DEPARTMENT OF BIOLOGY AND CHEMISTRY
APU MISSION STATEMENT:
Mission and Purpose Statement: Azusa Pacific University exists as an evangelical; Christian community of discipleship and scholarship to advance the work of God in the world through liberal arts and professional programs of higher education that encourage students to develop a Christian perspective on truth.
DEPARTMENT MISSION STATEMENT:
The Department of Biology and chemistry exists to serve God through the integration of a Christian perspective into the disciplines of biology and chemistry and the preparation of Christian men and women to assume leadership roles in these sciences.
COURSE: BIOL-220 General Microbiology
PROFESSOR: Dr. Scott S. Kinnes
Office: W-08 Ext. 3362
Real Office Hours: Tues. 8:30 am-9:30am/Thurs. 2:00pm-3:00pm
Virtual Office Hours: TBA
Other Office Hours: By appointment
A study of the fundamental principles and techniques of microbiology through lecture and laboratory experience. Prerequisite: Chem 111 or Chem 201
To develop an understanding of microorganisms and their impact on human life while gaining expertise in practical microbiological techniques.
Text: Microbiology: Principles and Applications; J. Black,
1999; Prentice Hall
Manual: Laoratory Exercises in Microbiology; Harley and
Prescott, 1999; WCB/McGraw-Hill
SUGGESTED READING: Study Guide to accompany text; Matthai and Berg
SUPPLEMENTAL READING: See supplemental reading list on website:
'A-' = 91.9-90
'B+' = 89.9-88
'B' = 87.9-82
'B-' = 81.9-80
'C+' = 79.9-78
'C' = 77.9-72
'C-' = 71.9-70
` 'D+' = 69.9-68
'D' = 67.9-62
'D-' = 61.9-60
'F' = 59.9-0
Graded Material: 40% 4 lecture tests
15% Comprehensive Lecture Final
18% 3 lab practicals
10% Unknown with chart & key
5% Lab preparation
NOTE: No student will receive a "C" or better course grade without achieving at
least a 70% average on the tests, final and lab practicals.
Papers, unknown, etc. cannot increase an "exam" average of less than 70%.
See "COURSE PHILOSOPHY" for other requirements.
This course is designed to teach you several things. In no particular order they are: biology, how to survive life after APU, and how to integrate your Christian faith with virtually everything you do. Granted, that may seem like a big statement, so let me explain what I mean.
MICROBIOLOGY: Hopefully, since this is a course entitled "General Microbiology" you will learn something about that subject through taking this course! This will be done through the lectures, the labs, the quizzes and exams and the papers. I assure you that everything we cover will be of value to you and you can verify this with some of my previous students.
This aspect of the course is to be a two-way street and will require work on your part that goes beyond the tests and papers. You will be expected to read the material prior to lecture or lab and to review those sections which you still do not understand after class. I stand ready, willing and able to help you through any difficulties that you may encounter but only after you have at least made an effort to understand it on your own.
LIFE AFTER APU: More importantly, perhaps, this course, like college in general, is designed to teach you how to survive after college. This includes life in graduate school, whatever job you may get and life in general.
1. Tests: will always include at least one essay question in which you will be required to put down in correct form a paragraph that will demonstrate your knowledge of the subject under discussion. If you omit important information or do not put the answer down in an essay format, you will lose points. Often, however, the questions will be short answers (usually lists of some type, often with short elaborations) or diagrams of something we have discussed and there will always be a vocabulary question with a list of important words for which you must furnish a short sentence type answer that completely defines the words as we discussed them. Scantrons are required for multiple choice matching, etc.
2. Attendance: The first three lecture absences will be ignored. After that, however, each absence will lower your final grade by four points so that an extra three absences will lower your grade one full letter. In lab, any unexcused absence will result in a drop of 10 points in your final lab grade. You are also responsible for attending the entire lab so do not make plans to leave early.
The lab component is an integral portion of this science course experience and the nature general studies requirement. Therefore any student missing two labs for any reason, excused or will automatically receive an "F" in the course.
It is your responsibility to explain your absences and to obtain all information presented during your absence. Excused absences include illnesses verified by a doctor's note, occasional absence due to extra-curricular activities and a few others as determined by me. An attendance sheet will be passed around during class for you to sign your name if you are present. Anyone caught signing another person's name will receive an "F" for the course.
3. Tardies: Three tardies will constitute an unexcused absence. If you are tardy be sure to see me after class to be sure that you are not counted absent. Failure to do so by the end of the period will result in an unexcused absence!!
4. Make-up Exams: Make-up exams will be given only in very special circumstances such as illness, verified by a doctor. No early tests will be given. All make-up tests will be given at the end of the semester on the last Monday of the week prior to finals. It is your responsibility to make arrangements with me to take the test on that day. If you fail to do so, you will get a zero for that grade. No early tests will be given.
5. Late Papers, etc.: NO late papers, projects, etc. will be accepted. The material is due during that day's lecture or lab period, depending on what it relates to, and not just prior to midnight of that day! No early presentations will be allowed.
6. Timed Tests: You will have a certain amount of time to take each test and at the end of that time all papers will be collected. It is, therefore, very important that you are not late on test days. If you have a disability of some type that prevents you from handling material at a normal rate, then please see me so that special arrangements can be made.
7. Cheating: If you are caught cheating on a test/paper, you will receive a zero for that test/paper. If you are caught cheating on a second test/paper, you will receive an "F" in the course. All cases of cheating will be reported to the Dean of Students. If you are suspected of cheating, I reserve the right to have you take another test on that material. If you are in doubt of what constitutes cheating, please refer to the University's Student Handbook.
8. Disability Statement: Any student in this course who has a disability that might prevent him or her from fully demonstrating his or her abilities should meet with an advisor in the Learning Enrichment center as soon as possible to initiate disability verification and discuss accommodations that may be necessary to ensure your full participation in the successful completion of course requirements.
9. Learning Enrichment Center: In an effort to assist students having difficulty in classes, the University has established an excellent Learning Enrichment Center which has become a model for Southern California schools. It is available to assist you with general and specific study programs. Unfortunately, very few students who need the help make the effort to get the help that could very well enable them to pass a course. Therefore, if any student getting a "D" or "F" on a lecture test in this class spends four hours in either group or individual tutoring sessions and their next test grade improves, the original grade will be raised by half the difference between the two grades or 5 points, whichever is higher. The LEC's records will be the only ones accepted as proof of attendance of these sessions.
FAITH AND LIFE: Finally, both by my example and the content of the course, I would like to help you learn that all aspects of your life can and must be brought under the Lordship of Jesus Christ. Too often we relegate God to those aspects of our lives that seem to have some obvious relation to Him, i.e., church activities, religion courses, etc. However, it is very important that God be involved and considered in all that you are involved in. Currently the Lord has called each of you to be students in this course and that must be your primary task over the next few weeks. God has also called you to be the best students you can possibly be and that means putting a lot of energy and effort into this course. I will attempt to teach you how God can be relevant to something that might seem as "unChristian" as microbiology throughout the course even though the author of the texts we'll be using is a strict evolutionist. You, however, must also do your part in being a responsible Christian student no matter how little you want to be taking this course!
TENTATIVE LECTURE SCHEDULE
DATE DAY TOPIC CHAPTER
Sept. 06 W Course Introduction Review 2
08 F History 1
11 M Micro Intro 9
13 W Prokaryotic Anatomy 4
15 F Metabolism 5 (knowledge of Ch. 2 assumed)
18 M Metabolism 5
20 W Metabolism 5
22 F Microbial Growth 6
25 M Test 1
27 W Microbial Growth 6
29 F Microbial Growth 6
Oct. 02 M Controls 12, 13,14
04 W Genetics 7
06 F Genetics 8
09 M Synbiosis 14
11 W Normal Flora 14
13 F Epidemiology 15
16 M Test 2
18 W Infections 14
20 F Vacation Day
23 M Bacteria 9
25 W Bacterial Diseases 19-24
27 F Fungi 11. 19-24
30 M Protozoans 11; 19-24
Nov. 01 W Helminthes 11: 19-24
03 F Test 3
06 M Viruses 10
08 W Viral Diseases 19-24
10 F Non-Specific Defenses 16
LAST DAY TO WITHDRAW FROM CLASS
13 M Immunology 17
15 W Immunology 17
17 F Immunology 17
20 M Immune Disorders 18
22 W Immune Disorders 18
24 F THANKSGIVING VACATION
27 M Test 4
29 W Environmental Micro. 25
Dec. 01 F Environmental Micro 25
04 M Food Microbiology 26
06 W Dairy Microbiology 26
08 F Water Microbiology 25
FINAL EXAM: Wed., Dec. 13, 1:00 PM to 3:00 PM
T/TH W/F Topic Lab Number
Sept. 7 8 No Lab, Review Manual pgs. 1-9
12 13 Culture Prep 14
14 15 Basic Techniques 15, 17, 18, 19
19 20 Staining 8, 9
21 22 Environmental Effects 42, 43, 44
26 27 Environmental Effects 20, 46
28 29 Chemical Control 47, 48
Oct. 3 4 Unknown Intro. 40, 41
5 6 Lab Practical
10 11 Unknowns 22, 24 - 37
12 13 Unknowns 22, 24-37
17 18 Medical Micro 65, 38, 39
19 20 Vacation Day No Lab
24 25 Staphyloccus 66
26 27 Streptococcus 67, 68
31 Nov. 1 Fungi 73, 74
2 3 Protozoans Handout
7 8 Multicellulars Handout
9 10 Lab Practical 2 (not including multicellulars)
14 15 Viruses Lab Kit
16 17 Immunology 60, 61, 64
21 22 Oil, N Cycle Oil kit, 76
23 24 Thanksgiving Break No Lab
28 29 Air and Water 51, 52
30 Dec. 1 Food and Dairy 53, 54, 55
5 6 Presentations
7 8 Lab Practical 3 (including multicellulars)
1. No food or drinks in the lab.
2. No bare feet.
3. Label all test tubes, petri dishes, etc. with the following information
Your name Media
a. Use white tape and ball point pen on glass, wax pencil on plastic.
b. Remove all labels when finished.
4. Place all glassware, cultures, pipettes, etc. in the appropriate area for
autoclaving. Dispose of nothing into the lab trash cans except regular
5. No horseplay in lab.
6. Keep desk top clean of all extra material.
7. Wash down desktop with 10% Clorox before and after lab.
8. Wash hands after lab.
9. Report any reagent or culture spills to me immediately.
10. Use test tube holders, tongs or asbestos gloves to handle hot glassware.
Note: Hot glass looks just like cold glass.
11. Wash out your table cloth thoroughly after lab.
12. Wear the lab coat provided at all times.
13. All long hair must be worn back in a manner to prevent contamination, etc.
14. Be sure that all cuts are bandaged or covered by gloves.
15. Females must wear gloves while performing any staining procedure.
16. Read labs before coming to class
17. Take notes, do diagrams and record dates, times, media, organisms,
incubation temps, etc.
18. Keep track of the various lab experiments.
19. Students may be present in the lab without the instructor's
presence only if:
a. they are with another person
b. they are not involved in any potentially dangerous activities-
for example: flaming, inoculating, staining, etc.
c. they are doing slide viewing, culture checking, Bergey's reading, etc..
Failure to abide by these rules and regulations may result in your dismissal from the class!!
1. In order to give you hands-on experience in basic lab techniques and lab instruction, 5%
of your grade will be based upon a lab preparation you will do.
2. For each prep you are responsible for:
a. determining what must be done for each experiment;
b. locating the materials required;
c. preparing the media, gathering glassware, special chemicals, etc.;
3. Grades will be determined by the quality, completeness and timeliness of the preparations.
4. An attempt will be made to assign experiments involving equal work to each
student. As some experiments are more involved than others, some people may work on several experiments while others may only work on only one.
5. Throughout your preparations you will be assisted by the Microbiology lab assistant.
However, it is always your responsibility to arrange for help and to arrange your
schedule to their's. Failure to do so is not excuse for incomplete or tardy preps. Please
note that the lab techs are not your servants. You are to do the work, collect the supplies,
and clean up.
a. You must see me before meeting with the lab TA to prepare your
material or the lab TA will not allow you to complete your prep and you will receive a zero.
b. You must arrange for T.A. assistance one week prior to the time you meet to work on your preparation. Failure to do so will result in the lab tech doing your preparation and your receiving a zero.
c. You must have the prep done at least two days before the first lab using that material meets.
1. 10% of your grade will be based upon your ability to identify an unknown bacterium correctly, using techniques explained in class.
2. As part of this lab experience you must develop, and turn in, a chart of
identifying characteristics for each of the microorganisms listed below.
3. You must then organize this information into a dichotomous key which would
allow someone else to identify an unknown microorganism using the key and
the test alone. These may be done with only minimal assistance from others
but do not copy anybody else's key or chart.
4. Grading will be done on a minimal basis for the chart and key (5% each) while your ability to identify the unknown on your first try will constitute the majority of the
grade. Each unsuccessful attempt to identify the microorganism will lower your grade 10%.
5. Due dates: Chart and Key Oct. 17, 18
Final Unknown ID Oct. 24, 25
1. 12% of your grade will be based upon your writing and presenting a 2-3 page paper on a
disease of your choice.
2. Papers are to be double-spaced and typed by the student on a computer. Students must be prepared to turn in a disk with the paper on it.
3. Students are to select a disease and have it approved by me. No duplicates will be allowed and they will be assigned on a first come, first serve basis. Only diseases due to microorganisms will be accepted, and once you have made your choice, no changes will be allowed. Therefore, choose wisely and thoughtfully.
4. Papers are to cover the following:
Historical Background Treatment
Causal Organism Prevention
Transmission Tie-in to class
Life/Cycle Progression Bibliography (not counted in page count)
(Do not break paper into these sections; just cover them all).
5. 10% will be based on college level presentation of paper under the following formula:
10 pts. each for spelling, glammar, references & bibliography, and
for covering the above points.
30 pts. for content
5 pts. will be subtracted for eact page, or part of a page, over or under the length requirement.
2% will be based on a 5-10 minute oral presentation graded by the attached sheet.
6. Due Dates:
Disease Selection: September 22
Paper Due Date: November 17
Oral Presentation: December 5, 6
ORAL PRESENTATION EVALUATION
SPEAKER ________________________ DATE __________________
TOPIC __________________________ GRADE _________________
POINTS POSSIBLE POINTS EARNED
A. Introduction (Preview) 5 ______________
B. Body 10 ______________
C. Conclusion (Review) 5 ______________
D. Logical development 5 ______________
E. Clarity 5 ______________
F. Apparent knowledge/
understanding of topic 5 ______________
G. Length (Time: _______) 10 ______________
H. Ability to answer questions 5 ______________
A. Posture/Poise 5 ______________
B. Use of notes not obvious 5 ______________
C. Eye contact with audience 5 ______________
D. Use of fillers (ahas, ums, etc.) 5 ______________
III. VISUAL AIDS
Type(s): Slides, overheads, whilteboard, PowerPoint, handouts, other (Circle ones used)
A. Visual clarity 5 ______________
B. Supports presentation 5 ______________
C. Relevance 5 ______________
D. Evidence of preparation 5 ______________
A Originality/Style 5 ______________
B. Overall impact 5 ______________
TOTAL 100 ______________
NOTE TO COMMENTORS: Please evaluate the presenter on each of the above areas according to
to how well they match the optimum in each category (points possible).
How to see them
Where they came from
What caused diseases
life from life
Berkeley and Phytophthora infestans
Koch and Bacillus anthracis
Isolate, culture, identify
Infect healthy host, it gets sick
Reisolate, reculture, reidentify
Where in prokaryotes?
Proteins: see Genetics section
see Genetics section
Carbohydrates and fats
Carbohydrates and amino acids
Function of cell wall
Gram positive vs. Gram negative
Comparison with eukaryotic flagellum
Growth in multicellular organisms
Growth in unicellular organisms
Limits to Growth:
Growth factor analogs
Disinfectants and Antiseptics
Antimetabolites/ Growth Factor Analogs
Prokaryotic vs. Eukaryotic
Codon/Amino Acid Key
CHANGING THE GENOME
Eukaryotes vs. Prokaryotes
MUTATIONS CHANGING THE GENOME
Wild type vs. Mutant
Mutagenesis vs. Carcinogenesis
RECOMBINATIONS CHANGING THE GENOME
MICRO to MICRO
Bacteria and Algae
Bacteria and Virus
MICRO to PLANT
MICRO to ANIMALS
Germ free animals
Definition: Transmission of infectious diseases in populations
Part of lifecycle?
hosts vs carriers
Relation to affected body part
Occurance in Population
Pathogen, et al.
Host, et al.
Classes of Diseases
Clinical Stages of Disease
Types of Infectious Diseases
Trichophyton, Microsporum, Epidermophyton
Athletes foot, groin itch, ringworm
Associated with water
Sporaozoan/Apicomplexanon-motile, spore forming, complex cycles
Pneumocystosis- PCPPneumocystis carinii
Roundorm diseaseAscaris lumbricoides
PLATYHELMINTHES: Flatworms- Introduction
Beef TapewormTaenia saginata
Pork TapewormTaenia solium
Fish TapewormDiphyllobothrium latum
Intestinal flukeFasciolopsis buski
Liver flukeFasciola helatica
Chinese liver flukeClonorchis sinensis
Blood flukeSchistosoma mansoni
Criteria for classification
Lyme DiseaseBorrelia burgdorferi
Relapsing FeverBorrelia recurrentis
Aerobic/Microaerophilic, Motile, Helical/Vibroid, Gram -
Gram - Aerobic Rods and Cocci
Urinary tract and burn infectionsPseudomonas aeruginosa
Legionnaires diseaseLegionella pneumophila
Bacteria meningitisNeisseria meningitidis
Facultatively Anaerobic Gram - Rods
Bubonic PlagueYersinia pestis
Sore throatHaemophilus influenzae
Anaerobic Gram - Rods
Anaerobic Gram - Cocci
Rocky Mountain Spotted FeverRickettsia rickettsii
Respiratory tract infectionsC. psittaci and C. pneumoniae
Primary Atypical PneumoniaMycoplasma pneumoniae
Gram + Cocci
Staphylococcus spps.Food poisonings: S. aureus
Toxic Shock Syndrome: S. aureus
Strep throat: S. pyogenes
Scarlet Fever, Rheumatic Fever
Endospore-forming Gram + Rods and Cocci
Gas GangreneC. perfringens
Irregular Nonsporing Gram + Rods
Leprosy/Hansen's DiseaseM. leprae
Any agent of disease
Obligate intracellular parasites
Non-living infectious units
Virulent vs. Temperate
Bacteriophages vs. Animal Viruses
modify binding sites
modify restriction enzymes
modify own DNA
Nucleic acid classificationpg. 276
Polymorphonuclear cells (PMN)neutrophil
Cell-mediated Immunity (CMI)
Antibody-mediated Immunity (AMI)
Complete vs. Incomplete (Haptens)
helper T cells
cytotoxic T cells
Natural Killer Cells
Cell Mediated Immunity
Primary and Secondary Responses
Type I- Anaphylactic Hypersensitivity
Type II- Cytotoxic Hypersensitivity
Type III- Immune Complex Hypersensitivity
Type IV- Cellular Hypersensitivity
Disorders- Immune Deficiencies
Involving just micros
In a macro world
Organic matter contribution
Nitrogen FixationRhizobium, Clostridium, Azotobacter, Nostoc
DenitrificationPseudomonas, Thiobacillus, Micrococcus
Acid Mine DrainageThiobacillus ferrooxidans
Acid Rain Damage
FOOD & DAIRY MICROBIOLOGY
Fruits and vegetables
Beneficial Aspects of Foods
5% Carbohydrates- lactose
4% Lipids- butterfats
2.5% ProteinCasein = color
Lactoalbumin = whey
Milk Borne Diseases
Bovine TBMycobacterium bovis
Q FeverCoxiella burnetti
Beneficial Aspects for Milk
Buttermilk and sour cream