CAS BI-311


(Spring Semester 2011/2012)

Instructor: Stjepko Golubic, Tel. 3-2436,, Office hours: by e-mail appointent, TR 1:00-2:30.

Prerequisite: Core biology courses, chemistry, cell biology, consent.

Objectives: The course promotes an understanding of microbial structures, functions and diversity. It reviews the basic biological principles as applied to microorganisms, and emphasizes the phylogenetic and metabolic diversity among them. The course exploits new advances in molecular research in dealing with microbial diversity, ecology and niche differentiation. It stresses microbial roles in biogeochemical cycling of elements in nature, and global importance of microorganisms. It deals with interactions among viruses, bacteria and macroorganisms and promotes a balanced view of beneficial vs. harmful effects of microorganisms on environmental and human health and society. The first part of the course introduces the subject and reviews basic structural and functional properties of microorganisms, microbiological methods of study and viruses. The second part deals with genetic basis, evolutionary history, and phylogenetic and metabolic diversity of microorganisms. The last part deals with the interrelations between microorganisms and humans as their hosts. Laboratory sessions are run independently. They provide hand-on experience in growing and observing microorganisms.

Evaluation: Best 3 of 4 exams (3+final): 75%; no makeups; Lab: 25% - must be passed to pass the course.

Textbook: Madigan, M.T, Martinko, J.M., Stahl, D.A. & Clark, D.P., 2012. Brock Biology of Microorganisms, 13th edition, Benjamin Cummings, Pearson 1043pp.+ Appendices. Older issues have different chapter schedule, but 11th and 12th Edition are accepted.



1. 17-19. Introduction to Microbiology

Microbiology as basic and applied science – T he importance of the microbial world – M icroorganisms as cells and organisms – Microorganisms in their environment – Microbiology in historic perspective – Prokaryotic and eukaryotic cellular organization – Diversity of microorganisms – Microorganisms seen at the level of macromolecules. – Microscopy - transmitted light, dark field, phase contrast and fluorescence microscopy. – Differential (Nomarski) interference contrast, atomic force and confocal scanning laser light microscopy - Scanning and transmission electron microscopy. – Cellular life and evolutionary history.  Chapters 1 – 2.

2. 24-26. Microbial Cells and their Interaction with the Environment

Cell Structure and function. –  Tthe plasma membrane and transport. – Cell walls: gram-positive, gram-negative bacteria, archaea. – Other cell surface structures. – Cellular inclusions. – Endospores. – Microbial locomotion: Bacterial flagella and flagellar motion - gliding movement. – B ehavioral responses: taxes. Ch. 3.


3. 31-02. Microbial Nutrition and Energy Generation

Nutrition and culturing – Culture media. – Aseptic procedures. – Energy generation and biocatalysis. – Enzyme structure and function. – Oxidation-Reduction. – NAD as redox carrier. – Phosphorylation. – E lectron carriers and electron transport systems. – Proton motive force: chemiosmosis. – Energy yielding metabolic systems. – Catabolic diversity. – Anabolism - Biosynthesis. Ch. 4.

4. 07-09. Microbial Growth and Control

Cell growth and cell division (binary and multiple fission). -  Peptidoglycan biosynthesis in cell division. – Growth of microbial populations – Growth cycle. – Growth measurements: direct and indirect. – Batch and continuous cultures. – Factors influencing microbial growth. – Heat: cardinal points, thermophilypsychrophyly. – Osmotic effects. – Oxygen. – Toxic forms of oxygen.  Ch. 5, 26.

5. 14-16. Viruses and Virology

Properties and types. – The virion. – The virus host. – Virus replication. – DNA and RNA viruses, double and single stranded, Positive and negative strand viruses. – Viral proteins. – Viral diversity – Baltimore classification. – Virulent and Lysogenic (temperate) bacteriophages. – Animal viruses. – Plant viruses. – Viruses and cancer. – Retroviruses. – Vectors. – Viroids and prions. Ch. 9, 21.

-----------------------EXAM-1: Feb. 23  


6. 28-01. Elements of Molecular Biology and Genetics of Microorganisms

Genetic information in Bacteria. – Genetic elements. – Chromosomes and plasmids - Gene arrangements, transfer and expression. – DNA and Replication. – Polymerase Chain Reaction (PCR). – RNA and Transcription; Proteins and Translation. – Genetic information in Archaea and Eukarya. – Cell division, Transcription and translation in Eukarya. – RNAi and MicroRNA regulation.  Gene expression and regulation. chromosome. – Mutation and recombination - Types of mutation – Mutagenesis. – Gene transfer: Transformation – Transduction – Conjugation. Mobile DNA – transposons.  Ch. 6, 7, 8, 10  

7. 06-08. Microbial Evolution, Phylogeny and Systematics

Microbial  Genomics, Proteoms and Metaboloms.  Early life on Earth – RNA-life - Early metabolism. – Cyanobacteria: Impact of oxygenic photosynthesis. – Microbial fossil record. – Origins of eukaryotic cellular organization. – Evolutionary chronometer molecules. – Ribosomal RNA sequences and cellular evolution. – The tree of life. – Phylogenetic probes. – Characteristics of the primary Domains. – Endosymbiotic origin of eukaryotes – Conventional and molecular taxonomy – Molecular clocks – Evolutionary analysis – Phylogenetic probes and FISH – Ribotyping – FAME – DNA-DNA hybridization.  – Bacterial species concept. – Classification and Nomenclature.  Ch. 12, 16.

------------------ SPRING RECESS: March 10-18.  

8. 20-22.Diversiy of Bacteria and Archaea

Metabolic and Phylogenetic Diversity of: (1) Bacteria – Phototrophy, Chemolithotrophy and Major Biosyntheses: Autotrophy, N-fixation. – Photosynthesis, pigments,  anoxygenic vs. oxygenic. (Ch. 13). – Phototrophy in the Phylogeny of Bacteria: Proteobacteria, Acidobacteria, Heliobacteria, Green sulfur bacteria, Green non-sulfur bacteria. – Oxygenic phototrophy and Cyanobacteria (Ch. 17-I, II; 18-II, VIII, XI). – Catabolism of organic compounds: Fermentation, Anaerobic and Aerobic Respirations (Ch. 14, 15). – Catabolism and Phylogeny (Ch. 17-III – V, 18-I, III – VII, IX, X, XII). –(2)  Metabolic and Phylogenetic diversity of Archaea – Methanogenesis (Ch. 14.10). – Euryarchaeota: Halophiles, Methanogens, Thermoplasmas, Hyperthermophiles. CrenarchaeotaSulfolobales, ThermoprotealesHyperthermal and nonthermal (Ch. 19). – (3) Phylogeny of Eucaryotes: Protozoa, Fungi, Slime Molds, Algae.  (Ch. 20). Ch. 13. 14, 17-20

9. 27-29.  Microbial Ecology

Microbial Habitats and Diversity. – E cological Concepts – Microbial Environments – Biogeochemical cycling. – Roles of microorganisms in ecosystems: functional guilds. – Biofilms, Microbial Mats. – Terrestrial environments. – Aquatic habitats, BOD. – E xtreme environments. – Deep sea hydrothermal vents and seeps. – Biodegradation.  – M icrobial integration with plants and animals. – Global cycling of elements: C, N, P, Fe. – Bioremediation. –  Methods in Microbial Ecology. Culture-dependent methods: Enrichment, Isolation, Stains. – Culture-independent methors. – Genetic stains, group specific probes, FISH, CARD-FISH PCR, DGGE, T-RFLP, ARISA, Microarrays, Philochips. – Metagenomics.  Microbial activities in Nature: Radio- and Stable isotopes. – Microelectrodes, Flow CytometryCh. 23, 24, 22. 


10. 03. Microbial Interaction with Humans

Humans as microbial hosts – Beneficial Microbial Interaction with Humans.Microflora of a healthy body: Skin, oral cavity, gastro-intestinal tracat, respiratory tract, urogenital tract. – Virulence and Pathogenesis – Exposure – Entry and Adherence – Colonization and infection. Invasion and Growth (Infection) – Tissue specificity - Virulence: Exotoxins incl. Enterotoxins – AB Toxins, Diphtheria and Cholera. Tetanus and Botulinum neurotoxins. Endotoxins LPS – Host factors: Age, stress and diet. Compromised host. – Innate Resistance to Infection.. Ch. 27. 

----------------------- EXAM-2: Apr. 05  (Topic 10 not included)

11. 10-12. Immunity and Host Defense

Cells and organs of the Immune system – Innate Immunity: Phagocytosis. – Pathogen-Associated-Molecular-Patterns (PAMP) recognition receptors. – A daptive Immunity. – Antigens and antibodies. – T-Cells and Antigen presentation system. – Major Histocompatibility Complex (MHC). – T-Lymphocyte subset and cell-mediated immunity:  T-cytotoxic and natural killer cells, – T-helper cells, – Macrophage activation, – B-cell activation. – Antibodies and immunity. – Immunoglobulin formation. – Complement system and opsonization. – Inflamation and septic shock. – I mmunization-Vaccination: active and passive immunity. – Hypersensitivity and Autoimmune diseases. – Immune Mechanisms. Ch. 28, 29, 30. 

12. 17-19. Diagnostics Microbiology and Immunology

Pathogen isolation and identification. – Growth-dependent identification – Antibiogram. – Lab safety – Immunodiagnostics – Polyclonal  and monoclonal antibodies. – Serology: Neutralization, Precipitation, Agglutination, Immunofluorescence. – Enzyme-linked Immunoassay EIA (ELISA) – Direct, Indirect, Competitive. – Radioimmunoassay (RIA). – Immunoblot. – Nucleic Acid-based Diagnostic Methods. DNA and RNA probes. - Diagnostic virology. Ch. 31. 

13. 24-26. Epidemiology

Principles of Epidemiology. – Mortality and morbidity – Disease progression – Disease Reservoirs and Epidemics – Zoonosis – Cariers – Infectious Disease Transmission. – Herd immunity. – Current  Epidemics: HIV/AIDS  Pandemic – Hedalthcare-Associated Infections (nosocomial) infections – Epidemiology and public health – Controls  - Immunization – Quarantine and isolation. - Emerging and reemerging diseases. Ch. 32.  


----------------------- EXAM-3: May, 01


------------FINAL EXAM scheduled is TBA


The background color approximates 
that of purple sulfur bacteria


Go to:
Lab schedule 


Powerpoint 1

Powerpoint 2

Powerpoint 3

Powerpoint 4

Powerpoint 5


Updated 01/17/2012