as the substrate for that
enzyme.
• The unique three-dimensional shape of an enzyme
enables it to fit the combining site of the substrate
like a key fits into a lock.
• An enzyme does not become altered during the
chemical reaction it catalyzes. (They don’t last
forever, however!)
Action of a Specific Enzyme (E1)

Breaking Down a Substrate (S1) Molecule
Metabolic Enzymes
Biologic Catalysts (cont.)
• Endoenzymes are enzymes produced within a cell

that remain within the cell to catalyze reactions.
– Example: digestive enzymes within phagocytes
• Exoenzymes are produced within a cell and then
released outside of the cell to catalyze extracellular
reactions.
– Examples: cellulase and pectinase, which are
secreted by saprophytic fungi to break down
cellulose and pectin, respectively
• Hydrolases and polymerases are examples of
metabolic enzymes.
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Metabolic Enzymes
Factors That Affect the Efficiency of Enzymes
• Many factors can affect the efficiency or effectiveness of

enzymes; for example, each enzyme has an optimum pH and
optimum temperature range at which it functions at peak
efficiency.
– Optimum pH range⎯efficiency can be adversely affected
if too acidic or too alkaline.
– Optimum temperature range⎯efficiency can be affected
if too hot or too cool.
– Optimum concentration of enzyme and/or substrate –
concentration might be too high or too low.
– Presence of inhibitors (e.g., heavy metals such as lead,
zinc, mercury, and arsenic) can affect efficiency.
Metabolism
• As previously stated, metabolism refers to all of the

chemical reactions within a cell. These reactions
known as metabolic reactions.
– A metabolite is any molecule that is a nutrient, an
intermediary product, or an end product in a
metabolic reaction.
• Metabolic reactions fall into two categories:
catabolism and anabolism.
– Catabolism refers to all catabolic reactions in a
cell.
– Anabolism refers to all anabolic reactions in a cell.
Metabolism (cont.)
• Catabolic reactions involve the breaking down of

larger molecules into smaller ones.
– Whenever chemical bonds are broken, energy is
released. Catabolic reactions are a cell’s major
source of energy.
• Anabolic reactions involve the assembly of smaller
molecules into larger molecules, requiring the
formation of bonds. Once formed, the bonds
represent stored energy.
• Much of the energy released during catabolic
reactions is used to drive anabolic reactions.
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Anabolic and Catabolic Reactions
Differences between
Catabolism and Anabolism
Metabolism (cont.)
• Energy can be temporarily stored in high-energy bonds in

special molecules, usually adenosine triphosphate (ATP).
– ATP molecules are the major energy-storing or
energy-carrying molecules in a cell.
• ATP molecules are found in all cells because they are
used to transfer energy from energy-yielding molecules,
such as glucose, to energy-requiring reactions.
• When ATP is used as an energy source, it is hydrolyzed
to adenosine diphosphate (ADP).
• If necessary, ADP can be used as an energy source by
hydrolysis to adenosine monophosphate (AMP).
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Metabolism (cont.)
• Energy is required not only for metabolic pathways

but also for growth, reproduction, sporulation, and
movement of the organism, as well as active
transport of substances across membranes.
• Some organisms (e.g., marine dinoflagellates) use
energy for bioluminescence.
• Cellular mechanisms that release small amounts of
energy as the cell needs it usually involve a
sequence of catabolic and anabolic reactions.
Metabolism
Catabolism
• Catabolic reactions release energy (by breaking bonds)

and are a cell’s major source of energy.
– Some energy is lost as heat in catabolic reactions.
• Biochemical pathways are a series of linked biochemical
reactions occurring in a stepwise manner, from a
starting material to an end product.
• Think of nutrients as energy sources for organisms and
think of chemical bonds as stored energy.
• Glucose, for example, can be catabolized by one of two
common biochemical pathways: aerobic respiration and
fermentation.
A Biochemical Pathway with Four Steps
Compound A is ultimately converted to compound E. Four

enzymes are required in this biochemical pathway. Compound
A is the substrate for Enzyme 1, Compound B for Enzyme 2,
etc.
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Metabolism
Catabolism (cont.)
• Catabolism of glucose by aerobic respiration occurs

in three phases (each is a biochemical pathway):
– Glycolysis
– The Krebs cycle
– The electron transport chain
• The first phase (glycolysis) is actually anaerobic, but
the other two phases are aerobic.
• Glycolysis (also called the glycolytic pathway, the
Embden–Meyerhof pathway and the Meyerhof–
Parnas pathway) is a nine-step biochemical pathway.
Each step requires a specific enzyme.
Number of ATP Molecules Produced from

One Molecule of Glucose by Aerobic
Respiration
32
36
aVariesdepending on the number of NADH molecules

produced during glycolysis that enter the mitochondria.
Anabolism
• Anabolic reactions require energy because chemical

bonds are being formed. The energy that is required
comes from catabolic reactions, which are occurring
simultaneously.
• Anabolic reactions are also called biosynthetic reactions.
• Biosynthesis of organic compounds requires energy. The
energy may be obtained through photosynthesis (from
light) or chemosynthesis (from chemicals).
– Photosynthetic reactions trap the radiant energy of
light and convert it into chemical bond energy in
ATP and carbohydrates (e.g., glucose).
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Bacterial Genetics
• Genetics is the study of heredity.

• An organism’s genotype (or genome) is its complete
collection of genes.
• An organism’s phenotype refers to its physical traits
(e.g., hair and eye color in humans).
• An organism’s phenotype is the manifestation of that
organism’s genotype.
• Genes direct all functions of the cell.
• A particular segment of the chromosome constitutes a
gene.
Bacterial Genetics
Mutations
• A change in a DNA molecule (genetic alteration) that is

transmissible to offspring is called a mutation.
– There are three categories of mutations:
• Beneficial mutations
• Harmful mutations (some are lethal mutations)
• Silent mutations
• Mutation rate (the rate at which mutations occur) can
be increased by exposing cells to physical or chemical
agents called mutagens.
• The organism containing the mutation is called a
mutant.
Bacterial Genetics
Ways in Which Bacteria Acquire
New Genetic Information
• Ways in which bacteria acquire new genetic information
(i.e., acquire new genes):
– Lysogenic conversion
– Transduction
– Transformation
– Conjugation
• An extrachromosomal DNA molecule is called a
plasmid. An organism that acquires a plasmid acquires
new genes.
• A plasmid that can either exist by itself or integrate into
the chromosome is called an episome.
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Plasmids
(A) A disrupted Escherichia coli cell, in which the DNA

has spilled out. A plasmid can be seen slightly to the left
of top center (arrow). (B) Enlargement of a plasmid.
Bacterial Genetics
Ways in Which Bacteria Acquire New Genetic
Information (cont.)
• Lysogenic conversion
– Temperate phages (or lysogenic phages) inject their
DNA into a bacterial cell.
– The phage DNA integrates into the bacterial chromosome
but does not cause the lytic cycle to occur. This is known
as lysogeny.
– A phage is called a prophage when all that remains of it
is its DNA.
– The bacterial cell containing the prophage is referred to
as a lysogenic cell.
– The bacterial cell exhibits new properties, directed by the
viral genes. This is referred to as lysogenic conversion.
Bacterial Genetics
Information, cont.
• Transduction (“to carry across”):
– This involves bacteriophages.
– In transduction, bacterial genetic material is
“carried across” from one bacterial cell to another
by a bacterial virus; thus, in transduction, bacteria
acquire new bacterial genes.
– Note how this differs from lysogenic conversion,
wherein bacteria acquire new genetic information
in the form of viral genes.
– Only small amounts of genetic material are
transferred by transduction.
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Generalized
Transduction
Bacterial Genetics
Information (cont.)
• Transformation
– A bacterial cell becomes genetically transformed
following the uptake of DNA fragments (“naked
DNA”) from its environment.
– The ability to absorb naked DNA into the cell is
called competence and bacteria capable of
absorbing naked DNA are said to be competent
bacteria.
– Transformation is probably not widespread in
nature.
Transformation
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Bacterial Genetics
Information (cont.)
• Conjugation
– This involves a specialized type of pilus called a sex
pilus.
– A bacterial cell with a sex pilus (called the donor cell)
attaches by means of the sex pilus to another bacterial
cell (called the recipient cell).
– Some genetic material (usually a plasmid) is transferred
from the donor cell to the recipient cell through a
conjugative pore.
– A plasmid that contains multiple genes for antibiotic
resistance is known as a resistance factor or R-factor. A
bacterial cell that receives an R-factor becomes a
“superbug.”
Conjugation
Conjugation in E. coli
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Genetic Engineering
• Genetic engineering or recombinant DNA technology

involves techniques to transfer eukaryotic genes
(particularly human genes) into easily cultured cells to
manufacture important gene products (mostly proteins).
• Plasmids are frequently used as vehicles for inserting
genes into cells.
• There are many industrial and medical benefits from
genetic engineering.
– Examples: synthesis of antibodies, antibiotics, drugs,
and vaccines, as well as synthesis of important
enzymes and hormones for treatment of diseases.
Recombinant
DNA
Technology
and Genetic
Engineering
Gene Therapy
• Gene therapy of human diseases involves the

insertion of a normal gene into cells to correct a
specific genetic disorder caused by a defective gene.
• Viral delivery is the most common method for
inserting genes into cells; specific viruses are
selected to target the DNA of specific cells.
• Genes may someday be regularly prescribed as
“drugs” in the treatment of diseases (e.g.,
autoimmune diseases, sickle cell anemia, cancer,
cystic fibrosis, heart disease, etc.)
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END OF UNIT 2
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2/16/2021

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Microbial Physiology • Metabolism

• Physiology is the study of the vital life processes of

• All living protoplasm contains six major chemical

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Terms relating to an organism’s energy source:

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Ecology is the study of the interactions between

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Decomposition of a Fallen Tree

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Metabolism refers to all of the chemical reactions

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Enzymes are specific, in that they catalyze only one

Action of a Specific Enzyme (E1)

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Endoenzymes are enzymes produced within a cell

• Many factors can affect the efficiency or effectiveness of

• As previously stated, metabolism refers to all of the

• Catabolic reactions involve the breaking down of

Anabolic and Catabolic Reactions

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Energy can be temporarily stored in high-energy bonds in

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Energy is required not only for metabolic pathways

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Catabolic reactions release energy (by breaking bonds)

A Biochemical Pathway with Four Steps

Compound A is ultimately converted to compound E. Four

• Catabolism of glucose by aerobic respiration occurs

Number of ATP Molecules Produced from

aVariesdepending on the number of NADH molecules

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Anabolic reactions require energy because chemical

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Genetics is the study of heredity.

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• A change in a DNA molecule (genetic alteration) that is

(A) A disrupted Escherichia coli cell, in which the DNA

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Genetic engineering or recombinant DNA technology

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

• Gene therapy of human diseases involves the

Copyright © 2015 Wolters Kluwer • All Rights Reserved

Copyright © 2015 Wolters Kluwer • All Rights Reserved

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