MODULE 5

Module Title: Microbial Physiology and Genetics

Overview:
This module introduces aspects of microbial physiology, such as enzymes, metabolism (catabolic
and anabolic reactions), oxidation-reduction reactions, biochemical pathways, aerobic respiration and
fermentation. It also covers microbial genetic topics like mutations, the various ways in which bacteria
acquire new genetic information (lysogenic conversion, transduction, transformation, conjugation),
genetic engineering and gene therapy.

Module Objectives:
At the end of the module, the student should be able to:
1.Categorize microorganisms according to their carbon and energy sources.
2. Discuss relationships biological catalysts.
3. Differentiate between anabolism and catabolism.
4. Explain the role of adenosine triphosphate molecules in metabolism.
5. Describe biochemical pathways involved in metabolism.
6. Explain the beneficial and harmful effects of bacterial mutations.
7. Explain how bacteria acquire genetic information.

Module Coverage:
A. Topic: Microbial Physiology
B. Topic: Microbial Genetics

TOPIC A
Topic Title: Microbial Physiology
Introduction:
This topic deals with the vital life processes of microorganisms. Microorganisms, especially the
bacteria, are ideally suited for use in studies of the basic metabolic reactions that occur within cells.
They are inexpensive to maintain in the laboratory, take up little space and reproduce quickly. Their
morphology, nutritional needs and metabolic reactions are easily observable.

Topic Objectives:
At the end of the topic, the student should be able to:
1. Define phototroph, chemotroph, autotroph, heterotroph, photoautotroph, chemo heterotroph,
endoenzyme, exoenzyme, plasmid, R-factor, “superbug”.
2. Discuss the relationships among apoenzymes, coenzymes and holoenzymes.
3. Differentiate between anabolism and catabolism.
4. Explain the role of ATP molecules in metabolism.
5. Describe aerobic respiration, glycolysis, Kreb’s cycle, electron transport system, oxidation-reduction
reactions, photosynthesis.

Topic Contents:
 PPP
 Use the internet or print resources to research articles on superbugs. Write one or two
paragraphs about the superbug, its effects and what is being done to combat it.
 Use the internet or print resources to research anabolic steroids. Write a paragraph or two
about how anabolic steroids work and how they relate to anabolism.
TOPIC B
Topic Title: Microbial Genetics
Introduction:
As with humans, animals and plants, the genetics of microbes involves DNA, genes, the genetic
code, chromosomes, DNA replication, transcription and translation- all part of molecular genetics. The
base sequence of any gene on a chromosome may be altered accidentally in many ways, resulting in a
mutation. Mutations are expressed not only in the cell where mutation occurred but in subsequent
generations a s well. The altered genetic code will result in an altered protein, which could affect any of
a number of different phenotypic characteristics (changes in colony characteristics, cell shape,
biochemical activities, nutritional needs, antigenic sites, virulence, pathogenicity, drug resistance).
Mutant bacteria are used in genetic and medical research and the production of vaccines.

Topic Objectives:
At the end of the topic, the student should be able to:
1. Explain what causes bacterial mutation.
2. Differentiate beneficial, harmful and silent mutations.
3. Discuss beneficial and harmful effects of mutations.
4. Describe lysogenic conversion, transduction, transformation and conjugation.

Topic Contents:
 PPP
 Use the internet or print resources to research on products that are produced by genetically
engineered bacteria and yeasts.
 Students should make a list of terms that are not familiar to them and later on quiz each other.

Review of Key Points

 Microbial physiology is the study of the life processes of microorganisms.
 Scientists have learned a great deal about cells—including human cells—by studying
the nutritional needs of bacteria, their metabolic pathways, and why they live, grow,
multiply, or die under certain conditions.
 All living organisms require sources of energy and carbon so that they can produce the
molecules necessary for life. In addition, organisms must be provided with certain
materials (called essential nutrients) that they themselves are unable to synthesize, but
are required for survival; these essential nutrients vary from species to species.
 The energy source for certain organisms (called phototrophs) is light and for other
organisms (called chemotrophs) is organic or inorganic chemicals.
 Chemolithotrophs and chemoorganotrophs are subcategories of chemotrophs.
Chemolithotrophs (or simply lithotrophs) use inorganic chemicals as an energy source,
whereas chemoorganotrophs (or simply organotrophs) use organic chemicals as an
energy source.
 An organism’s carbon source may be CO2 (in which case the organism is called an
autotroph) or other organic compounds (in which case the organism is called a
heterotroph). Humans, animals, protozoa, and fungi are heterotrophs, as are most
bacteria.
 Interrelationships among the different nutritional types are of prime importance in the
functioning of the ecosystem. Phototrophs (plants, algae, and certain bacteria) are the
producers of food and oxygen for the chemoheterotrophs (animals). Dead plants and
animals are recycled by the chemoheterotrophic saprophytic decomposers (certain
fungi and bacteria) into nutrients for phototrophs and chemotrophs.
 Metabolism refers to all of the chemical reactions (metabolic reactions) that occur
within a living cell, including the production of energy and the synthesis of new
molecules.
 Metabolic reactions include catabolic reactions and anabolic reactions. Catabolic
reactions (also called degradative reactions) involve the breaking of chemical bonds
and the release of energy. Anabolic reactions (also called biosynthetic reactions)
require energy because they involve the formation of chemical bonds.
 Most metabolic reactions are regulated by enzymes.
 Enzymes are biologic molecules (proteins) that serve as catalysts to control the rate of
metabolic reactions. The enzymes produced by any particular cell are governed by the
genotype of that cell, and the presence or absence of any particular enzyme is part of
the phenotype of that cell.
 The substance upon which an enzyme acts is known at that enzyme’s substrate.
 All the enzymes that a cell is capable of producing need not be present in the cell at a
given moment in time. They are produced to meet the metabolic needs of the cell, as
determined by the internal and external environments.
 Endoenzymes are enzmes that remain within the cell that produced them, whereas
exoenzymes are enzymes that leave the cell to catalyze reactions outside of the cell.
 Apoenzymes are proteins that are unable to catalyze reactions on their own. To
catalyze reactions, apoenzymes must first link up with a cofactor (either a mineral ion
or a coenzyme).
 An enzyme operates at peak efficiency within a particular pH and temperature range
and when an appropriate concentration of the substrate for that enzyme exists. If the
environment is too acidic, basic, hot, or cold, or contains too much or too little
substrate, the enzyme will not operate at peak efficiency and the reaction will not
proceed at its maximum rate.
 Catabolic reactions involve the breaking of chemical bonds and the release of energy.
Anabolic reactions involve the formation of bonds, which requires energy.
 Adenosine triphosphate (ATP) is the principal energy-storing or energy-carrying
molecule in the cell. Should a cell require energy, one of the high-energy bonds in an
ATP molecule can be broken, producing energy, an ADP molecule, and a free
phosphate. The energy can then be used for growth, reproduction, active transport of
substances across membranes, sporulation, movement, anabolic reactions, and other
energy-requiring activities.
 Nutrients should be thought of as energy sources, and chemical bonds should be
thought of as stored energy.
 A common pathway by which bacteria catabolize glucose is aerobic respiration, which
consists of three phases: glycolysis, the Krebs cycle, and the electron transport chain.
 Most of the energy that is produced by aerobic respiration is produced by the electron
transport chain. The breakdown of one molecule of glucose by aerobic respiration
yields either 36 ATP molecules (procaryotic cells) or 38 ATP molecules (eucaryotic
cells).
 Aerobes and facultative anaerobes are able to produce more energy than anaerobes,
because they can catabolize glucose molecules via aerobic pathways. Anaerobes must
catabolize glucose by fermentation, a relatively inefficient method that yields only two
ATP molecules from a molecule of glucose.
 Oxygen does not participate in fermentation reactions.
 Oxidation reactions involve the loss of an electron, whereas reduction reactions involve
the gain of an electron.
 Phototrophic organisms (algae, plants, and photosynthetic bacteria) derive their energy
from the sun by photosynthesis. Chemosynthetic organisms use a chemical source of
energy and raw materials to synthesize metabolites and macromolecules for growth
and function of the organisms.
 As with humans, animals, and plants, the genetics of microbes involves DNA, genes,
the genetic code, chromosomes, DNA replication, transcription, and translation—all
part of molecular genetics.
 An organism’s genotype (or genome) is its complete collection of genes, whereas an
organism’s phenotype is all the physical traits, attributes, or characteristics of the
organism.
 Genes direct all functions of the cell, providing it with its own particular traits and
individuality. An organism’s phenotype is the manifestation of that organism’s
genotype.
 Constitutive genes are expressed at all times, whereas inducible genes are expressed
only when the products that they code for (gene products) are needed.
 The base sequence of any gene on a chromosome may be altered accidentally in many
ways, resulting in a mutation. Mutations are expressed not only in the cell in which the
mutation occurred, but in subsequent generations as well. The altered genetic code will
result in an altered protein, which could affect any of a number of different phenotypic
characteristics (e.g., changes in colony characteristics, cell shape, biochemical
activities, nutritional needs, antigenic sites, virulence, pathogenicity, drug resistance).
Mutant bacteria are used in genetic and medical research and the production of
vaccines.
 Mutations may be beneficial, harmful, or of no consequence to the cell or organism
containing the mutation. Those of no consequence are called silent or neutral
mutations.
 Beneficial mutations are of benefit to an organism, whereas harmful mutations result in
the production of structurally altered proteins (often, nonfunctional enzymes). Some
harmful mutations are lethal to the organism.
 Physical or chemical agents that cause an increased mutation rate are called mutagens.
  In addition to mutations, genetic changes in a bacterial cell may be the result of
lysogenic conversion, transduction, transformation, or conjugation, all of which occur
in nature as well as in the laboratory.
 Lysogenic conversion involves temperate bacteriophages. In lysogenic conversion,
bacteria gain new genetic information in the form of viral genes.
 Transduction also involves bacteriophages. In lysogenic conversion, bacteria gain new
genetic information in the form of bacterial genes.
 In transformation, a bacterial cell becomes genetically transformed following uptake of
DNA fragments (“naked DNA”) from the environment.
 Conjugation involves the transfer of genetic material (usually a plasmid) from a donor
cell to a recipient cell through a hollow sex pilus.
 A plasmid that contains multiple genes for antibiotic resistance is called a resistance
factor or R-factor.
 The field of genetic engineering involves the introduction of new genes into cells.
When a cell receives a new gene, it can produce the gene product that is coded for by
that gene. Genetically engineered bacteria are used to produce products such as insulin,
interferon, human growth hormone, and materials for use as vaccines.
 Gene therapy involves the use of viruses and plasmids to introduce normal genes into
cells that contain abnormal genes.

Why Anaerobes Die in the Presence of Oxygen

When molecular oxygen (O2) is reduced (i.e., when O2 gains electrons; as in certain oxidation–
reduction reactions), extremely reactive substances are produced (as shown in the following
equations).
O2 + e–  –O2 (superoxide anion)
O2 + 2e–  H2O2 (hydrogen peroxide)
O2 + 3e–  H2O + OH– (hydroxyl radical)
These reduction products (superoxide anion, hydrogen peroxide, and hydroxyl radicals)
are capable of causing severe damage to enzymes and cell membranes; they are potentially
lethal to cells. To survive in the presence of oxygen, organisms must possess enzymes (e.g.,
superoxide dismutase and catalase) that can neutralize these toxic substances. Obligate
anaerobes are killed in the presence of oxygen because they lack one or more of these
enzymes. Aerotolerant anaerobes produce these enzymes, but not in high enough
concentrations to enable the organisms to survive in high concentrations of oxygen.
Genetically Engineered Bacteria and Yeasts
The term genetic engineering refers to the manufacture and manipulation of genetic material in
vitro (in the laboratory). Genetic engineering has been possible only since the late 1960s, when
a scientist named Paul Berg demonstrated that fragments of human or animal DNA can be
attached to bacterial DNA. Such a hybrid DNA molecule is referred to as recombinant DNA.
When a molecule of recombinant DNA is inserted into a bacterial cell, the bacterium is able to
produce the gene product, usually a protein. Thus, microorganisms (primarily bacteria) can be
genetically engineered to produce substances (gene products) that they would not normally
manufacture. Paul Berg won a Nobel Prize in 1980 for his pioneering genetic engineering
experiments.
Molecules of self-replicating, extrachromosomal DNA, called plasmids, are frequently
used in genetic engineering and are referred to as vectors. A particular gene of interest is first
inserted into the vector DNA, forming a molecule of recombinant DNA. The recombinant DNA is
then inserted into or taken up by a bacterial cell. The cell is next allowed to multiply, creating
many genetically identical bacteria (clones), each of which is capable of producing the gene
product. From the clone culture, a genetic engineer may then remove (“harvest”) the gene
product.
The Gram-negative bacillus, Escherichia coli, has often been used because it can be
easily grown in the laboratory, has a relatively short generation time (about 20 minutes under
ideal conditions), and its genetics are well understood by researchers. A Gram-positive
bacterium (Bacillus subtilis), a yeast (Saccharomyces cerevisiae), and cultured plant and
mammalian cells have also been used by genetic engineers to produce desired gene products.
An example of a product produced by genetic engineering is insulin, a hormone
produced in E. coli cells and used to treat diabetic patients. Human growth hormone
(somatotropin), bovine growth hormone (BGH), porcine growth hormone (PGH), somatostatin
(a hormone used to limit growth), tissue growth factors, clotting factors, and interferon are also
produced by genetically engineered E. coli. Genetically engineered bacteria are being used to
produce industrial enzymes, citric acid, and ethanol, and to degrade pollutants and toxic
wastes. The hepatitis B vaccine that is administered to healthcare workers is produced by a
genetically engineered yeast, called Saccharomyces cerevisiae.
New uses for recombinant DNA and genetic engineering are being discovered every day,
causing profound changes in medicine, agriculture, and other areas of science.

Learning Activities:
Post summative assessments.
Critical Thinking
Assume that you are a microbiologist who has been doing research on a penicillin-sensitive strain of
Staphylococcus aureus for many months. One day you discover that the organism is now resistant to
penicillin. You know that it has not come in contact with any other species of bacteria, nor has it come in
contact with the DNA from any other species of bacteria. What are two possible explanations for its
sudden change from penicillin susceptibility to penicillin resistance?

Matching Questions
_____ 1. These are chemotrophs that use inorganic chemicals A. autotrophs
as their energy source. B. heterotrophs
_____ 2. Organisms that use organic compounds as their C. lithotrophs
source of carbon are called _________. D. organotrophs
_____ 3. Organisms that use organic compounds as their E. phototrophs
energy source are called _________.
_____ 4. Organisms that use carbon dioxide as their source
of carbon are called ___________.
_____ 5. Organisms that use light as their energy source are
called ___________.

_____ 6. In _____________, bacteria acquire new genetic A. conjugation

information in the form of viral genes. B. lysogenic conversion
_____ 7. Oswald Avery and his colleagues discovered that C. mutation
DNA is the hereditary molecule while performing D. transduction
_________ experiments with Streptococcus E. transformation
pneumoniae.
_____ 8. In ___________, bacteria acquire new genetic
information as a result of absorbing pieces of naked
DNA from their environment.
_____ 9. In ___________, genetic information is passed
from one bacterial cell to another via a hollow sex
pilus.
_____ 10. In __________, bacteria acquire new genetic
information when bacteriophages inject bacterial genes.

True/False Questions
_____ 1. Dehydration synthesis reactions always involve the removal of a molecule of water.
_____ 2. The biosynthesis of polysaccharides, polypeptides and nucleic acids are examples of catabolic
reactions.
_____ 3. Oxidation-reduction reactions are paired reactions that involve the transfer of electrons.
_____ 4. Breaking a disaccharide down into its two monosaccharide components is an example of a
hydrolysis reaction.
_____ 5. Anabolic reactions are a cell’s major source of energy.
_____ 6. The majority of energy produced in aerobic respiration is produced by the Kreb’s cycle.
_____ 7. In glycolysis, a 6-carbon glucose molecule is broken down into two 3-carbon molecules of
pyruvic acid.
_____ 8. Aerobic respiration is a more efficient method of breaking down glucose than is fermentation.
_____ 9. Virulent bacteriophages are responsible for lysogenic conversion.
_____ 10. Mutations are always harmful.

Answers:
Matching Questions True/False Questions
1. C 1. True
2. B 2. False (these are examples of anabolic reactions)
3. D 3. True
4. A 4. True
5. E 5. False (catabolic reactions are a cell’s major source of energy)
6. B 6. False (the majority of energy is produced by the electron transport
7. E chain)
8. E 7. Ture
9. A 8. True
10. D 9. False (temperate bacteriophages are responsible for lysogenic
conversion)
10.False (mutations may be harmful, beneficial, “silent”)

Reference:
Engelkirk, P. G. and G. R. W. Burton. 2011. Burton’s Microbiology for the Health Sciences. Lippincott
Williams & Wilkins. Baltimore, MD, 398 pp.