Microbial Physiology Fall, 2010 MICRO-3445

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1 Microbial Physiology Fall, 2010 MICRO-3445 Objective: This course is designed to provide the student with a foundation of physiology and biochemistry of bacteria, including the growth, division, adaptation, fermentation, energy production and chemotaxis. Laboratory courses will include the hands on experiences on: 1) measuring the growth of bacteria; 2) isolating and quantifying DNA, protein and lipid molecules; 3) beer and yogurt productions, and 4) the assay of bacterial enzymes. Lecture: TR PM (UGLC 220) Lab: Will be informed later Instructor: Dr. Sid Das Office: Biosciences Building ( ) sdas@utep.edu. Office Hours: TEXT: M, W, F: 3-4 PM (or through prior appointment). 1. Microbial Physiology (4 th Edition) Moat, Foster and Spector 2. The Physiology and Biochemistry of Prokaryotes by David White (3 rd Edition (Oxford University Press) 2007 Reference Text: 2) Lehninger s Biochemistry or any Standard Biochemistry Text Book. Examination Procedure There will be three exams and the final (which is must). In addition, there will be classroom presentations and quizzes, which will be counted. Your grade will be distributed as follows: Three Class Exams: 45%. Presentation: 15% Final Exam: 20% Lab Grade: 20% Grand Total: 100%

2 Note: 1) You are strongly encouraged to form groups consisting of three people-this will be helpful in discussing and presenting materials in the class. 2) Try not to miss any exam without proper notification. 3) Final Exam- mandatory (December 7 th, Time: PM) A = B = C = D = F = Below 60 Grading Policy Course Materials 1. Introductory Lectures on Enzyme, Carbohydrates and Lipids (Any standard Biochemistry Textbook: I will follow Lehninger s Biochemistry) Enzymes: I) Introduction II) How Enzymes Work III) Enzyme Kinetics to understand reaction mechanisms IV) Acid-base Catalysis V) Regulatory Enzymes Carbohydrates and Glycobiology: I) Monosaccharides, Disaccahrides and Polysaccahrides II) Glycoconjugates: Proteoglycans, Glycoproteins and Glycolipids III) The Sugar code IV) Carbohydrate Analysis Lipids: I) Fatty acids and triglycerides II) Membrane Lipids III) Lipids as Signals 2 P a g e

3 IV) Lipid Analysis Exam-I 2. Bacterial Cell Surfaces: Structure and Function. (Chapter 7: pp ): Microbial Physiology by Moat, Foster and Spector. I) Cell Structure II) Surface Layers of Bacteria III) Peptidoglycan of Bacterial Cell Walls IV) Peptidoglycan synthesis V) Teichoic Acids & Lipoptiechoic Acids VI) Membranes of Gram Negative Bacteria VII) Lipopolyscacchardies VIII) Lipopolysacchardie Biosynthesis IX) Bacterial Antigen X) Cytoplasmic and Intra cytoplasmic membranes. XI) Capsules XII) Cellular Locomotion XIII) Bacterial Flagella XIV) Chemotaxis XV) Motility Ref: (Chapter 1: 1-52): The Physiology and Biochemistry of Prokaryotes by White 3. Growth and Cell Division (Chapter 2: The Physiology and Biochemistry of Prokaryotes) I) Measurement of Growth II) Growth Physiology III) Adaptive responses to nutrient limitation IV) Diauxic Growth V) Catabolite repressor VI) Septum formation and cell division VII) Proteins required for septum formation and cell division VIII) Growth yields and growth kinetics Exam-2 4. Central Metabolic Pathways (Chapter 8: pp , Microbial Physiology; Chapter 8: The Physiology and Biochemistry of Prokaryotes) I) EMP Pathway and its Enzymes II) Alternate Pathways of Carbohydrate Metabolism III) Ketoglutarate Pathway 3 P a g e

4 IV) Phosphoketolase Pathway V) Pentose Phosphate Cycle VI) Gluconeogenesis VII) TCA Cycle VIII) Glyoxylate Cycle 5. Fermentation Pathways (Chapter-11: pp , Microbial Physiology; Chapter 14, pp , Physiology and Biochemistry of Prokaryotes) I) Fermentation Balances II) Yeast Fermentation III) Lactate Fermentations IV) Butyric Acid and Solvent Production V) Mixed type Fermentation VI) Propionic Acid Fermentation VII) Acetate Production Exam-3 6. Export of Bacterial Proteins and Host-Bacteria Interactions (Chapter-20, , Microbial Physiology by Moat, Foster and Spector) I) Host-parasite Relationships II) Adherence/Colonization III) Virulence IV) Exotoxins V) Quorum Sensing VI) Bacterial Pathogenesis VII) Escherichia coli VIII) Salmonella IX) Listeria monocytogens X) Chlamydia EXAMINATION (FINAL) 4 P a g e

5 The Topic of Presentations Cloning and Sequencing Gene Replacement and Gene Arrays Proteomics-I Mutant Haunts PCR, RT-PCR and Real time PCR Gel Shift and Supershifts Southern, Northern, Western and Southwestern Blots ELISA Assay 2D Gels and LC/MS SDS-PAGE/Western Blot Separation of Lipids by TLC and HPLC Bacterial Expression Systems Eukaryotic Expression Systems BLAST Search ELISA and FACS Confocal Microscopy Or, any selective topic 5 P a g e

6 Microbial Physiology Lab Fall 2010 Instructor: Sid Das Lab Instructors: Mr. Joaquin DeLeon Mr. Jorge Sierra Office Hours: By appointment or through s. Office: Lab: Bioscience 5.200, x6897 The focus of this lab is twofold. First we will use selected protocols to examine the physiology of the cell and the many processes the cell uses to produce energy and the metabolites required for survival. Second we will examine a multitude of techniques, including the principles behind, the uses for, and interpretation of these and other techniques. Understanding this information will be essential to your performance in this class. Your grade will be based on attendance, 6 quizzes, 1 exam, and a final project. It is recommended that you maintain a notebook. However this is for your own study purposes and will not constitute a grade in the class. Lab follow-ups are required and will be performed on the Friday after the lab. The grade in this lab will constitute 20% of your overall grade. The grading policy is as follows: 6 quizzes 20 pts each 120 Points Midterm exam 50 Points Final 50_ Points 220 Points Total There is no textbook or lab manual for the lab. All protocols will be discussed in the lab prior to the lab in which the protocol is performed. It is recommended that you perform all protocols on paper, prior to lab and before attempting the protocol in lab. This will give you an idea of where and what kinds of problems to expect in lab. This is also a good way to learn the protocols and to understand where the theory of these protocols applies. Materials for this lab: Sharpie (Required) Lab Coat (Required) Notebook (Not required but recommended) Lab appropriate clothing is required for this lab. Open toe shoes and shorts are not acceptable and long hair must be tied back. If you are not dressed appropriately, you will be asked to leave. 6 P a g e

7 Be aware that absences will hurt your grade. If you miss a lab, you will not be able to make up any quizzes or assignments you may have missed. If you know you will be missing a lab and need to attend another section that week, please notify me at least 1 week prior to your absence so that I can inform the other AI that you will be attending his/her lab. **This is only tentative and is subject to change. Quizzes, assignments, and lab activities may be moved, cancelled, or added. Lab 1 Growth curves Lab 2 Growth curves cont QUIZ 1 Lab 3 DNA extraction and electrophoresis QUIZ 2 Lab 4 Lipid Extraction Lab 5 Thin Layer Chromatography QUIZ 3 Lab 6 Midterm Lab 7 Fermentation Beer/Yogurt Lab 8 Enzyme Kinetics - Lecture by Das QUIZ 4 Lab 9 Enzyme assay QUIZ 5 Lab 10 Feedback Inhibition Lab 11 Final 7 P a g e