Chapter 7.

Microbial Physiology and

Genetics
 Chapter 7 Outline
• Microbial Physiology • Metabolism
– Introduction – Catabolism
– Microbial Nutritional – Anabolism
Requirements
• Bacterial Genetics
– Categorizing
Microorganisms – Mutations
According to Their
Energy and Carbon – Ways in Which Bacteria
Sources 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.
 Microbial Physiology
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).
 Microbial Physiology
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.
Microbial Physiology
Categorizing Microorganisms According
to Their Energy and Carbon Sources
(cont.)
• Terms relating to use
– Autotrophs an organism’s carbon
carbon dioxide (COsource:
2) 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.
Microbial Physiology
Categorizing Microorganisms According
to 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.
 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.
 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.
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).
Interrelationships between ATP, ADP, and
AMP Molecules
 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.
 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.
Glycolysis (First Step in the Aerobic
Respiration of Glucose)
 Catabolism
Aerobic Respiration of Glucose (cont.)
• The Krebs cycle (also known as the citric acid cycle, the
tricarboxylic acid cycle, and the TCA cycle):
– A biochemical pathway consisting of eight separate
reactions, each controlled by a different enzyme.
– Only two ATP molecules are produced, but a number
of products (e.g., NADH, H+, FADH2) are formed,
which enter the electron transport chain.
• In eukaryotes, the TCA cycle and the electron transport
chain occur in mitochondria.
• In prokaryotes, both occur at the inner surface of the cell
membrane.
The Krebs Cycle
 Catabolism
Aerobic Respiration of Glucose (cont.)
• The electron transport chain (also referred to as the
• electron transport system or respiratory chain):
– A series of oxidation–reduction reactions,
whereby energy is released as electrons which
are transferred from one compound to another.
– Many enzymes are involved in the electron
transport chain, including cytochrome oxidase,
which transfers electrons to oxygen (the final
acceptor).
– A large number of ATP molecules are produced
by oxidative phosphorylation.
• Aerobic respiration is very efficient!
Number of ATP Molecules Produced from
One Molecule of Glucose by Aerobic
Respiration

aVaries depending on the number of NADH molecules

produced during glycolysis that enter the mitochondria.
 Catabolism
Fermentation of Glucose

• Fermentation reactions do not involve oxygen. They take place in

anaerobic environments. There are many industrial applications of
fermentation reactions.
– First step is glycolysis (anaerobic).
– The next step is conversion of pyruvic acid into
an end product. The end product varies from
one organism to another. For example, yeasts
are used to make wine and beer; the end
product is ethanol.
– Fermentation reactions produce very little
energy (~2 ATP molecules).
 Catabolism
Oxidation–Reduction (Redox) Reactions

• Oxidation–reduction reactions are paired reactions in

which electrons are transferred from one compound to
another.
• Oxidation occurs whenever an atom, ion, or molecule loses one
or more electrons in a reaction, in which case, the molecule is
said to be oxidized.
• The gain of one or more electrons by a molecule is called
• reduction, and the molecule is said to be reduced.
• Within a cell, an oxidation reaction is always paired with a
reduction reaction, hence the term oxidation–reduction reaction.
 Catabolism
Oxidation–Reduction (Redox) Reactions (cont.)
• In a redox reaction, the
electron donor (compound A)
is the reducing agent, and
the electron acceptor
(compound B) is the
oxidizing agent.
• Many biologic oxidations are
referred to as
dehydrogenation reactions
because hydrogen ions, as
well as electrons, are
removed.
 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).
 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.
 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
Ways in Which Bacteria Acquire New
Genetic 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.
Generalized
Transduction
Bacterial Genetics
Ways in Which Bacteria Acquire New
Genetic 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
Bacterial Genetics
Ways in Which Bacteria Acquire New
Genetic 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
 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.)