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Chapter Outline
7-1
iii. Opportunistic pathogens
d. Parasitic microorganisms
i. Pathogens
ii. Obligate parasites
iii. Obligate intracellular parasite
D. Transport mechanisms for nutrient absorption
E. The movement of water: Osmosis
1. Selectively or differentially permeable membranes
2. Tonicity conditions (concentration)
a. Isotonic
b. Hypotonic
c. Hypertonic
d. Direction of net water movement and osmotic pressure
3. Adaptations to osmotic variations in the environment
F. The movement of molecules: Diffusion and transport
1. Diffusion
a. Simple diffusion
b. Facilitated diffusion
c. Specificity
d. Saturation
2. Active transport: Bringing in molecules against a gradient
a. Transport of nutrients against the diffusion gradient
b. Transport of nutrients in the same direction as the natural gradient but faster
than diffusion alone.
c. Presence of specific membrane proteins
d. Expenditure of energy
e. Examples:
i. Sodium, potassium, and hydrogen pumps
ii. Group translocations
G. Endocytosis: Eating and drinking by cells
a. Phagocytosis
b. Pinocytosis
7.2. Environmental Factors That Influence Microbes
A. Temperature adaptations
1. Minimum, optimum, and maximum temperature
2. Psychrophile
3. Mesophile
4. Thermophile
B. Gas requirements
1. How microbes process oxygen
a. Aerobe
b. Obligate aerobe
c. Facultative anaerobe
d. Microaerophile
e. Anaerobe
f. Strict or obligate anaerobe
g. Aerotolerant anaerobes
2. Capnophiles—higher CO2
C. Effects of pH
1. Acidophiles
2. Alkalinophiles
7-2
D. Osmotic pressure
1. Halophiles
2. Facultative halophiles
E. Miscellaneous environmental factors
1. Barophiles
2. Dehydrated cell stages
F. Ecological associations among microorganisms
1. Symbiosis and symbionts
2. Mutualism
3. Commensalism and satellitism
4. Parasitism
5. Synergism
6. Antagonism
a. Antibiosis
G. Interrelationships between microbes and humans
1. Normal microbial flora
2. Lactobacillus spp. in vagina
7.3. The Study of Microbial Growth
A. The basis of population growth: Binary fission
B. The rate of population growth
1. Generation or doubling time
2. Mycobacterium leprae and Salmonella enteriditis
3. Exponential: Geometric increase
C. The population growth curve
D. Stages in the normal growth curve (Fig. 7.15)
1. Lag phase
2. Exponential or logarithmic (log) phase
3. Stationary phase
4. Death phase
5. Practical importance of the growth curve
i. Chemostat
E. Other methods of analyzing population growth
1. Turbidity assessment
2. Enumeration of bacteria
a. Direct or total cell count
b. Cytometer counting
c. Coulter counter
7-3
Endocytosis Aerotolerant Normal microbial flora
Phagocytosis Capnophiles Binary fission
Pinocytosis Acidophiles Generation or doubling time
Minimum temperature Alkalinophiles Exponential
Maximum temperature Halophiles Lag phase
Optimum temperature Barophiles Exponential (log) phase
Psychrophile Symbiosis Stationary phase
Mesophile Mutualism Death phase
Thermophile Commensalism Turbid
Aerobe Parasitism Chemostat
Anaerobe Synergism Direct (total) cell count
Microaerophile Antagonism
The most complex issue for most students, in this chapter, continues to be the concept of osmotic
pressure. The terms isotonic, hypotonic, and hypertonic should be reviewed. The students need a clear
understanding of these terms to apply the material in this chapter. Additionally, students will need
reinforcing of nutritional requirement concepts (autotrophs, heterotrophs, etc.). Students could be placed
in discussion groups and directed to create lists of specific organisms and how they would best grow
them. The clinical infective applications of the growth curve and the rate of infection spread in humans
should be discussed.
7-4
Chapter 8
Microbial Metabolism: The Chemical Crossroads of Life
Chapter Outline
8-1
v. Decarboxylases
7. The role of microbial enzymes in disease
a. Streptokinase: Streptococcus pyogenes
b. Elastase and collagenase: Pseudomonas aeruginosa
c. Lecithinase C: Clostridium perfringens
8. The sensitivity of enzymes to their environments
a. Labile
b. Denaturation
C. Regulation of enzymatic activity and metabolic pathways
1. Metabolic pathways
a. Multistep series of reactions
b. Interconnected and merge at many sites
2. Direct controls on the actions of enzymes
a. Competitive inhibition
b. Noncompetitive inhibition through negative feedback
3. Controls on enzyme synthesis
a. Enzyme repression
b. Enzyme induction: Escherichia coli
8.2. The Pursuit and Utilization of Energy
A. Energy in cells
1. Exergonic
2. Endergonic
B. A closer look at biological oxidation and reduction
1. Redox reactions
a. Redox pair: electron donor and electron acceptor
2. Phosphorylation and ATP synthesis
3. Electron transfer
4. Dehydrogenation
5. Electron carriers: Molecular shuttles
a. NAD and NADH
b. Final electron acceptor in aerobic metabolism is oxygen
c. In anaerobic metabolism, final electron acceptor is some other organic or
inorganic compound.
C. Adenosine triphosphate: Metabolic money
1. The molecular structure of ATP
a. Phosphate, sugar (ribose), and a base (adenine)
2. The metabolic role of ATP
a. Substrate-level phosphorylation
b. Oxidative phosphorylation
c. Photophosphorylation
8.3. The Pathways
A. Introduction
1. Metabolism
a. Enzymes
b. Catabolize
c. Precursor molecules
d. Anabolize
e. Reducing power
f. Energy
B. Catabolism: Getting materials and energy
1. Glycolysis
8-2
2. Aerobic respiration
a. Glycolysis
b. Krebs cycle
c. Respiratory chain
3. Anaerobic respiration
a. Glycolysis
b. Final electron acceptor is not oxygen
C. Aerobic respiration
1. Glucose: The starting compound
2. Glycolysis: The starting lineup
i. An anaerobic step
ii. Pyruvic acid synthesis
iii. Steps in the glycolytic pathway
b. Pyruvic acid: A central metabolite
c. The Krebs cycle: A carbon and energy wheel
i. The processing of pyruvic acid
ii. Role of acetyl coenzyme A
iii. Role of NADH
iv. Steps in the Krebs cycle
3. The respiratory chain: Electron transport and oxidative phosphorylation
a. Elements of electron transport: The energy cascade
i. ATP synthase
ii. Oxidative phosphorylation
b. Formation of ATP and chemiosmosis
c. Potential yield of ATPs from oxidative phosphorylation
4. Summary of aerobic respiration
a. Total possible yield
b. The terminal step
i. Formation of water
ii. Neisseria, Pseudomonas, Bacillus
iii. Klebsiella, Enterobacter
iv. Streptococcus
v. Superoxide dismutase and catalase
D. Anaerobic respiration
1. Nitrate and nitrite reduction systems
a. E. coli
2. Denitrification
a. Pseudomonas and Bacillus
E. Fermentation
1. Products of fermentation in microorganisms
a. Alcoholic fermentation
i. Converting pyruvic acid to ethanol
b. Acidic fermentation
i. Streptococcus and Lactobacillus: Homolactic fermentation
ii. Leuconostoc: Heterolactic fermentation
c. Mixed acid fermentation
i. Propionibacterium
F. Catabolism of noncarbohydrate compounds
1. Lipid catabolism:
a. Lipases: break down lipids to fatty acids and glycerol
b. Fatty acids are broken down through beta oxidation
8-3
2. Protein catabolism:
a. Proteases
b. Deamination
8.4. Biosynthesis and the Crossing Pathways of Metabolism
A. The frugality of the cell: Waste not, want not
1. Amphibolic sources of cellular building blocks
a. Gluconeogenesis
b. Beta-oxidation
c. Amination
d. Transamination
B. Anabolism: Formation of macromolecules
1. Carbohydrate biosynthesis
2. Amino acids, protein synthesis, and nucleic acid synthesis
C. Assembly of the cell
8.5 It All Starts with the Sun
A. Photosynthesis
1. Two phases
a. Light-dependent reactions require sunlight
b. Light-independent reactions proceed in light or dark conditions
c. Photons are energy packets from the sun
d. Photosynthetic pigments absorb energy:
i. Chlorophylls
ii. Carotenoids
iii. Phycobilins
2. Light-dependent reactions
a. Take place in the thylakoid membranes (grana) of the chloroplast
b. Photosystem I
c. Photosystem II
i. Photolysis
ii. Cytochromes
3. Light-independent reactions
a. RuBP
b. Carbon fixation
4. Other mechanisms of photosynthesis
a. Oxygenic
b. Anoxygenic
8-4
FAD ETS Transamination
ATP Fermentation Beta oxidation
Glycolysis Amphibolism Chemiosmosis
Krebs Cycle Photosynthesis Gluconeogenesis
Aerobic respiration Light-dependent reactions Photolysis
Ferment Light-independent reactions RuBP
Anaerobic respiration Chlorophylls Carbon fixation
Pyruvic acid Amination Chloroplast
A review of cellular metabolism, both anabolic and catabolic, will help the student with the material in
this chapter. Students should have had some coverage of this material from prerequisite courses.
Students should compare the effectiveness of aerobic versus anaerobic reactions that produce energy.
Discuss the role of vitamins, minerals, and nucleotides in energy production. Create a list of useful
products of fermentation. The process of photosynthesis can be discussed in terms of its importance to
the development of life on earth.
8-5
Chapter 9
Microbial Genetics
Chapter Outline
9-1
B. The gene-protein connection
1. The triplet code and the relationship to proteins
a. Structural genes
b. Phenotype
C. The major participants in transcription and translation
1. RNAs: Tools in the cell's assembly line
a. Single-stranded molecule
b. Composed of nucleotides with a phosphate group, ribose sugar, and a
nitrogenous base (uracil, adenine, guanine, and cytosine)
c. Include mRNA, tRNA, rRNA, miRNA (micro), riboswitch RNA, and siRNA
(small interfering)
2. Messenger RNA: Carrying DNA's message
a. Codons: a sequence of three nucleotides
3. Transfer RNA: The key to translation
a. Anticodon: complements mRNA codons
4. The ribosome: A mobile molecular factory for translation
a. Prokaryotic ribosome (70S)
D. Transcription: The first stage of gene expression
1. RNA polymerase
2. Template strand
3. Coding strand
4. Promoter region
5. mRNA transcript
E. Translation: The second stage of gene expression
1. The initiation of translation
2. The master genetic code: The message in messenger RNA
a. Redundancy and “wobble”
3. The beginning of protein synthesis
a. Start codon: AUG
4. Continuation and completion of protein synthesis: Elongation and termination
a. tRNA
b. Translocation
c. Termination (nonsense) codons
d. Posttranslational modifications
e. Polyribosomal complex
F. Eucaryotic transcription and translation: Similar yet different
1. Introns
2. Exons
3. Split gene
4. Spliceosome
G. The genetics of animal viruses
9.3. Genetic Regulation of Protein Synthesis and Metabolism
A. The lactose operon: A model for inducible gene regulation in bacteria
1. Regulator
a. Repressor
b. Allosteric
2. Control locus
a. Promoter
b. Operator
3. Structural locus
4. Inducer
9-2
B. A repressible operon
1. Corepressor
C. Antibiotics that affect transcription and translation
1. Actinomycin D
2. Erythromycin and spectinomycin
3. Chloramphenicol
4. Streptomycin
9.4. Mutations: Changes in the Genetic Code
A. Introduction
1. Mutation
2. Wild type strain
3. Mutant strain
B. Causes of mutations
1. Spontaneous mutation
2. Induced mutation
a. Mutagens
C. Categories of mutations
1. Point mutations
2. Missense mutation
3. Nonsense mutation
4. Silent mutation
5. Back-mutation
6. Frameshift
D. Repair of mutations
1. Photoactivation or light repair
2. Excision repair
a. Xeroderma pigmentosa and the enzyme photolyase
3. Mismatched bases
E. The Ames Test: Salmonella typhimurium
F. Positive and negative effects of mutations
1. Adaptation
2. Natural selection
9.5. DNA Recombination Events
A. Transmission of genetic material in bacteria
1. Conjugation: Bacterial “sex”
a. Fertility or F factor
b. Conjugative pilus
c. Donor and recipient
d. Resistance plasmids or R factors
2. Transformation: Capturing DNA from solution
a. Streptococcus pneumoniae
b. Transformation
c. Competent
d. Transfection
3. Transduction: The case of the piggyback DNA
a. Generalized transduction
b. Specialized transduction
c. Corynebacterium diphtheriae
4. Transposons: "This gene is jumpin''
9-3
Genetics tRNA Exons
Heredity rRNA Split gene
Genome Genotype DNA polymerase
DNA Phenotype Corepressor
RNA Single stranded Mutation
Chromosome Double stranded Spontaneous mutation
Deoxyribose sugar Codons Missense mutation
Nitrogenous base Anticodon Point mutation
Purine RNA polymerase Induced mutation
Pyrimidine Promoter region Nonsense mutation
Adenine Start codon Photoactivation
Thymine Translocation Ames Test
Guanine Nonsense codons Conjugation
Cytosine Triplets Transformation
Uracil Carcinogenic Transduction
Replication Operon Sex pilus
Okazaki fragments Locus Transposons
Transcription Posttranslational Allosteric
Translation modifications
mRNA Introns
The students will appreciate a review of the nature of the genetic material. A good historical discussion
can center on the work of Watson, Crick, Wilkins, and Rosalind Franklin. Animations, 3D graphics, and
interactive tutorials are available on the Internet and will aid in the students' understanding of the
replication process. A good discussion of mutations and adaptation will include the topic of antimicrobial
resistance in bacteria and its increase in hospital as well as community settings.
9-4
Chapter 10
Genetic Engineering: A Revolution in Molecular Biology
Chapter Outline
10-1
c. Bacillus subtilis
C. Construction of a recombinant, insertion into a cloning host, and genetic expression
10.4. Biochemical Products of Recombinant DNA Technology
A. Human growth hormone
B. Insulin
C. Clotting factor VIII
10.5. Genetically Modified Organisms
A. Recombinant microbes: Modified bacteria and viruses
1. Pseudomonas syringae and Frostban
2. Pseudomonas fluorescens, Bacillus thuringiensis and insecticide genes
B. Transgenic plants: Improving crops and foods
1. Agrobacterium
C. Transgenic animals: Engineering embryos
1. Pharming
10.6. Genetic Treatments: Introducing DNA into the Body
A. Gene therapy
1. Adenosine deaminase (ADA) deficiency
2. SCID
B. DNA technology as genetic medicine
1. Antisense DNA: Targeting messenger RNA
10.7. Genome Analysis: Maps, Fingerprints, and Family Trees
A. Genome mapping and screening: An atlas of the genome
1. Locus and alleles
2. Linkage, physical and sequence maps
3. Genomics and bioinformatics
B. DNA fingerprinting: A unique picture of a genome
1. Single nucleotide polymorphism
2. Markers
a. Variable number of tandem repeats (VNTRs)
b. Microsatellite polymorphisms
3. Microarray analysis
10-2
A major topic of discussion should be on the heightened awareness of bioterrorism and what impact
advances in biotechnology have had on this issue. Student discussions should include modern products,
including the Hepatitis B vaccine and why they should all receive it. Students should be encouraged to
list current uses of recombinant DNA in medicine, criminal investigations, and paternity suits, as well as
hypothesize about future developments. Discuss possible positive and negative aspects of using
genetically modified crops and/or animals.
10-3
Chapter 11
Physical and Chemical Control of Microbes
Chapter Outline
11-1
a. Cells deprived of functional cell wall lyse easily
2. How agents affect the cell membrane
a. Surfactants lower surface tension of cell membranes
3. Agents that affect protein and nucleic acid synthesis
a. Ribosome function
b. DNA and RNA function
4. Agents that alter protein function
a. Denaturation of proteins
11.2. Methods of Physical Control
A. Heat as an agent of microbial control
1. Mode of action and relative effectiveness of heat
a. Moist heat
b. Dry heat
2. Heat resistance and thermal death of spores and vegetative cells
3. Practical concerns in the use of heat: Thermal death measurements
a. Thermal death time
b. Thermal death point
c. Common methods of moist heat control
i. Steam under pressure
1. Autoclave
ii. Nonpressurized steam
1. Tyndallization (intermittent sterilization)
iii. Pasteurization: Disinfection of beverages
1. Thermoduric microbes
2. Sterile milk
iv. Boiling water: Disinfection
b. Dry heat: Hot air and incineration
i. Incineration: most rigorous heat treatment
ii. Hot-air oven
iii. Dry oven
B. The effects of cold and desiccation
1. Cold retards activities of microbes
2. Dessication
3. Lyophilization
C. Radiation as a microbial control agent
1. Modes of action of ionizing versus non-ionizing radiation
2. Ionizing radiation: Gamma rays, X rays, and cathode rays
a. Cold sterilization
b. Applications of ionizing radiation
3. Non-ionizing radiation: Ultraviolet rays
a. Pyrimidine dimers
b. Applications of ultraviolet radiation
D. Decontamination by filtration: Techniques for removing microbes
1. Pore diameters
2. Applications of filtration
11.3. Chemical Agents in Microbial Control
A. Choosing a microbicidal chemical
1. Levels of chemical decontamination
a. High
b. Intermediate
c. Low
11-2
B. Factors that affect the germicidal activity of chemicals
1. Nature of microorganism
2. Nature of material being treated
3. Degree of contamination
4. Time of exposure
5. Strength and chemical action of germicide
C. Germicidal categories according to chemical group
1. The halogen antimicrobial chemicals
a. Chlorine and its compounds
b. Chlorine compounds in disinfection and antisepsis
i. Hypochlorites
ii. Chloramines
c. Iodine and its compounds
i. Free iodine
ii. Iodophors (alcohol and iodine complex)
d. Applications of iodine solutions
i. Iodine tincture
1. Surgical antiseptic
ii. Iodophore
1. Betadine
a. Surgical handscrub
2. Phenol and its derivatives
a. Phenolics
b. Aromatic carbon ring with added functional groups
3. Applications of phenolics
a. Triclosan
4. Chlorhexidine
a. Surgical hand scrub
b. Obstetric antiseptic
5. Alcohols as antimicrobial agents
a. Applications of alcohols
b. Ethanol, isopropyl alcohol
6. Hydrogen peroxide and related germicides
a. Applications of hydrogen peroxide
i. 3% hydrogen peroxide as an antiseptic
ii. Vaporized hydrogen peroxide
iii. Ozone used to disinfect air and water
7. Chemicals with surface action: Detergents
a. Surfactants
i. Anionic detergents (negatively charged): limited microbicidal power
ii. Cationic detergents (positively charged): much more effective
b. Applications of detergents and soaps
i. Quaternary ammonium compounds:
1. Benzalkonium chloride
2. Zephiran
8. Heavy metal compounds
a. Oligodynamic action
b. Drawbacks:
i. Toxic to humans
ii. Allergic reactions
iii. Neutralized by biological fluids and wastes
11-3
iv. Resistance can develop in treated microbes
c. Applications of heavy metals
i. Merthiolate
ii. Metaphen
iii. Silver nitrate
9. Aldehydes as germicides
a. Glutaraldehyde; formaldehyde
b. Applications of the aldehydes
10. Gaseous sterilants and disinfectants
a. Ethylene oxide
b. Chlorine dioxide
c. Applications of gases and aerosols
11. Dyes as antimicrobial agents
a. Crystal violet and malachite green
b. Acridine dyes
12. Acids and alkalis
Discuss why it is not wise to kill all microorganisms in certain areas. Bring to their attention the issue of
the pervasive use of antimicrobial soaps, and possible drawbacks to its overuse.
What are the most effective ways of eliminating harmful contaminating agents, especially when
dealing with contaminants such as HIV, anthrax, and prions? The issue of bioterrorism and the spate of
misinformation (stocking up on duct tape and plastic) will also encourage vigorous discussion.
Students will be interested in a general discussion on food handling and preparation and the
sterilization of medical equipment and supplies. An introduction to wound care is a good way to
introduce the chemical compounds (and their relative efficacies) for disinfection or antisepsis.
11-4