Exam Guide
Chapter 1. Microbial Life: Origin and Discovery







A microbe is a microscopic organism
Microbial genomes are sequenced
Microbes shape human history
Microscopes reveal the microbial world
-Robert Hook observes…., Antoni van Leeuwenhoek observes…
The debate over spontaneous generation
Medical microbiology
-Kock’s postulates
Antiseptic and antibiotics control pathogen
Chapter 2. Observing the Microbial Cell
Observing Microbes



Light Interacts with an object
Refraction Enables Magnification
Maginfication and Resolution
Bright_Field microscopy





Increasing resolution
Fixation and staining
Differential stains: Gram staining
Other differential stains
Negative staining
Dark-Field Microscopy
Other Microscopy




Phase-Contrast Microscopy: familiarize its application
Fluorescence Microscopy: familiarize its application
Confocal Microscopy: familiarize its application
Electron Microscopy: familiarize its application
Chapter 3. Cell Structure and Function
The Bacterial Cell: An overview

Biochemical composition of bacteria
The Cell Membrane and Transport




Phospholipids and Proteins
Important functions of plasma membrane
Transport across the cell membrane
-Osmosis, Passive diffusion, Facilitated diffusion, Active diffusion
Membrane lipids and their various structure and function
The Cell Wall and Outer layer






Peptidoglycan structure and its functions
Peptidoglycan in Gram positive
Peptidoglycan in Gram negative
Gram positive cell envelop
Gram negative outer membrane
Familiarize the major differences in cell walls of Gram positive and Gram
negative cells
The Nucleoid and Gene Expression


DNA organization in the nucleoid
Supercoiling and the role of DNA binding proteins
Cell Division:


The DNA is replicated biodirectionally
Formation of septa in spherical, and rod-shaped organisms
Specialized Structures: Readup on the followings




What are thylakoids and Carboxysomes. And with what activity in microbes
these structures are associated?
Storage granules
Magnetosomes and their role
Pili, fimbriae, and stalks- their specific functions
Flagella – familiarize about different type of flagella and their role in chemotaxis.
Chapter 4. Bacterial Culture, Growth, and Development
Micorbial Nutrients


Macronutrient, Micronutrients, Trace minerals, and Etc.
Autotrophy and Heterotrophy: Photoautotrophy, Photoheterotrophy,
Chemoautotrophy and Chemoheterotrophy
Nutrient Uptake:





Simple diffusion and facilitated diffusion
Active transport: Symport and Antiport;
Active transport: ABC Transporters
Active transport: Siderphores
Active transport: Group translocation
Culturing Techniques: Readup on various techniques for culturing bacteria in the lab
Culture media: Readup on various types of growth media
Counting Bacteria: Understand the concept/theory for some of the below techniques



Cell counting with the Petroff-Hausser chamber
Cell counting using fluorescent dyes (live and dead cells)
Cell counting with Fluorescence-activated cell sorter
The Growth Cycle


Batch growth: familiarize with the four microbial growth phases
Exponential growth: what is generation time? Methods to estimate generation
time and other growth parameters.
Biofilms: Read the entire material on this topic (pp 139-141)
Cell Differentiation:



Read up on the formation of endospores
Nitrogen-fixing heterocysts in Cyanobactetria.
Differentiation in Streptomyces cell structure (pp144-145)
Chapter 5: Environmental Influences and Control of Microbial Growth
Environmental limits of growth
Adaptation to temperature
Microorganisms are classified by growth temperature:



What is a cardinal temperature?
Microbial adaptation to cold and heat shock
Biotechnological application of psychrophiles and thermophiles
Adaptation to Pressure




What are barophiles or piezophiles?
What are barotolerants?
Molecular adaptation to pressure
Application of barophiles/barotolerants
Water Activity and Salt




What is water activity?
Osmotic stress
How do cells minimize osmotic stress?
What are halophiles?
Oxygen and Other Electron Acceptors

Read all sections related to this topic, especially about “Reactive Oxygen
Species” and about those enzymes that help overcome toxicity (pp 164-167)
Oligotrophs (page 168)
Physical, Chemical, and Biological Control of Microbes
Physical:





Have a clear understanding of the term “D-value” and “z-value”
Effects of high temperature and pressure
Pasteurization and how this differs from sterilization
Filtration
Irradiation
Chemical:



What is the Phenol Coefficient?
Chemical disinfectants
Biological control of microbes
Chapter 7: Genomes and Chromosomes (DNA Replication)
DNA: The genetic material
 Bacterial genome and genome organization
 Chemical structure of DNA
 DNA supercoiling
 Topoisomerases
DNA Replication (Pp 232-239):





What is semiconservative replication?
Where on chromosome the replication is initiated and terminated?
Familiarize yourself about replication forks, major enzymes, steps, and direction
of replication.
What are Okazaki fragments?
Be familiar about event that occur on the lagging strand
DNA Polymerase 3: Read about this enzyme and other associated enzymes (don’t go
into too details of this process)
DNA Polymerase 1: Read about this enzyme and other associated enzymes (don’t go into
too details of this process)
DNA replication generates supercoils (page 239): DO NOT READ FOR EXAM
Terminating Replication (page 240): DO NOT READ FOR EXAM
Plasmids (pp 242-243)


Plasmids Replicate Autonomousely
Plasmids Have Tricks to Ensure Their Inheritance
DO NOT READ (f) THE MATERIAL ON PAGES 244-256.
Chapter 8: Transcription, Translation, and Bioinformatics
RNA Polymerase and Sigma factor

Read about the promoter and its binding sites (pp 259-261)
Transcription of DNA to RNA: Have a clear understanding of this process


Initiation: Major enzymes and events
Elongation: What happens during this step

Termination: How does this happens (Rho-dependent and Rho-independent)
Different Classes of RNA and their functions
Translation of RNA to protein
 What is a code and codon?
 What is t-RNA ? Familiarize with its structure and role in translation
 What are aminoacyl-tRNA synthetases?
 What are ribosomes: be familiar about its structure and function
 What is an “Open Reading Frame” and how do ribosomes find the right reading
frame?
The Three Stages of Protein Synthesis(pp 275-280): Read and have a clear
understanding of the entire translation process (do not have to remember the small details
but know the major steps).
Prokaryotic Transcription and Translation are coupled (pp 281-282)
Bioinformatics



Annotating the genome
Computer analysis and web sciences- What are open reading frames?
Orthologs and paralogs: have clear understanding of the terms.
Chapter 9: Gene Transfer, Mutation, and Genome Evolution
The Mosaic Nature of Genomes
Transformation of genetic material in nature


Transformation in Gram Positive organisms (competent cells, competence factors,
transformasomes)
Transformation in Gram Negative organisms: have a clear understanding of how
the transformation in Gram positive and Gram negative organisms differ?
Conjugation





What is a conjugative plasmid?
How does the conjugation occurs in Gram negative organisms?
What happens when F+ and F- mate?
What is meant by the term “Hfr”?
What happens when an Hfr mates with an F- cells?
Transduction




What is a bacteriophage?
Generalized Transduction: familiarize with the process
Specialized Trasndution: familiarize with the process
How generalized tansduction differs from the specialized transduction?
DNA restrictions and Modifications
Recombination
Generalized recombination and RecA
Site-specific recombination
Mutation: Review the difference between various mutations (pp 319-322)
Chapter 13: Energetics and Catabolism
Energy carriers and Electron Transfer (pp 465-468)
Enzymes catalyze metabolic reactions (pp 469-471)
Catabolism: The microbial buffet
Classes of catabolism: Have a basic understanding about the following items:



Fermentation
Respiration
Phototrophy
Diverse substrate for catabolism
 Carbohydrate catabolism
 Lipid and amino acid catabolism
 DO NOT READ ABOUT AROMATIC CATABOLISMS FOR EXAM
Glucose Breakdown and fermentation: Overview of EMP and ED pathways for glucose
(pp 478-482)
DO NOT STUDY THE PENTOSE PHOSPHATE PATHWAYS FPR THE EXAM
DO NOT STUDY FERMENTATION
The Tricarboxylic acid cycle (TCA) cycle (pp 487-492): Have a clear understanding of
the major steps. **Refer to my power point slides.
Chapter 14: Respiration and Lithotrophy: **This chapter is bit confusing and
repetitious. You need to refer to both book sections and my slides in a clever way.
Need help, just ask!!
Have a basic understanding of the following concepts:





Energy Storage: The Reduction potential (pp 503-504)
An ETS functions within a membrane (pp 504-506)
The protonmotive force (pp 507-508)
The p drives many cell functions (pp 509 and 512)
Cofactors allow small energy transition.
Oxidoreductase Protien complexes (pp 514-516)
The proton potential drives ATP synthesis (pp 518-520)


The F 0and F1 ATP Synthase
DO NOT READ Na+ PUMP: AN ALTERNATE TO H+ PUMPS
Anaerobic Respiration (pp 521-522)


Electron acceptors and donors
Nitrogen and sulfur
DO NOT STUDY DISSIMILATORY METAL REDUCTION
Lithotrophy (pp 525-527)


Nitrogen oxidation
Sulfur oxidation
Chapter 19: Archaeal Diversity
Archaeal Traits (pp 717-720)



Archaeal cell structure and metabolism
Unique metabolic pathways
Nucleic acid structure
Crenarchaeota: Hyperthermophiles



Habitats for thermophiles
Desulfurococcales: Reducing sulfur from hot springs
Barophilic hyperthermophiles

Sufolobales: High temperature and extreme acid
Crenarchaeota: Mesophiles and Psychrophiles


Psychrophilic crenarchaeotas
DO NOT READ AMMONIA-OXIDIZING CRENARCHAEOTES (Page 732)
Euryarchaeota: Methanogens




Different paths to methane
Methanogens have diverse cell morphologies
Anaerobic habitats (soil and landfills, digestive methanogenic symbionts, human
digestion, methane hydrates)
Biochemistry of methanogensis
-methanogenesis from CO2
-methanogenesis from acetate
Euryarchaeota: Halophiles



Haloarchael form and physiology
DO NOT READ IFFERENT HYPERSALINE HABITATS SUPPORT
DIFFERENT HALOARCHAEA (Page 742)
Retinal-based phototrophy
Euryarchaeota: Thermophiles and Acidophiles




Thermococcales
DO NOT READ ARCHAEOGLOBUS
Thermoplasmatales
Nanoarchaeota
Chapter 26: Microbial Diseases
Characterizing and Diagnosing Microbial Diseases
Skin and Soft-Tissue Infection
Respiratory Tract Infections
Gastrointestinal Tract Infections
Genitourinary Tract Infections
DO NOT STUDY CENTRAL NERVOUS SYSTEM INFECTIONS FOR THE EXAM
DO NOT STUDY CARDIOVASCULAR SYSTEM INFECTIONS FOR THE EXAM
Systemic Infections




The plague
Lyme disease
Hepatitis
Ebola