Microbiology 229 Spring 2000
Course Syllabus Prof. Thomas Terry

A. General Information

Welcome to Fundamentals of Microbiology , MCB 229. This course is a comprehensive, one-semester introduction to the world of bacteria and viruses, with a little material on fungi. We will begin our course by looking at the world revealed by microscopy the shapes, sizes, and structures of microbes. We will next examine how microbes grow and how their growth is controlled, both by environmental and human activities. We will then examine microbial physiology the complex chemical pathways by which they obtain matter and energy, and the ways in which they dispose of wastes. We will examine the role of nucleic acids in storing and expressing genetic information, and apply this information to the study of viruses, our information parasites . We will look at some mechanisms that allow genes to move between different microbes, and will examine ideas about how microbes evolved over time into many taxonomically different groups and three domains. We will next examine how microbes interact with their environments and with other organisms in a variety of symbiotic relationships ranging from mutual benefit to parasitism. We will end our semester with a detailed study of the role of microbes as disease agents, including study of some of the specialized virulence systems that allow microbes to survive in the host, the role of host immune systems in restricting microbial growth, and an introduction to epidemiology, the study of disease control and transmission.

We cannot possibly do justice to all topics in microbiology in this short time, so I have had to make choices about what to exclude as well as what to include. We will not have time to cover such important topics as industrial microbiology, genetic engineering, a systematic survey of microbial diversity, clinical immunology, or a thorough study of many microbial diseases.

Microbiology is a laboratory science, and the laboratory is an integral and important part of this course. During the semester, we will be training you in the basic skills needed to work with bacteria: proper use of the microscope, how to prepare stained slides, aseptic technique for transfer and inoculation of bacteria, use of various media to select, isolate, and characterize bacteria. We will challenge you with a number of learning tasks: isolating and identifying unknowns, a scavenger hunt  where you will have to isolate specific organisms from your body or other environmental sources, examination of a variety of food, water, and other environmental samples.

What preparation do you need to take this course? I strongly recommend that you have had at least one prior course in biology, preferably Biology 107 or a comparable course that introduces the structure and function of cells and the genetic code. In addition, you will need a decent background in chemistry, including a semester of organic chemistry, which can be taken concurrently. The machinery of microbes is chemical, and the only way to understand how microbial processes work is to examine some of the details of this machinery. I will regularly use diagrams that show organic molecules, and expect you to understand what I am talking about without my having to go back and explain what these diagrams mean. If you have never looked at an organic structural formula, don't know what valence is, and have no conception of acids and bases (to pick just a few chemical concepts we will use), you should not be taking this course at this time.

B. Course Logistics.

Lectures meet Tues. and Thurs. from 8:00 - 9:20 a.m. in TLS 154. Labs are scheduled for one 2 1/2 hour period per week in TLS 207; you will on occasion be expected to come back a day or two later, when the lab is not in scheduled use, to monitor results and (occasionally) for extra inoculations. Most of these extra visits will be brief, perhaps only five minutes, but there will be times when you will want extra time. I have tried to list these occasions in the laboratory syllabus so that you can plan ahead. Each lab section is limited to 20 students unfortunately, the course is filled to capacity; as a result it is not possible to attend different lab sections unless someone drops and you are able to change sections via the registrar's office.

Course instructor: Prof. Thomas Terry
Office hours: Tues 9:30-10:30; Thurs 9:30-10:30 and 2-3, or by appointment
Phone: 486-4255. If you leave a message, pronounce your name and phone number slowly and clearly! About 10% of student calls are unintelligible and I cannot respond because I don't get your name or you fail to leave a number that I can unscramble.
e-mail terry@uconnvm.uconn.edu (Note: this is the easiest way to reach me).

C. Materials needed. Available at the UConn Coop.

  1. Required Text:
    Microorganisms, 4th Ed., by Prescott, Harley and Klein. Available at UConn Co-op. Used copies should be available. This is an expensive text, but an excellent and comprehensive one. You should consider keeping it as a reference.
  2. Required Text: Fundamentals of Microbiology Laboratory Manual, January 2000 version.
  3. Recommended Supplementary Text: Photographic Atlas for the Microbiology Lab. Morton.
  4. Required Supplies for Laboratory:
    " Wax marking pencil (dark color) or felt-tipped indelible marking pen (not water soluble). Available in supply dept at UConn Coop.
    " Disposable Lab Coat. State and federal regulations make lab coats a requirement when working with certain microorganisms. Bring your coat to the first lab, with your name marked on the coat. Store coats in drawers under your lab bench, or as indicated by lab instructor. Lab coats are assumed to be contaminated and may not to leave the lab after initial use. At the end of the semester, all lab coats will be autoclaved and disposed of.
    " Safety goggles. Available from the Coop (with elastic bands to hold them on); also available from Biology stockroom (TLS 461) in glasses-style (no elastic) at $3.50.
  5. Required: Access to the World Wide Web. I will be posting many class materials on the Web, and expect every student to check the Web site for announcements at least once a week. There will be required quizzes preceding all lectures -- you will have to log on through the WebCT environment to take quizzes and access administrative data such as grades (see separate handout).
  6. Strongly recommended: an e-mail account. I can be reached more easily by e-mail than by any other method, and will reply to any concern or question you raise if you have an e-mail account. Go to the computer center help desk to find out how to obtain and use e-mail (available free to all students).
    Note: when sending me e-mail, you must list MCB 229 + your subject  as the subject.

(1) Subject: MCB 229. I have a question.
(2) Subject: MCB 229. Feedback about the course. And so forth.
All my e-mail is sorted, and your failure to include this subject may cause your message to be delayed or ignored. I receive up to 100 e-mails a day, and there are days when I simply do not have time to go through e-mail in detail, so things may get delayed or lost if they are not clearly identified. I never deal with office matters from home-- if you send e-mail to my home account, it will eventually be forwarded back to my UConn account, and only then will it come to my attention.

D. Reading Assignments, Study Guides, and Quizzes:

Reading assignments in the text are listed on a separate page. Readings and lectures will complement each other I cannot cover every detail in lecture, and will expect you to obtain certain information from reading the text rather than from lecture. Exams will be based on both assigned reading and lecture material. You should plan on reading approximately 20-40 pages in the text per class period. Don't fall behind! Read the assignment before each class, as you will have to take an online quiz prior to each class to demonstrate familiarity with that material (see below). Reading a text is not like reading a novel. Keep a pad of paper next to your text while reading and use it to sketch diagrams, make outlines or concept maps, jot down unfamiliar terms, and make other notes to yourself. Stop frequently to ask yourself What did I just read ? Work with practice questions to see what you don't understand.

I will make study guides available for each reading assignment (i.e., each lecture). Typically these will be handed out at the previous lecture. I will also post the study guides on the class web site as soon as possible. If you miss class, download your copy from the Web -- I do not bring paper copies of previous materials to lecture. Study guides are designed to be used while you read the text, and will focus your attention on what to learn. Quiz questions (see below) will be written as I consult the study guide -- if you can answer the questions on the study guide, you should be well-prepared for each online quiz, and for exams.

There will be a short quiz (10 multiple-choice questions), to be completed in not more than 15 minutes) on each reading assignment. Quizzes will be posted on the course WebCT site (see below). You can use your text during quizzes, but be warned that it you haven't already read the material and worked with the study guide, you will probably run out of time. If you fail to complete the quiz in 15 minutes, it still counts as one of your two possible graded attempts. You will each access WebCT with your own userID and password. In order to receive credit for the quiz, you must complete it by midnight of the day preceding each lecture. For example, the quiz for a Tuesday lecture must be taken by midnight on Monday, and the quiz for a Thursday lecture must be taken by midnight on Wednesday. Quizzes will not be available after these deadlines. You may take each quiz up to two times; only the highest score will count. Each quiz is generated from a database of questions, hopefully more than 10, so there will be some variation from quiz to quiz. There are 26 lectures, so there will be 25 quizzes (assigned reading for the first lecture will be included in quiz 1, which also includes the second lecture. I will drop the lowest three grades (if you miss any quizzes, those are included in the grades dropped). Please don't come begging for excuses or makeups for quizzes that you missed -- the "drop 3 low grades" is meant to include zero marks for all possible reasons for missing a quiz (the computer crashed, I couldn't log on, the lab was full, the power was out, my car wouldn't start, the cat ate my password, I had flu, etc. etc. etc.) Setting the WebCT environment to allow individuals to bypass the deadlines is not technically feasible within the constraints of my time. No quiz makeups or extensions will be given -- take the quizzes on time or suffer the consequences. Individuals who have unusual circumstances (e.g. out with mono for 3 weeks) should see me; under some special circumstances I will prorate quiz grade on fewer than 22 grades.

Why am I doing this? It is inefficient use of my lecture time to attempt to go through all the details of each subject. Some information is easy to acquire even from a cursory reading. Lecture time is much better spent by giving more attention to "problem areas", and a certain amount of group work to help reinforce important concepts. By requiring you to read the assigned reading in advance of each lecture, I am convinced that you will learn more, make better use of lecture time, and achieve better grades. The only way I can think of to encourage you to read lecture material regularly and in timely fashion is to make part of your course grade dependent on your reading, with appropriate quizzes and deadlines.

E. Laboratory:

The separate lab schedule lists exercises to be done. You should come to lab having read the lab exercise beforehand! The lab will generally take 2 to 2 1/2 hours, and you will need to return on some occasions to record observations and/or carry out further inoculations (these dates are noted in the schedule to assist you in planning your time). There is no opportunity to make up labs missed. You should make every effort to attend all labs.

The lab will count for 30% of your course grade. Lab grades will be based on satisfactory completion of exercises, on keeping clear and accurate records, on demonstrated mastery of critical lab skills such as the use of a microscope, pure colony isolations, identification of microorganisms, and ability to correctly interpret diagnostic test results, and on lab quizzes.

F. Grades.

Two-hour exams will be given during scheduled class times; each will cover approximately 1/3 of the course material. The final exam will cover the final third of material.
Best 22 of 25 Quizzes on reading (from WebCT) 25%
Exam #1: Tuesday, Feb. 29 15%
Exam #2: Tuesday, April 11 15%
Final Exam: Saturday, May 13 (time TBA) 15%
Laboratory: 30%
Total: 100%

Exams may include a mixture of different types of questions, such as short-answer, multiple-choice, true-false, and/or short essay. Each exam will include both an individual and a group exam component. The final exam will follow the same format as the first two-hour exams for the first hour; the second hour will require you to write essays as a way of reviewing and bringing together major themes from the course.

G. Class Groups:

Learning improves when students work together in groups. All students will be asked to form a class group of 4 students by the end of the second week of the semester. I prefer that you form groups of your own choosing; if necessary, I will assign you to a group. Group members are asked to sit together in every lecture. Occasionally, groups will be asked to work together during class on a problem designed to reinforce lecture material. In addition, class groups will be allowed to work together at each exam, in the following way. For the first part (40 minutes) of the exam, students will work individually, and turn in individual answer sheets. After that time, students will assemble by groups and go over the exam together, turning in one group answer sheet. No student will lose points if the group score is lower than his/her individual score. If the group score is higher than the best individual score from the group, then each student in the group will earn bonus points (maximum limit 5 points out of 100 added to exam score). This format does not apply to the cumulative portion of the final exam, nor to untimed or make-up exams.

Groups are also encouraged to spend time studying together. You should exchange phone numbers with members of your class group early on, and schedule occasional meetings outside of class to review course material and quiz each other. After the first exam, you will have a chance to join a different group if you are unhappy with your existing group.

H. Students with Language Difficulty or other special needs; extra time on exams

Some of you may want extra time during exams, due perhaps to learning disabilities or language problems. On exam days, I will be in the lecture hall at 7:30 a.m. Any student who wants extra time can the exam as early as 7:30, and in any case you should start by 8 a.m. If English is not your native language, you may bring a translation dictionary. You don't have to have any disability or difficulty to take advantage of this offer, and you can come in any time after 7:30 if you want a little extra time. Once you have begun the exam, I ask that you not leave until the exam is complete, so please use the restrooms before starting.

I. Make-Up Policy:

Makeup exams are available only to students who have a legitimate excuse for missing an exam, such as illness, sanctioned athletic team event out of town, or death in the immediate family. If you know in advance that you must miss an exam, see me in advance and bring documentation to support your anticipated absence. If you miss an exam unexpectedly because of last-minute illness or accident, contact me when you return to campus (or by phone if you will be away for some time) with documentation of your situation.

Makeup exams will be given on the following days for those students who missed the scheduled exam and who have received permission to make up the exam. Room will be announced if you are not sure of location, it will be posted on my office door (TLS 276) on the day of the makeup, as well as posted on the class announcements page. Make-ups may include short-answer, short essay, and/or multiple-choice questions.

Makeup for Exam #1 Monday, March 6, 3 p.m.
Makeup for Exam #2 Monday, April 19, 3 p.m.

J. Extra credit option

Students wishing to make up for poorer than expected exams or quizzes, or to boost scores, can write up to three short essays. Topics on specific microbiological issues will be posted at different stages of the course on the class Web site, with appropriate due dates. You may write up to three short (3 page, double-spaced) essays on suggested topics during the semester, if you meet the appropriate deadlines. Each paper submitted on time will earn up to 1 point added to the course grade, as follows:
" one point (good work, appropriate references),
" 1/2 point (basically acceptable content but marred by mechanical problems such as incorrect spelling or grammar, or lack of clarity in explaining the topic, lack of or inappropriate references)
" 0 point (unacceptable) or plagiarized.
Any evidence of plagiarism will result in zero points for all students involved and denial of any extra credit points otherwise earned. Essays should include at least two citations to primary literature, not textbooks.

K. How to succeed in this course:

In order to succeed in this course, you should plan to attend all lectures, take careful notes, and allow ample time to read and study the assigned material before lecture. You should plan on spending at least two hours of study time for each hour of lecture. If you begin to fall behind, make every effort to catch up quickly; otherwise you may find yourself swamped with too much material to assimilate before an exam.

Some of you may find that attending lectures and reading the text is all the support you need. Others will have problems with some of the material. I offer several forms of support to help you with difficulties you may experience. Different students have different optimum learning stratagems; experiment with the options listed, and find what best helps you.