Biology 331 Course Information – Spring 2011
General Microbiology (Writing Intensive, 4 credits)
This document contains a LOT of information, including a study guide and learning outcomes, and
everything related to lab (policies, lab notebook rules). Make sure you read and follow it carefully!
Lecture Meeting Times: MW, 10:00-10:50 a.m.
Laboratory: T AND R, 8-10 a.m.
Instructor: Sarah Boomer, Ph.D.
Office/Hours: 219; 8-8209; office hours will be posted on-line and on my door
Website: www.wou.edu/~boomers/boomer.html (has links to course materials)
This writing intensive biology core course is designed to give you a broad knowledge of microbiology
in the context of the planet, humankind, and general science. Course pre-requisites include 200-level
biology (Bi211-3) and chemistry (Bi221-3). Genetics and Cell Biology are strongly recommended and
if you have not taken them, you may need to do additional background reading from the course text.
Text and Required Course Materials: Brock's Biology of Microorganisms (12th Edition). Each
person will maintain a lab notebook using a graph-ruled composition notebook (~$2.50 at bookstore).
Writing: Informal writing is based on lab notebooks and video summaries. Formal writing is based
on reports that accompany several lab assignments, and essay questions on the final.
Exams: 1 lecture exam and 1 lab exam during term, and 1 final. Owing to pre-professional exam
format (MCAT, DAT, GRE), 40% all exams will be multiple-choice. Missed exams cannot be made-
up without a valid excuse (e.g. university-sanctioned trip, note from doctor).
In-Class Videos: Two or three videos will be shown in class, most from a PBS series on global
health issues called Rx for Survival. Each presentation is accompanied by 10 pts. of short answer
questions due in class. So - don't miss class.
Grade Breakdown and Scale 90-100% (A)
Lecture and Lab Exams: 2 X 100 = 200 pts. 80-89% (B)
Final: 130 pts. 70-79% (C)
Lab Assignments and Pop Quizzes: 277 pts. 60-69% (D)
Video Summaries: 20 or 30 pts. 59% or less = F
Course Syllabus – Spring 2011
This is TENTATIVE Because I May Be Called To Do Federal Grant Review For One Week in May
Topics/Exams Lab (Tuesdays & Thursdays)
3/28 Syllabus and Pre-Test Introduction Set-Up
3/30 Introduction and Diversity Introduction (FINAL)
4/4 Prokaryotic Cell Biology Nitrogen Set-Up
4/6 Unique Chemotrophs TBA
4/11 Phototrophic Bacteria Applied - Soil and Antibacterial Set-Up
4/13 Video - Superbugs Applied - Yogurt & Feces Set-Up - Nitrogen PAPER DUE
4/18 Prokaryotic Central Dogma All Projects Follow-Up
4/20 Microbial Control All Projects Follow-Up (All Gram Staining!)
4/25 Ecology of You - Normal Flora Microbial Evolution and All Projects Follow-Up
4/27 Unit One Exam Food Set-Up, Evolution Follow-Up
5/2 Immunology Food & Evolution (FINAL) - Genome PAPER DUE
5/4 Bacterial Pathogens/Virulence TBA
5/9 Video - Vaccines All Projects Follow-Up, Start Plasmid Lab
5/11 Applied Immunology Plasmid Isolation - Campy PAPER DUE
5/16 Eukaryotic Pathogens Plasmid Fingerprinting
5/18 Virology I Immunodiagnostics and Epidemiology
5/23 Virology II All Projects Follow-Up - Immunology PAPER DUE
5/25 Virology III, Epidemiology No Lab – Academic Showcase
5/30 Memorial Day Holiday Lab Exam – Notebooks Due
6/1 TBA TBA
Final Exam – Monday, June 6 at 10-11:50
Study Guide, Learning Outcomes, Final Overview
Guide to Your Text
Your text is a resource for helping you master course materials and answering questions during lab.
Unless stated, exams are only based on information from my lecture notes and labs. These materials
only sometimes follow the structure of the textbook. Therefore, you will be jumping around a lot in the
book to follow my materials; for this reason, you might want to consult with the index.
Here are my top tips for working with the textbook:
(1) Understand that the following chapters cover diversity for specific groups of PROKARYOTES.
Even though I have not included these in the summary below, you will be consulting each
whenever a specific microbe is named, which is OFTEN!
Chapter 15 = Proteobacteria Phylum Chapter 16 = All Other Bacterial Phyla
Chapter 17 = All Archaea
(2) Chapters 34-37 cover infectious pathogens. Even though I have not included these in the
summary below, you will be consulting each whenever a new pathogen is described!
(3) Some chapters contain material that should be review: Chapter 3 (macromolecules), parts of
Chapters 7 & 9 (molecular biology/gene expression), and Chapter 5 (metabolism). Even though I
have not included these in the summary below, you may need to review them.
Study Tip Throughout Term: for every named GENUS, you need to know which DOMAIN, PHYLUM
and/or GROUP it belongs to - in addition to other specific features or processes highlighted in lecture.
It is therefore wise to develop study note-cards based on each named GENUS.
Unit One Learning Outcomes = Prokaryotic Diversity - Ecology, Metabolism, Genetics, Control
Lecture Chapter Key Course-Specific Learning Outcomes - Things to Know, Be Able To Do
Introduction 1, 2 Ways to categorize and describe microbes, examples thereof
Microbiology applications and landmarks in microbiology history
Prokaryotic Cell 2, 4 Compare/contrast domain membranes, walls, surface & cytoplasmic structures
Biology Environmental bacteria with unique structures and/or lifestyles
Chemotrophy 20-1, Recognize e- donor and acceptor in prokaryotic reactions
23-24 Prokaryotic chemolithotrophic and anaerobic respiration examples
Phototrophy 14, 20, Compare/contrast domain photosynthesis reactions, pigments, membranes
23-24 Earth history landmarks, emphasizing metabolic features
Central Dogma, 8, 11, Compare/contrast domain structures and processes related to central dogma
Antibacterials 27 Antibacterial drugs - history, source, spectrum, target, resistance
Control 27, 36 Physical and chemical factors that affect microbial growth
Pathogens Environmental microbes that evade control, contaminate food
Ecology of You 28, 33 Ecology of normal flora, emphasizing body regions and their control
Nosocomials Nosocomial infections, emphasizing overall trends and examples
Unit Two Learning Outcomes = Medical - Immunology and Pathogens (Prok, Euk, Viral)
Immunology 29 Distinguish nonspecific (1st, 2nd) vs. specific (3rd) defenses, players for each
For specific, understand humoral, cell-mediated, mucosal - all players, all Ab
Know strategies pathogens use to exploit the defenses - examples
Pathogens, 28 Understand steps of bacterial pathogenesis, virulence factors that facilitate
STD's All lecture pathogens (including STD's) that illustrate virulence factors, how
Compare/contrast STD agents - all levels (structure, classification, disease…)
Applied 30 Compare/contrast active and passive immunity - natural and artificial
Immunology Example vaccines & neutralizing Ab treatments - pathogens/virulence factors
Eukaryotic 18 All major eukaryotic classification groups from lecture
Microbes Unique features of fungi and protozoa, example pathogens
Virology I 10, 19 Attributes of viruses - compare/contrast with cells, history/discovery
Viral classification, structures and replication cycle features
Class I viruses, emphasizing structures, replication, host/diseases
Virology II 10, 19 Class IV-VII viruses, emphasizing structures, replication, host/diseases
Compare/contrast viruses in terms of unique evolution, features
Compare/contrast viruses in terms of cancer - cis/trans capabilities
Virology III 33 Compare/contrast antivirals - natural and synthetic drugs
Epidemiology Prions - all levels of understanding (structure, function, disease)
Epidemiology vocabulary, strategies, agencies, top 10 global killers
Lab Learning Outcomes = Culture-Dependent and -Independent Approaches to Microbiology
Basic Techniques 2, 4, 5, Describe media and septic techniques, including all tools and procedures
6, 32 Microbial division and growth curve, counting methods - pros, cons, and math
Nitrogen Cycle, 20-24 Nitrogen cycle chemistry, example genera - their ecology and applications
Enrichments N fixation diversity, how different genera handle the oxygen problem
Describe enrichment strategies, procedures – advanced methods (paper!)
Applied Micro 21, 25- Industrial microbiology, example products, all aspects of fermentation
Gram Positives 26, 27 Compare/contrast Gram Positive phylum subgroups, microbes - all levels
Soil procedures, microbes and useful products (all antibacterial facts/data)
Evolution 8, 11, Compare/contrast prokaryotic recombination - transformation methods
12 Deino/Thermus applications, genomic biology (paper, review genome lecture!)
Food/Fecal 32, 36 Compare/contrast food/feces-associated Proteobacteria subgroups, microbes
Proteobacteria Understand medical ID testing, on-line tools for archiving and analyzing DNA
Compare/contrast diarrhea agents, toxins, disease/pathogenicity
16S Analysis 12, 26 All molecular tools and procedures - especially plasmid isolation flow chart
Studying/Using All vector/plasmic features, how they are used in cloning
Plasmids Principles of gel electrophoresis, fingerprinting, restriction enzymes
Immunology, 29, 30, Immunodiagnostic tests – agglutination, ELISA, fluorescence, gel (paper)
Epidemiology 32 Epidemiology vocabulary and example pathogens from lab (including paper)
The final for this course will include 110 points of typical exam questions that will cover lecture
material from the second half of the class, which - in part - emphasizes the top 10 global infectious
disease killers below. Thus, you should use the following "worksheet" to both organize your notes
and research. In addition, you will also be answering long answer essay questions (20 pts, ~2X10 pt.
questions) about research or review papers I provide about global killers ~2 weeks before final.
Kind of Microbe Disease Information
Agent If Prokaryotic - Wall, Shape? Anything From
If Virus - Envelope? Lecture
If Eukaryotic - Classification?
Hepatitis B Lecture Lecture Research Lecture
N. meningitidis Lecture Lecture Research Lecture
C. tetani Lecture Lecture Research Lecture
B. pertussis Lecture Lecture Research Lecture
Measles Not In Lecture Not In Lecture Research Lecture
Plasmodium Lecture Lecture Research Lecture
M. tuberculosis Lecture Lecture Research Lecture
S. typhi Lecture Lecture Research Lecture
HIV Lecture Lecture Research Lecture
Influenza Lecture Lecture Research Lecture
Lab attendance is mandatory and you CANNOT miss the first week because that is when we go over
and practice key safety activities. There are no opportunities to make up labs because each lab
involves significant preparation, including growing fresh materials overnight. For these and other
safety reasons, access to the lab is only during scheduled lab times.
Lab Assignments and POP Quizzes
This is a writing intensive course, with most writing based on lab. Although some lab activities are
done in pairs, assignments are completed and graded individually. There will be SEVEN 10-point pop
quizzes; 40% of these points are extra credit. Note: if you miss a lab with a quiz, you cannot make
up the quiz because of the extra credit component.
Project Turn-In Materials & Notebook Report Theme
Introduction 25 pts. None
Nitrogen Cycle 25 pts. Advanced Research – 20 pts.
Applied 25 pts. None
Evolution 10 pts. Genome Research – 20 pts.
Food/Feces 25 pts. Advanced Detection – 20 pts.
Plasmid/16S Methods 25 pts. None
Immunology/Epidemiology 20 pts. Advanced Detection – 20 pts.
Lab Notebook Rules
NOTEBOOKS DO NOT LEAVE THE LAB until the final lab (in preparation for your LAB EXAM). ALL
work on the notebooks MUST OCCUR in the lab and I will collect them at the end of every lab and
grade them at random times throughout the term. At the end of the term, you may keep your
notebook if you sign a “notebook honor promise” statement not to share your materials with others.
The goal of a notebook is to keep a legible, organized, detailed account of EVERYTHING you do,
see, or generate. Before the first day of lab, divide your notebook into 7 sections (reflecting projects
above), leaving 10-15 pages between each and making labeled tabs that identify each section above.
Within each project section, DATED entry(ies) must appear every day you work on a given project.
Within each project section, you need to treat entries as linear-temporal journals (i.e. write down
everything you do each day, in dated time-order within each project section). Throughout each lab
handout, there are BOLD instructions for project-specific things I will be looking for. In addition and
for ALL projects, remember to do the following:
(1) Record what you label your plates and tubes so you can identify things later
(2) Record where materials are at end of each day (incubator, refrigerator, discarded, etc.)
(3) For visual tests, describe what you see (i.e. avoid just saying "test was +").
For 4/7 lab projects, you will also write formal reports (see lab handouts for specific instructions).
Each is worth 20 points and will require significant homework in the form of careful reading, thinking,
and computer activities. In fact, you might want to read them ASAP because you can start some of
them earlier than a given lab. These assignments must be typed/word processed with 1.5 spacing
and printed out hard-copy; the length of each report should be 3-5 pages.
Comprehensive Lab Exam
At the end of the term, you will take a comprehensive 100-pt. exam covering ALL lab topics, including
lab lectures, procedures, results, on-your-own problems, and some report topics. Pop quizzes and
on-your-own problems (see lab handouts for specific instructions) are good ways to study for this.
Pathogens and Safety Rules in the Lab
During lab, you will handle some known pathogens (e.g. Staphylococcus, Salmonella, Shigella). You
may also encounter unknown pathogens from personal and grocery samples. The following rules will
be applied at all times to prevent contamination and promote safety. Misconduct or failure to abide by
these rules in lab will result in automatic expulsion and course failure.
1. Bring lab handouts and your individual lab notebook to every lab, along with writing tools,
course text, and a calculator. Label materials carefully and keep organized records.
2. Store all other items in the shelf beneath lab benches - NOT on the floor or in your work
area. Absolutely no drinks or food in lab. No gum-chewing, nail-biting, or pen-nibbling.
3. Wash desktops with 10% bleach at the beginning and end of lab. Wash hands at the
beginning and end of lab, and before/after using the restroom.
4. Follow appropriate sterile technique when handling ALL materials in lab. Handle materials
with care and don't waste anything.
5. Many items in this lab cannot be replaced if you drop, lose, or squander them. If you spill a
live culture, there will not be a back-up available. If you misuse or break expensive
supplies, second copies will not be available and you will lose points.
6. If you spill or break contaminated materials, follow these procedures:
a. If personal injuries occur, stabilize bleeding and clean wound first.
b. Next, disinfect spill by soaking with bleach for at least five minutes.
c. Alert your instructor while spill is disinfecting and she will direct further clean-up
7. Equipment that can be flame/alcohol sterilized at the bench (e.g. loops, forceps, dally rods)
is kept in white trays on your bench after you have appropriately decontaminated them.
8. All other trash goes in the following designated areas: small items go in waste buckets on
benches; large items go on front autoclave cart.
9. Be careful with Bunsen burners. Double-check that they are off as you leave the lab.
Microscopes cost hundreds to repair, thousands to replace; handle and clean microscopes and
prepared slides as directed (if you don’t, you will lose points):
a. Avoiding moving microscopes; if you have to, use both hands, carrying upright and gently
b. Clean oil from lenses with lens paper; clean stage with Kimwipe tissues and cleaner
c. Store microscope covered with lowest power down when finished