Chapter 7
Microbial Physiology and Genetics
Learning Objectives
Chapter 7 introduces aspects of microbial physiology, such as enzymes, metabolism (catabolic
and anabolic reactions), oxidation–reduction reactions, biochemical pathways, aerobic
respiration, and fermentation. Microbial genetic topics discussed in Chapter 7 include mutations,
the various ways in which bacteria acquire new genetic information (lysogenic conversion,
transduction, transformation, and conjugation), genetic engineering, and gene therapy. The
information in Chapter 7 is considered essential in an introductory microbiology course.
Terms Introduced in This Chapter
After reading Chapter 7, you should be familiar with the following terms. These terms are
defined in Chapter 7 and in the Glossary.
Adenosine triphosphate (ATP)
Ames test
Anabolic reactions
Anabolism
Autotroph
Beneficial mutation
Catabolic reactions
Catabolism
Chemoautotroph
Chemoheterotroph
Chemolithotroph
Chemoorganotroph
Chemosynthesis
Chemotroph
Competence
Competent bacteria
Dehydrogenation reactions
Ecology
Ecosystem
Electron transport chain
Endoenzyme
Episome
Essential nutrients
Exoenzyme
Fermentation
Gene therapy
Genetics
Glycolysis
Harmful mutation
Heterotroph
Krebs cycle
Lethal mutation
Lysogenic bacterium
Lysogenic conversion
Lysogeny
Metabolic reactions
Metabolite
Microbial physiology
Mutagen
Mutant
Mutation
Oxidation
Oxidation–reduction reactions
Phenotype
Photoautotroph
Photoheterotroph
Phototroph
Prophage
R-factor
Reduction
Silent mutation
Transduction
Transformation
Review of Key Points
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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,
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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 photosynthetic 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 exerts its effect is known as 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.
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 energyrequiring activities.
Nutrients should be thought of as energy sources, and chemical bonds should be thought
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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 38 ATP molecules (in prokaryotic cells) or 36 to 38 ATP molecules (in eukaryotic
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 of
which are aspects of molecular genetics.
An organism’s genotype (or genome) is its complete collection of genes, whereas an
organism’s phenotype is all of the organism's physical traits, attributes, or characteristics.
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.
As the name implies, beneficial mutations are of benefit to an organism, whereas harmful
mutations result in the production of structurally altered proteins which do not function
properly (e.g., nonfunctional enzymes). Some harmful mutations are lethal to the
organism; these are called lethal mutations.
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
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well as under laboratory conditions.
Lysogenic conversion involves temperate bacteriophages. In lysogenic conversion,
bacteria gain new genetic information in the form of viral genes.
Transduction also involves bacteriophages. In transduction, 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. Donor cells possess sex pili.
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.
A Closer Look:
• Why Anaerobic Bacteria 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 anions, 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.
• Transduction
There are actually two types of transduction: specialized and generalized. The explanation in
Chapter 7 describes specialized transduction, in which the infecting phage integrates into the
bacterial chromosome or a plasmid. As the virus genome breaks away to replicate and produce
more viruses, it carries one or more bacterial genes with it to the newly infected cell. In this way,
genetic capabilities involving the fermentation of certain sugars, antibiotic resistance, and other
phenotypic characteristics can be transduced to other bacteria. This process has been shown in
the laboratory (in vitro) to occur in bacterial species of Bacillus, Pseudomonas, Haemophilus,
Salmonella, and Escherichia, and it is assumed to occur in nature. In generalized transduction,
the bacteriophage is a virulent lytic phage that does not incorporate into the bacterial genome or
plasmid. Rather, it picks up fragments of bacterial DNA during the assembly of new virus
particles and carries these bacterial genes to other cells that the new viruses infect. Generalized
transduction has been observed in bacterial species of Streptococcus, Staphylococcus, and
Salmonella, and in Vibrio cholerae.
• Fertility Factors
Bacteria possessing F+ or Hfr+ genes have the ability to produce sex pili and become donor cells.
If the fertility factor is on a plasmid, it is called an F+ gene, whereas if it is incorporated into the
chromosome, it is referred to as an HFr+ gene. A complete copy of the F plasmid (the plasmid
containing the F+ gene) usually moves to the recipient (F) cell; therefore, the recipient cell
usually becomes F+ (i.e., the recipient cell becomes capable of producing a sex pilus and
becoming a donor cell). On the other hand, the recipient cell usually receives only a portion of
the chromosome from an HFr+ cell, and that portion does not include the HFr+ gene; therefore,
in this case, the recipient cell remains Hfr–, does not produce a sex pilus, and cannot become a
donor cell.
• 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
one or more new gene products (usually proteins). Thus, microorganisms (primarily bacteria) can
be genetically engineered to produce substances (gene products) that they would not normally
manufacture. Paul Berg won the 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 in genetic engineering
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 Grampositive 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 daily,
causing profound changes in medicine, agriculture, and other areas of science.
Increase Your Knowledge
1.
Learn more about enzymes at
www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swf
2.
View the following animations on the TCA cycle and electron transport:
(a) Click here to view TCA cycle.
(b) Click here to view electron transport.
3.
There are many good videos on genetics on YouTube. Search for “genetics” or
“microbial genetics.”
4
Try your hand at some advanced microbial genetic problems at
www.sci.sdsu.edu/~smaloy/MicrobialGenetics/problems/
5.
Learn more about gene therapy at
science.howstuffworks.com/life/genetic/gene-therapy.com
6.
View many interesting videos on bacterial genetics at www.DNATUBE.com; type in the
appropriate term in search (e.g., transcription or translation).
Critical Thinking
1.
Give two possible explanations why an obligate anaerobe is unable to live in the presence
of oxygen?
2.
Assume that you are a microbiologist who has been doing research on a penicillinsensitive 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?
3.
Several products were mentioned in this chapter that are being produced by genetically
engineered bacteria and yeasts. Using the Internet, can you find others?
4.
Use the Internet to learn why some people are against genetically modified food.
5.
Be prepared to discuss these processes: lysogenic conversion, transduction,
transformation, and conjugation.
6.
Using the Internet, prepare a brief written report on the current status of gene therapy in
medicine.
Additional Chapter 7 Self-Assessment Exercises
(Note: Don’t peek at the answers before you attempt to solve these self-assessment exercises.)
Matching Questions
A.
autotrophs
B.
heterotrophs
C.
lithotrophs
D.
organotrophs
E.
phototrophs
_____ 1.
_______________ are chemotrophs that
use inorganic chemicals as their energy
source.
_____ 2.
Organisms that use organic compounds
as their source of carbon are called
_______________.
_____ 3.
Organisms that use organic compounds
as their 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 _______________.
___________________________________________
______________________________
A.
conjugation
B.
lysogenic conversion
C.
mutation
D.
transduction
E.
transformation
_____ 1.
_____ 2.
In _______________,
bacteria acquire new
genetic information in
the form of viral
genes.
Oswald Avery and his
colleagues discovered
that DNA is the
hereditary molecule
while performing
_______________
experiments with
Streptococcus
pneumoniae.
_____ 3.
In _______________, bacteria acquire
new genetic information as a result of
absorbing pieces of naked DNA from
their environment.
_____ 4.
In _______________, genetic
information is passed from one bacterial
cell to another via a hollow sex pilus.
_____ 5.
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 biosyntheses 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 Krebs
cycle.
_____ 7.
In glycolysis, a six-carbon glucose molecule is broken down into two threecarbon 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 to the Additional Chapter 7 Self-Assessment Exercises
Matching Questions
1.
2.
3.
4.
5.
C
B
D
A
E
1.
2.
3.
4.
5.
B
E
E
A
D
True/False Questions
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
True
False (These are examples of anabolic reactions.)
True
True
False (Catabolic reactions are a cell’s major source of energy.)
False (The majority of the energy is produced by the electron transport chain.)
True
True
False (Temperate bacteriophages are responsible for lysogenic conversion.)
False (Mutations may be harmful, beneficial, or “silent.”)