Instructor: Dr. Michael T. Madigan, Professor

Lecture: 9:00–9:50 a.m., M, W, F Room 450, Life Science II

Office/Office Hours:

ROOM 187 LS II.  Office hours: T/R 2:00–4:00 p.m.

  or by appointment. If I am not in Rm. 187 during my

  office hours, I should be in my laboratory, Rm. 109

  Office phone/fax: 618-453-5130

  E-mail:

(1)            To explore the microbiology of the major groups of prokaryotes that catalyze important biogeochemical transformations in nature

(2)            To contrast the major physiological processes of these organisms and relate them to the ecology of their ecosystems

(3)            To investigate the microbiology of specialized microbial habitats

(4)            To employ bioenergetic principles to predict the ecology of microbial ecosystems

Required Readings: Brock Biology of Microorganisms, 12th edition (2009). Madigan, M.T., J.M. Martinko, P.V. Dunlap, and D.P. Clark. Benjamin Cummings, San Francisco. Available at University, Saluki, and 710 Bookstores.

Enrichment and Reference Reading:  Optional and more detailed coverage of the major groups we will cover in class are available in Morris Library. The major source in this regard is:

The Prokaryotes, 2nd edition (1992). Balows, A., H.G. Trüper, M. Dworkin, W. Harder and K-H. Schleifer (editors). Springer-Verlag, New York.

Readings from The Prokaryotes are listed on page 5 of this syllabus. This source is the most complete compendium on Bacteria and Archaea available. An electronic updated edition is also available and access details will be announced in class. 

A web site for MICR 470 can be found at: www.science.siu. edu/microbiology/micr470. The web site contains lecture outlines and other study aids.

Your grade in MICR 470 is based on three quizzes, two exams, and a final exam. Each quiz is worth 30 points and each exam, 100 points. Your lowest quiz score will be dropped to make the total points for the course 360. Coverage for each quiz will be announced in class at least one period prior to the quiz, and quiz questions will be at the same difficulty level as exam questions. Bonus points may show up on quizzes. Each quiz will be short-answer format; quizzes may also contain some definitions of key terms. Exams will be a mixture of objective (multiple choice/true-false) and essay questions. The final exam will consist of 40 points covering material since the third quiz and 60 points comprehensive and will be entirely objective. NO MAKE-UP QUIZZES OR EXAMS WILL BE GIVEN. Grades will be based on a scale of: 93% or above = A; 81–92% = B; 70–80% = C; 60–69% = D; < 60% = F.  Although I shouldn’t need to remind Jr., Sr., and grads of this, I will anyway: Students who do well in MICR 470 typically have a perfect attendance record, or nearly so.

*Readings from Balows, A., Trüper, H.G., Harder, W., and Schleifer, K-H (eds.).  1992.  The Prokaryotes.  Second edition.  Springer-Verlag, New York.  Available in Morris Library.

It is important in MICR470 for you to be familiar with many common and several specialized microbiological/biochemical terms.  Most of these can be found in the glossary of your textbook.  Some of these, for example, the term acetyl, refer to chemical structures that you should know.  These terms will be used, in some cases quite often, in MICR470 and your familiarity with them and a few core chemical structures will help you get more out of this course.  Many of these terms, e.g. acetyl, amino acid, or carbon dioxide, will be used without explanation if I feel you should already know the term.  Other, more technical and specialized terms, such as anoxygenic or denitrification, will be defined as we go along.  In addition, you may see some of these terms as definition questions on quizzes or exams.  Thus you may wish to write out definitions here for use in your studying.  The words listed below in boldface refer to chemical structures or chemical concepts that you should know by memory.

Acetyl
Acetyl-CoA
Acid
Acidophile
Active transport
Adenosine triphosphate (ATP)
Aerobe
Aerobic respiration
Alcohol
Aldehyde
Algae
Alkaliphile
Amino acid
Anion
Anaerobe
Anoxic
Anoxygenic
Archaea
Autotroph
Bacteria
Bacteriochlorophyll
Bacteriorhodopsin
Barophile
Base
Bicarbonate
Biosynthesis
Buffer
Butyrl
Calvin Cycle
Carbohydrate
Carbon dioxide
Carbonate
Carboxyl
Catabolism
Catalyst
Cation
Cellulose
Cell wall
Chemiosmotic
Chemolithotroph
Chemoorganotroph
Chemotaxis
Chlorophyll
Chlorosome
Chromosome
Coenzyme
Compatible solute
Concentration gradient
Covalent bond
Cytochrome
Cytoplasm
Denaturation
Denitrification
Deoxyribonucleic acid (DNA)
Electron acceptor
Electron donor
Electron transport system
Endergonic
Endospore
Enrichment culture
Enzyme
Equilibrium
Ester
Ethanol
Ether
Ethyl
Eukarya
Eukaryote

Exergonic
Exponential growth
Facultative
Fat
Fatty acid
Fermentation
Ferric Iron (Fe³⁺)
Ferrous Iron (Fe²⁺)
Free energy (G₀^')
GC ratio
Gas vesicle
Generation time
Genotype
Genus
Glucose
Gram-negative
Gram-positive
Heterocyst
Hexose
Homoacetogen
Hybridization
Hydrocarbon
Hydrogen bond
Hydrolysis
Hydrophilic
Hydrophobic
Hydrothermal vent
Inorganic
Ion
Ionic bond
Isomer
Isotope
Lipid
Lipopolysaccharide
Lysis
Macromolecule
Membrane
Mesophile
Messenger RNA (mRNA)
Metabolism
Methane

Methanogen

Methanotroph

Methyl
Methylotroph
Microaerophile
Microenvironment
Micrometer (µm)
Mixotroph
Molecule
Molecular weight
Monosaccharide
Monomer
Morphology
Nicotinamide adenine dinucleotide (NAD⁺ and NADH)
Nitrification
Nucleic acid
Nutrient
Organic
Osmotic pressure
Oxidation
Oxidative phosphorylation
PCR

Peptide
Peptidoglycan
pH
Phenotype
Phospholipid
Phosphorylation
Photosynthesis
Photoautotroph
Photoheterotroph
Photophosphorylation
Phototroph
Phylogeny
Plasmid
Polymer
Polymerase Chain Reaction

Polysaccharide
Polypeptide
Primary production
Prokaryote
Propionyl
Protein
Proton motive force
Psychrophile
Purine
Pyrimidine
Reduction
Reduction potential (E₀^')
Ribose
Ribonucleic acid (RNA)
Ribosome
Ribosomal RNA
RNA polymerase
Rumen
Salt
Sanger (dideoxy) sequencing

Stoichiometry
Solute
Species
Substrate
Sugar
Symbiosis
Syntrophy
Taxonomy
Thermophile
Thiosulfate
Transcription
Translation
Viable
Vitamin

Before the exam

1. Predicting the exam.

Try to identify everything that was emphasized in class.  Indeed, you should be able to predict many of the questions you will face by:  (a) checking the syllabus and doing the required reading before class;  (b) attending class religiously and taking good notes (based on a and b the list of possible questions should be fairly obvious);  (c) noting material that is covered in BOTH lecture and in the text; and (d) brainstorming with other students in MICR 470.

2. Preparing for the exam.

Once you have formulated a list of potential essay questions, prepare a "study sheet" for each question.  To do this, review your lecture notes and textbook highlights.  Make a bullet list of major points that you would use to answer each question and then fill in this general outline with a few specific points that you want to be sure and discuss.

During the exam

1. Read each question quickly and develop a time budget.

For those questions that you feel can be answered quickly, mark these in some way so you can answer them first.  Also, as you look through the questions, list any major points that you want to discuss in a brief outline in the margin of the answer space.

2. Answer the question posed.

Don't get off on tangents.  My goal in writing MICR 470 essay questions is for them to be precisely worded.  You should strive in your answer to be likewise. Thus, you won't receive credit for answering things you haven't been asked (you also don't want to waste time writing something you don't need to).

3. Use the outline to your advantage.

For each question use the list of major points you made earlier and then answer the question.  Before you begin, check the list of points, embellish them if necessary, and rearrange the order if need be.  The best answers to essay questions are ones that employ a series of arguments that flow logically, one from the other.

4. Be direct when you write.

As they say in the newspaper business: write short sentences and short paragraphs.

5. Legibility.

Although MICR 470 is not a course in penmanship, you could easily lose partial credit if I cannot read what you have written. Sloppy handwriting, non-standard abbreviations, multiple cross-outs, and confusing circles and arrows, all make grading difficult.

updated 1/9/09 doj