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Micro 161 - Microbial PhysiologySyllabusSpring 2002 Instructor: Dr. Alice D. Wright Office Number & Hours: Wednesday 1:00 to 3:00, Thursday 10 to noon, and by appointment Email: awright@csufresno.edu Telephone: 559 - 278-7692 Course website: http://zimmer.csufresno.edu/~awright/micro161.htm
Introduction and Course DescriptionMicrobial physiology studies the structure, function, energy metabolism, growth and regulatory mechanisms of microorganisms. We will look at microorganisms as models for metabolic processes common to all living things and emphasize the incredible metabolic diversity exhibited by microorganisms in widely diverse environments. We will examine reaction thermodynamics, reaction catalysis, metabolic pathways and their regulation, and regulatory networks that support cellular survival and growth. Studies will lead us to develop a concept of integrative rules governing biological systems leading to the survival and growth of those cells. This course is for students who are interested in microbiology and desire experience and knowledge in microbial physiology, microbial cell biology and the techniques used to study microbial physiology. This course will satisfy Biology requirements for graduation in Organismic and General Biology Option in category A.4, Ecology Option in category B, Molecular, Cellular, and Developmental (Option C), and Physiology and Anatomy (Option A2). Microbial Physiology (Micro161) is a four-credit course consisting of Lecture on Tuesdays and Thursdays from 1:00 to 1:50 meeting in Room S226 Lab on Tuesdays and Thursdays from 2:00 to 4:50 meeting in Room S226 The lab and lecture schedules are flexible to accommodate the lab exercises. Some labs require more than three hours. Other labs have a long incubation period and I will lecture during the incubation. A few laboratory exercises will regularly require time outside of the scheduled three-hour lab period.
Course GoalsGoals of the course are for each student to:
PrerequisitesPrerequisites for this course are introductory microbiology (Micro140) and organic chemistry (a prerequisite for Micro 140). This is an advanced course for upper level undergraduate students in the biological and chemical sciences. A comprehensive background in basic biology and chemistry is necessary. The following are some of the concepts and techniques that students are expected to know. If some of these concepts are not clear or are new to you, please let me know and I will provide additional reading material for you. Students should understand sterile technique, sterilization procedures, how to work safely in the laboratory, how to work with microorganisms, and how to use basic lab equipment, including use of the spectrophotometer, vortex, pH meter, and analytical balance. Students are expected to have a basic understanding of cell structure and function, central metabolic pathways, transcription, and translation. We will review these topics in the first few lectures students needing a more in depth review should see Dr. Wright.
What You Will Need to Purchase for this CourseText book: The Physiology and Biochemistry of Prokaryotes, by David White; Oxford University Press Students are required to have email access and to have Internet access. Instructions for the laboratory exercises will be available on the class website before the lab exercise. Students are required to access information for lab and for assignments from the web ahead of scheduled periods. The University provides free email accounts to all students. Internet access is also available for $9.95 per month. Students may sign up for email or for Internet access through CVIP at Barstow and Cedar or in the University Student Union. Students should bring the following laboratory supplies to each lab period: 2 ml and 10 ml Pipette aids Sharpie marking pen, blue or black Lab notebook Lab coat
GradingTotal 1000 points Grade distribution, 900 - 1000 A, 800 - 899 B, 700 - 799 C, 600 - 699 D. 450 exams - see above section for description of examinations 150 exam 1 150 exam 2 150 final 25 for mini report 375 Lab Attendance, safety, and good manners required 200 Lab notebook including answers to lab related problems, a description of what is required in the lab notebook is provided below. 100 Lab quizzes 75 Participation 150 2,4-D paper Attendance and participation in the laboratory exercises is required and points will be lost for unexcused absences. Repeated absences will lower the course grade. No make up experiments will be scheduled and if you miss an experiment, the lab report or lab book entries should be written with a classmate's data (clearly indicate the source of the data). Students are required to follow safety rules. Students should come prepared to begin the laboratory exercise by taking the on-line quiz for that lab on the course website and by briefly writing the purpose or objective of the lab exercise and the steps for that exercise in their lab notebook. The instructor will periodically check that the student before class completes this. Points will be lost if the student is not prepared. Chronically unprepared students may be asked to leave the lab section and not return until they are prepared. Some lab exercises will require the entire lab period and students must be prepared in order to complete the lab on time. The instructor will decide participation grades. In the laboratory this is evaluated on whether or not the individual shows up on time, leaves before the other members of his group have completed the lab work, takes part in the lab work, cleans up after lab, and takes part in their assigned lab duties outside of the scheduled lab periods. Sometimes the instructor will ask questions of specific class members (all students will be asked a questions at different times). Participation grades are not determined by the student being able to provide the correct answer to a question (mistakes are part of learning) but are determined if the student is prepared and willing to intelligently discuss a question or subject. Participation points may be lost in lecture for disruptive or distracting behavior. The instructions for each laboratory will be published on the course website. Most of the lab exercises will have a short quiz associated with it. The quiz is designed to ensure that the students are prepared for the lab. Students are required to take the quiz by 10:00 pm the evening before the particular lab starts. No credit will be given after the lab period.
Examinations and Major AssignmentsThere will be three examinations, including the final. The exam dates are listed on the class schedule. There will not be a comprehensive section on the final examination. Examinations will consist of definitions, problem solving, a take home component, and short essay. Students will be given a choice of short essay questions (e.g. pick two out of three questions to answer). Approximately 50% of the examination questions will require students to use the knowledge they have learned in different ways than it was presented in class. More than memorization of the material is required, students are expected to understand the material and be able to discuss it and use it. The examinations will cover material presented in lab, theory and science behind lab exercises, material presented in lecture, material on the course website, material passed out in class, and assigned sections of the text. The exact text chapters or pages covered may be different from those listed in the syllabus - these changes will be announced in class. If you are absent, please get the announcements from your fellow students. Make up examinations will be allowed for serious and compelling reasons. If the student is ill, they should provide a written physician's excuse from class. Students are expected to contact the instructor as soon as possible if they miss an exam. Make up exams will be 100% essay and may be completely different from the exam given in the regularly scheduled period. Written assignments for this course include a lab notebook, quizzes or questions that are to be answered before each lab (on the course website), and a paper on the 2,4-D studies performed in the lab. Presentations include a mini presentation on an assigned pathway or chemical reaction. A paper on a specific microbial physiology application or a presentation on a specific microbial physiology application may be done for extra credit. If you choose to do the presentation, you will need to turn in an abstract of your paper and references for the presentation. Instructions for the 2,4-D paper and for the microbial physiology presentation are available on the course website. Please see the instructions for the lab notebook provided below. There will be one extensive written report required. This report will cover the experiments performed on the 2,4-D degrading organisms that we isolate and characterize in class. This report will be written as a paper to be published in the prestigious journal Applied and Environmental Microbiology. Students will follow the instructions to authors provided by the American society for Microbiology, the publisher of the journal, for writing their reports. There will be a field trip. Tentative date for the trip is 4/12/2001 during scheduled class time (lecture and lab). Though students are not required to write a report about the trip, the trip will be discussed in lecture and students are expected to take active part in the discussion as part of their participation grade.
Laboratory Note BookEach student must prepare a lab notebook. For each laboratory activity or experiment, there should be a report in you notebook. Lab notebook grading is rigorous. Someone should be able to repeat your experiment and obtain similar results from the information provided in your notebook and material that you reference in you notebook. Lab notebooks will be collected and graded three times on 2/15/2001, 3/29/2001, and at the time of the final exam. There may be questions for you to answer about a given lab exercise in addition to the routine components of the lab notebook for that lab. These questions will be provided with the laboratory protocol on the course website. You need to come prepared to go straight to work in the lab. This is an upper division course and instructor provided lab introductions will be kept to a minimum. Students should read the material for the lab exercise before lab (it will be available on the course website). Prepare for each laboratory experiment before coming to class by completing the introduction, preparing an outline of the procedures, taking the on-line quiz, and preparing charts and tables for recording data. Points will be lost for coming to lab unprepared. Students should ask questions before starting protocols that they do not understand. Most lab experiments will have a quiz associated with them. This quiz must be taken before coming to lab - by 10 pm the night before the lab. The quiz is an important part of preparation for the lab period. Students who fail to take the quizzes or are chronically unprepared for lab will not be allowed to participate in lab and will receive a zero for that day. The lab manual instructions are not always explicit and your work will go more smoothly if you detail the protocols before class. Enter observations and the collected data in your lab books during the lab period. You should complete the calculations, data analysis, and the discussion parts of the lab notebook within one-week after the completion of the experiment.
Each lab report in your notebook should have six sections -
Tables and Figures
Subject to ChangeThis syllabus and schedule are subject to change. If you are absent from class, it is your responsibility to check on announcements made while you were absent.
Course PoliciesThis course requires a high degree of collaboration between students to achieve the course goals. Examinations require that each student work independently. Students must work in groups in the laboratory exercises. Though the work in lab is performed in groups, each individual is required to complete a lab note book about each lab exercise. Some lab exercises include questions or problems and these may be worked on in groups, however each individual must write their own answer in their own lab notebook.
Safety issues NO FOOD OR DRINKS ARE ALLOWED IN THE LABORATORY AT ANY TIME. The experiments that you will be doing may involve the use of toxic chemicals and bacteria that are opportunistic pathogens. Other safety concerns include the use of electrical equipment. I will discuss safety rules during the first lab period. Specific safety concerns for individual lab periods will be discussed before that laboratory session. Students are responsible for knowing the safety rules and following them. No food or drinks in the laboratory at any time. Students must wear closed shoes and lab-coats. Personal belongings that are not needed for the lab period should be placed apart from your work area. This avoids accidental contamination and provides you with more workspace. It is essential that you properly label all samples and solutions. Samples and cultures should be labeled with your name, course, date, and contents. Any solution or buffer made should be clearly labeled with identification of the chemicals, date, name, and course. All labels must be removed from glassware that is to be washed and glass ware that is to be washed should be put ion the designated cart.
University PoliciesBelow is a short description of university policies. For a more detailed description, please the schedule of classes or the university catalog. Cheating and Plagiarism: "Cheating is the actual or attempted practice of fraudulent or deceptive acts for the purpose of improving one's grade or obtaining course credit; such acts also include assisting another student to do so. Plagiarism is a specific form of cheating which consists of the misuse of the published and/or unpublished works of others by misrepresenting the material (i.e., their intellectual property) so used as one's own work." Penalties for cheating and plagiarism range from a 0 or F on a particular assignment, through an F for the course, to expulsion from the university. Computers: "At California State University, Fresno, computers and communications links to remote resources are recognized as being integral to the education and research experience. Every student is required to have his/her own computer or have other personal access to a workstation (including a modem and a printer) with all the recommended software. In the curriculum and class assignments, students are presumed to have 24-hour access to a computer workstation and the necessary communication links to the University’s information resources." Disruptive Classroom Behavior: " It is essential to this learning environment that respect for the rights of others seeking to learn, respect for the professionalism of the instructor, and the general goals of academic freedom are maintained. Student conduct which disrupts the learning process shall not be tolerated and may lead to disciplinary action and/or removal from class." Students with Disabilities: Upon identifying themselves to the instructor and the university, students with disabilities will receive reasonable accommodation for learning and evaluation.
Kurt, Matt, and Dr. Wright in Micro 161 lab making beer.
Micro 161 - ScheduleSpring 2002
Chapters shown are in The Physiology and Biochemistry of Prokaryotes, by David White; Oxford University Press. This schedule is subject to change, changes are announced in class. Presented in italics is one possible sequence for the 2,4-D experiments. Students will receive further advice on organizing the experiments in class. Suggested problems for each chapter will be announced in class.
Micro 161 - Lab Procedures
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