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SYLLABUS
MICROBIOLOGY
Biology 342 Spring 2007
Lectures: Monday/Wednesday/Friday 10:30-11:30 Room: 201 Irving 1
Lab: Tuesday 9:45-12:45 (F01) or 14:00-17:00 (F02) Room: 207 Irving
Instructors:
Dr. Patrick Kuss
Email: ffhpk1@uaf.edu
Office phone: 474-2459
Office: 254 Arctic Health
Hours: 12:00-1:00 MW, or by appointment
T.A.s:
Alexis Hansen (fsamh5@uaf.edu)
Prof. Dr. Karsten Hueffer
Email: karsten.hueffer@uaf.edu
Office phone: 474-6313
Office: 302 A Irving 1
Hours: 12:00-1:00 MW, or by appointment
NA
@uaf.edu
Web resources:
Lab Manual:
Bauman, Robert W. (2007) Microbiology. 2nd edition. Pearson/Benjamin
Cummings, San Francisco, USA.
The Microbiology Place (www.microbiologyplace.com)
Microbiology Lab Manual, Spring 2004. Martinson.
Other materials:
Black permanent marker, old shirt/lab coat for lab (recommended).
Text:
Course objectives/goals:
1. To provide students with a foundation in the fundamentals of microbiology
2. To provide students with skills in basic microbiol. lab techniques (aseptic technique,
microscopy, staining, identification, and control/assessment of microbial growth)
Course outline:
Lecture and lab topics are coordinated so that the concepts introduced in lecture are reinforced
through the lab exercises. The lecture portion of the course is divided into 4 main sections:
1. The biology of bacteria:
a. Structure of bacterial cells
b. Microbial nutrition and growth
2. Microbial genetics:
a. Basics of DNA replication, transcription, and translation in prokaryotes
b. Recombinant DNA technology
c. Viruses and prions
3. Controlling microbial growth
4. Microbial diseases:
a. Principles of infectious disease and epidemiology
b. The innate and adaptive immune responses
c. Overview of microbial diseases
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Prerequisites:
Biology 105, 106, and Chem 105 are prerequisites for this course.
Grading:
There are two parts to this course: lecture and lab, worth a total of 900 points. The lecture
portion of the course accounts for 520 points (58%), while the lab portion accounts for 380
points (42%).
Breakdown of assignments:
Lecture
Student project:
Poster/brochure:
Presentation (~5 min):
Weekly journal assignments:
Weekly concept maps:
Problem sets:
Exams:
Final exam:
Lab
Lab exercises/handouts:
Lab practical:
Lab quizzes:
1 @ 15 points
1 @ 15 points
10 @ 1 point each
10 @ 2 points each
3 @ 20 points each
2 @ 100 points each
1 @ 200 points
15 points
15 points
10 points
20 points
60 points
200 points
200 points
varies with exercise 160 points
1 @ 100 points
100 points
12 @ 10 points each 120 points
Explanation of assignments:
Lecture:
1. Student Project: At the beginning of the semester, you will be assigned a disease to
study. Towards the end of the semester, you will turn in either a poster or a brochure
covering certain aspects of your disease (more details later). In addition, you will give a
brief (5 minute) presentation to the class on your disease during the last few lectures of
the semester when we are covering diseases.
2. Weekly journal assignments: To help ensure steady progress on your Disease Project,
weekly journal assignments will be given. Each journal assignment will address one of
the aspects required for your poster/brochure and presentation. Journal assignments will
be due on Monday. Late journals will be docked 50% (0.5 point).
3. Concept maps: Every Monday (except after spring break), you will be given a list of 1020 terms from the material we are covering in lecture that week. You will create a
concept map that relates these terms to each other in some creative way, and provide a
brief, one-paragraph summary of your concept map. The goal here is to help you form
the “Big Picture” in your mind. Note that there are very few wrong ways to do this.
We all think and learn differently. The only unacceptable concept maps would be ones
that consist merely of definitions, or contain large portions of figures/tables from the text.
If you completely misunderstand a term and relate it incorrectly to the other terms, I will
make corrections but will not dock you points unless I feel that you have not made an
honest effort to understand the material and create your map. Please remember that the
maps are not collaborative. In your map, feel free to use flow-charts, arrows, drawings,
etc. Be creative! This is meant to be a learning tool. Concept maps will be due on
Monday the following week. Late concept maps will be docked 50% (1 point).
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4. Problem sets: There will be 3 problem sets given over the course of the semester, worth
20 points each. The problem sets are due ~2 weeks after they are handed out (see lecture
schedule). You may work together on the problems, but each student must turn in their
own answers.
5. Exams: There will be two exams during the semester and one final exam. The final
exam will be split between new material (100 points) and material from the first two
exams (100 points). Please make every attempt to be present for exams. Make-up
exams will consist of all essay questions. If you are going to be absent, you must take
the exam prior to the regular exam time. If you are sick, please contact me as soon as
possible so we can make other arrangements.
Lab:
Lab exercises are an integral part of this course. Missing three labs (unexcused) is
equivalent to dropping the lab portion of the class, and a grade of F will be given. In general,
missed labs cannot be made up due to the extensive amount of prep work that goes into setting
up for the lab. If you are going to miss a lab, please let myself and/or your T.A. know as soon as
possible so that we can attempt to accommodate you. Keep in mind that many of the exercises
are completed over the course of two or more lab periods. Completion of the lab exercises
(recording results and observations), as well as developing good lab techniques are critical to
successful completion of this course. Please come to lab prepared (review the lab exercise(s)
beforehand), and be on time. Short quizzes are given at the beginning of lab. I have tried to
arrange the labs so that they correlate with lecture topics as much as possible (e.g. we will do
experiments on microbial growth at the same time we are learning about it in class).
You are responsible for completing all parts of your lab manual. This includes recording
results and observations, and answering brief questions about your results. Since each lab
exercise is different, the number of points varies for each exercise. Basically, if you do all the
exercises, record your results, and provide thoughtful answers to all questions, you will receive
full credit. Failure to completely answer questions will result in partial credit being given. Your
lab manuals will be due twice during the semester: Tuesday, March 6 and Tuesday, May 1.
When a handout is used for the lab, it is due at the end of the lab period. Handouts will be given
out in class the week before the lab.
Your proficiency in and understanding of general microbiological techniques will be
assessed during the lab practical, given at the end of the semester (May 1). It is important to
thoroughly understand the concepts covered in lab, as well as to be proficient in standard
methods such as pure culture techniques, Gram staining, and microscopy. So as you go through
the lab exercises, take your time and make sure you understand what you are doing. You will
have plenty of opportunities to practice your techniques, as well. Don’t be afraid to ask
questions!
Lecture outlines and exams:
Lecture outlines are provided at the beginning of each lecture. I include a series of
questions on the key points of the lecture. On exams, my questions come from the key points
section of the lecture outlines. This is the best tool for studying. The online quizzes/interactive
learning tools provided by The Microbiology Place may be of use to you, as well, but if you have
limited time, I would focus on the lecture outlines and your notes. Another good study tool is to
review the Summaries and Review Questions at the end of each chapter. I generally do not hold
review sessions. There is ample time during lecture to ask questions and have things clarified. If
you review your lecture outlines, you will be fine.
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Attendance:
It is strongly recommended that you attend lectures every week. I have found that
students who attend class do far better than those who do not. In addition, depending on the
lecture topic, there may be some hands-on learning activities and demonstrations. Remember,
journal assignments and concept maps are due in lecture every Monday. I do not take attendance
as a rule, but I make a point of getting to know each of my students. Attendance will be noted in
lab.
Courtesy issues:
Food: Food and drink are strictly prohibited in lab. Please do not bring food into the lecture, as
it is a distraction to other students. Drinks may be brought in to lecture, but please try to avoid
making a lot of noise.
Cell phones: Cell phones may not be brought into the lab, where they could easily become
contaminated with pathogens and/or chemicals. Please do not bring cell phones into lecture.
This is your time to listen and learn. Few things are more important than that.
Laptop computers: I prefer it if students do not bring laptop computers to class for note taking,
as some students are distracted by the clicking of the keyboard.
Disabilities Services:
The Office of Disability Services insures that UAF students have equal access to campus and
course materials. I will work with the Office of Disabilities Services (Whitman Bldg., room 203,
474-7043) to provide reasonable accommodation to students with documented disabilities.
Academic integrity:
It is assumed that the work you do for this course is your own, and not that of someone else. All
aspects of the UAF Student Code of Conduct apply (UAF catalog 2006-2007
www.uaf.edu/catalog/current/academics/regs3.html). In lab we will sometimes be working with
partners, and it is expected that each partner will contribute equally to the exercise.
Grades: Grades are given as follows:
A
B
C
D
F
90% or higher
80-89%
70-79%
60-69%
<60%
I generally do not curve grades because I do not write my exams based on a curve. I provide
current grade information at regular intervals during the semester (generally every time
something is graded and returned to you).
Extra credit options:
Opportunities for extra credit will likely be available during the course of the semester. These
may include additional questions on exams, a short summary of a seminar on some aspect of
microbiology, and/or a short report to the class on a current event involving some aspect of
microbiology. I will make announcements regarding seminars, but keep in mind that there may
not be any this semester that deal with microbiology.
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Biology 342 Microbiology Spring 2007
Tentative lecture and lab schedule
Instructors: Dr. Patrick Kuss (PK), Prof. Dr. Karsten Hueffer (KH)
Date
Jan 17W
Lecture 1
Jan 19F
Lecture 2
Jan 22M
Lecture 3
Jan 23T
Lab 1
Jan 24W
Lecture 4
Topic
Introduction: history of
microbiology
Introduction (cont.)
Assignment of study topics
Review of chemistry and
macromolecules
Introduction, Lab safety
Microscopy
Structure of prokaryotic
cells
Jan 26F
Lecture 5
Structure of prokaryotic
cells
Jan 29M
Lecture 6
Microbial metabolism:
Basic principles, enzymes
Jan 30T
Lab 2
Jan 31W
Lecture 7
Aseptic technique
Staining
Microbial metabolism:
Carbohydrate catabolism,
lipid and protein catabolism
Microbial metabolism:
electron transport, ATP
production, fermentation,
Microbial nutrition:
environmental requirements,
biofilms, quorum sensing
Microbial ubiquity
Identification of bacteria
Culturing microorganisms,
pure cultures, culture media
Culturing microbes and
measuring microbial growth
Survey of prokaryotes
Feb 2F
Lecture 8
Feb 5M
Lecture 9
Feb 6T
Lab 3
Feb 7W
Lecture 10
Feb 9F
Lecture 11
Feb 12M
Lecture 12
Feb 13T
Lab 4
Feb 14W
Feb 16F
Lecture 13
Pure culture techniques
Bacterial population counts
Exam I
Microbial genetics I:
Replication
Text pages
Chapter 1:
Pp 1-11
Chapter 1:
Pp 11-24
Chapter 2
Assignment(s) due
Exercise 1
Quiz 1
Chapter 3:
Pp 55-67; 88
ff
Chapter 3:
Pp 67-76;
88ff
Chapter 5:
Pp 123-133
Exercise 2+3
Inst.
PK
KH
PK
PK
PK
PK
PK
Concept map 1
Journal assignment 1
Hand out Problem set #1
Quiz 2
Chapter 5:
Pp 133-140,
147-149
Chapter 5:
Pp 142-147,
PK
PK
PK
PK
Chapter 6:
Pp 166-174
Concept map 2
Journal assignment 2
PK
Exercise 4+5
No quiz
PK
Chapter 6:
Pp 174-184
Chapter 6:
Pp 184-192
Chapter 11:
Pp 313-318
Exercise 6+7
Covers
Chapters 1-6
Chapter 7:
Pp 197-205
PK
Problem set #1 due
PK
Concept map 3
Journal assignment 3
Quiz 3
PK
PK
PK
PK
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Date
Feb 19M
Lecture 14
Feb 20T
Lab 5
Feb 21W
Lecture 15
Topic
Microbial genetics II:
transcription and translation
Microbial growth curves
Text pages
Chapter 7:
Pp 205-219
Exercise 8
Microbial genetics III:
control of transcription,
mutations
Microbial genetics IV:
Mutation demo,
Transformation,
transduction, conjugation
Recombinant DNA
technology I
Chapter 7:
Pp 219-227
PK
Chapter 7:
Pp 227-234
PK
Feb 27T
Lab 6
Feb 28W
Lecture 18
Mar 2F
Lecture 19
Mar 5M
Lecture 20
Mar 6T
Lab 7
Bacterial transformation
Handout
Recombinant DNA
technology II
Polar microbiology
Guest: Dr. Derek Mueller
Controlling microbial
growth I
Chemical control of
microbial growth
Chapter 8
Pp. 250-258
www.ipy.org
Mar 7W
Lecture 21
Mar 9F
Lecture 22
Mar 12-16
Mar 19M
Controlling microbial
growth II
Antimicrobial drugs
Chapter 9:
Pp 276-281
Chapter 10:
Pp 287-304
Mar 20T
Lab 8
Mar 21W
Lecture 23
Mar 23F
Lecture 24
Mar 26M
Lecture 25
Mar 27T
Lab 9
Mar 28W
Lecture 26
Mar 30F
Lecture 27
Tobacco mosaic virus lab
Feb 23F
Lecture 16
Feb 26M
Lecture 17
Spring Break
Exam 2
Viruses I
Viruses II
Processes of infection
Flora of the oral and nasal
tract
Epidemiology
Innate immunity
Chapter 8:
Pp 240-250
Chapter 9:
Pp 261-276
Exercise 9
Chapters 711
Handout
Chapter 13
Pp 375-389
Chapter 13
Pp 389-403
Chapter 14
Pp 404-419
Exercise 10
Chapter 14
Pp 419-436
Chapter 15
Pp 437-447
Assignment(s) due
Concept map 4
Journal assignment 4
Quiz 4
Concept map 5
Journal assignment 5
Hand out problem set #2
Quiz 5
Inst.
PK
PK
PK
PK
PK
Concept map 6
Journal assignment 6
Quiz 6
Turn in lab manual for
grading
PK
DM
PK
PK
PK
Problem set #2 due
PK
Concept map 7
Journal assignment 7
No quiz!
PK
KH
KH
KH
Concept map 8
Journal assignment 8
No quiz!
KH
KH
KH
KH
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Date
Apr 2M
Lecture 28
Apr 3T
Lab 10
Apr 4W
Lecture 29
Apr 6F
Lecture 30
Topic
Innate immunity
Apr 9M
Lecture 31
Immunization
Chapter 17
Pp 486-493
Concept map 10
Journal assignment 10
KH
Apr 10T
Lab 11
Ice-nucleating bacteria
Handout
Quiz 8
Turn in lab manual for
final grading
KH
Apr 11W
Lecture 32
Immune testing
Chapter 17
Pp 493-506
Apr 13F
Lecture 33
Apr 16M
Lecture 34
Apr 17T
Lab 12
Apr 18W
Lecture 35
Apr 20F
Lecture 36
Apr 23M
Lecture 37
Apr 24T
Lab 13
Immune system disorders
Chapter 18
Pp 508-516
Chapter 18
Pp 516-528
Handout
Hand out problem set #3
KH
Concept map 11
KH
Quiz 9
KH
Pathogenic gram-positive
cocci and bacilli
Pathogenic gram-negative
cocci and bacilli
Miscellaneous bacterial
infections
Synthetic epidemic
Disease tracking using
ELISA
Parasitic protozoa,
helminthes + arthropod
vectors
Pathogenic DNA viruses
Chapter 19
Poster/brochure due for all
Student presentations
Student presentations
KH
Pathogenic RNA viruses
Apr 25W
Lecture 38
Apr 27F
Lecture 39
Apr 30M
Lecture 40
May 1T
Lab 14
May 2W
Lecture 41
May 4F
Flora of the GI tract
Specific immune response
Specific immune response
Immune system disorders
Synthetic blood typing
Text pages
Chapter 15
Pp 445-460
Exercise 11
Assignment(s) due
Concept map 9
Journal assignment 9
Quiz 7
Chapter 16
Pp 462-472
Chapter 16
Pp 472-484
Chapter 20
Chapter 21
Inst.
KH
KH
KH
KH
KH
KH
Concept map 12
Student presentations
Quiz 10
KH
Chapter 23
Problem set #3 due
Student presentations
KH
Chapter 24
Student presentations
KH
Chapter 25
Student presentations
KH
Handout
KH
Lab practical exam
KH
Topics in applied and
Chapter 26
environmental microbiology
No class
KH
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Date
May 9W
Topic
Final exam
Text pages
1st half: Ch.
13-18, plus
diseases
2nd half:
material from
first two
exams
Assignment(s) due
10:15-12:15
Inst.
KH