Burton's Microbiology
for the Health Sciences
Chapter 7.
Microbial Physiology and Genetics
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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
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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 Physiology
Nutritional Requirements
• All living protoplasm contains 6 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).
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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.
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Microbial Physiology
Categorizing Microorganisms According to
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 a carbon source and CO2 as an
energy source.
– Chemoautotrophs use chemicals as a carbon source and CO2 as
an energy source.
– Chemoheterotrophs use chemicals as a carbon source and
organic compounds other than CO2 as an energy source.
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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.
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Metabolic Enzymes
• Metabolism refers to all 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 only catalyze one
particular chemical reaction.
• A particular enzyme can only exert its effect on one
particular substance, known as the substrate for that
enzyme.
• The unique 3-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!)
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Action of specific enzyme (E1) breaking down a
substrate (S1) molecule
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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 affect the efficiency or effectiveness of
enzymes; enzymes function best under optimum
conditions.
– pH - extreme acidity for example
– Temperature - heat can denature enzymes by
breaking bonds
– Concentration of enzyme and/or substrate – may be
too high or too low
– Inhibitors, for example heavy metals like lead, zinc,
mercury and arsenic
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Metabolism
• As previously stated, metabolism refers to all of the
chemical reactions within a cell - 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 2 categories: catabolism and
anabolism.
– Catabolism refers to all catabolic reactions in a cell.
– Anabolism refers to all anabolic reactions in a cell.
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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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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
like glucose, to energy-requiring reactions.
• When ATP is used as an energy source, it is hydrolyzed
to adenosine diphosphate (ADP).
• ADP can be used as an energy source by hydrolysis to
adenosine monophosphate (AMP).
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Interrelationships
among ATP, ADP, and
AMP molecules.
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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.
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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 2
common biochemical pathways: aerobic respiration and
fermentation.
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A biochemical pathway with 4 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 3
phases (each is a biochemical pathway):
– Glycolysis
– The Krebs cycle
– The electron transport chain
• The 1st phase (glycolysis) is actually anaerobic, but the
other 2 phases are aerobic.
• Glycolysis (also called the glycolytic pathway, the
Embden-Meyerhof pathway and the Meyerhof-Parnas
pathway) is a 9-step biochemical pathway. Each step
requires a specific enzyme.
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Aerobic Respiration of
Glucose:
First Step = Glycolysis.
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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 8 separate
reactions, each controlled by a different enzyme.
– Only 2 ATP molecules are produced, but a number of
products (e.g., NADH, H+, FADH2) are formed, which
enter the electron transport chain.
• In eucaryotes, the TCA cycle and the electron transport
chain occur in mitochondria.
• In procaryotes, both occur at the inner surface of the cell
membrane.
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The Krebs Cycle.
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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!
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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. Example: yeasts are used to
make wine and beer; the end product is ethanol.
– Fermentation reactions produce very little energy
(~ 2 ATP molecules).
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Catabolism
Oxidation-Reducton (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.
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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.
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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 = the study of heredity.
• An organism’s genotype is its complete collection of
genes.
• An organism’s phenotype refers to its physical traits
(e.g., includes 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.
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Bacterial Genetics
Mutations
• A change in a DNA molecule (genetic alteration) that is
transmissible to offspring is called a mutation.
– 3 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.
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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 can integrate
into the chromosome is called an episome.
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(A) A disrupted E. 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 plasmid.
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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.
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Bacterial Genetics
Ways in Which Bacteria Acquire New Genetic
Information, cont.
• Transduction (“to carry across”):
– Also 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
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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.
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Transformation
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Bacterial Genetics
Ways in Which Bacteria Acquire New Genetic
Information, cont.
• Conjugation
– 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 through the hollow sex pilus from the
donor cell to the recipient cell.
– A plasmid that contains multiple genes for antibiotic
resistance is known as a resistance factor or R-
factor. A bacterial cell that receives a R-factor
becomes a “superbug.”
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Conjugation
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Conjugation in Escherichia coli.
Sex pilus
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Genetic Engineering
• Genetic engineering or recombinant DNA technology
involves techniques to transfer eucaryotic 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; also, for synthesis of important
enzymes and hormones for treatment of diseases.
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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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