MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
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Elementary Microbiology (MICRB 106)
Spring 2003
Lecture Room 40 MCB
MWF 1:00 – 1:50 p.m.
Microbiology Laboratory (MICRB 107) is mandatory.
Instructor: Dr. Matthew P. Hoch
E-mail: mph13@psu.edu
Campus Phone: 4016
Website: www.yk.psu.edu/~mph13/
Office/Lab: MCB Rm 6 / MCB Rm 124 “Biology Lab”
Office Hours: W 4:00-5:00 p.m., F 3:00-4:00 p.m., or by appointment
Required Textbook: Microbiology: An Introduction, 7th ed. Tortora, G.J., B.R.Funke, and C.L.
Case. Benjamin Cummings, 2002.
Course Perspective:
Microorganisms play an omnipotent role in our human lives. They have influenced the atmosphere and
climate of Earth for billion and years and continue to do so today. They obviously have immense influence
of individual human health as well as that of whole communities. Human societies have been shaped by
both the deleterious and beneficial functions of microbes, from changing the course of history via epidemic
infectious disease to defining cultural elements like unique foods and beverages. Today, new
biotechnologies employ microorganisms for industrial production of chemicals, including pharmaceuticals.
To understand and appreciate how microbes have done and do all these things, we must establish a
fundamental understanding of the relevant chemistry and biology of microbes and gain appreciation for their
diversity. A specific focus is then placed on bacterial and viral involvement in the infectious disease process
of humans, from the perspectives of microbial pathogenicity and human defenses and medical intervention.
Course Goals and Objectives:
 Understand the theory and application of microscopy technology for studying microbes.
 Students will describe the basic differences between light and electron microscopes
and various versions of each.
 Understand basic chemical principles pertinent to elementary microbiology.
 Students will learn basic principles of chemical bonds and reaction thermodynamics.
 Students will learn the major biomolecules and their involvement in cellular function.
MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
 Learn basic prokaryotic cell biology terminology and concepts.
 Students will master the form and function of prokaryotic cell structures to the
molecular level.
 Given environmental conditions, student will correctly predict the degree of growth
for particular physiological categories of prokaryotes.
 Students will correctly list, in order, metabolic pathways used for energy yield and cell
growth for a bacterium fed particular substrates in the presence of absence of oxygen.
 Students will determine the regulation and flow of genetic information within and
between prokaryotic cells at the molecular level.
 To become familiar with the phylogenetic and physiological diversity of prokaryotes.
 Students will offer accurate examples of how microbes are used by man for industrial
and biotechnical applications.
 Based on the current system of prokaryotic taxonomy, student will provide
characteristics (structural, biochemical, and genetic) and techniques used to identify
bacteria.
 Using knowledge of microbial physiology, students will correctly determine the
microbes involved in the biogeochemical cycling of major elements in different
natural communities.
 Understand basic concepts in virology
 Students will correctly distinguish prokaryotic viruses (phage) based on lytic and
lysogenic replication cycles, viral particle structure, information storage molecules.
 Students will correctly distinguish eukaryotic viruses (phage) based on replication
cycles, viral particle structure, information storage molecules, and unique viral
enzymes.
 Understand terminology and unifying concepts of host defenses and infectious disease.
 Using principles of epidemiology, students will make predictions on the spread and
prevention of infectious disease.
 Given details of pathogenicity and host symptoms and signs, students will correctly
identify specific microbial infections.
 Students will accurately determine mechanisms of non-specific host defenses.
 Student will correctly differentiate between humeral and cellular immunity and how
they relate to each other in there role of containing and stopping microbial infections.
Student Evaluation:
The majority (88%) of your course evaluation will be based on quiz and exam performance, and the
remainder of the evaluation will be on an oral presentation and your individual class participation. The oral
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MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
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presentation, “Bad Bug” Talk, is an opportunity for you to independently learn about a particular pathogenic
microorganism of interest to you and then share your knowledge with the class. Course participation will be
based on weekly lecture attendance (body and brain) and other criteria (see below for details).
Participation
4 Quizes (2% each)
Exam I
Exam II
Exam III
Exam IV
Bad Bug Talk
Total
9%
8%
15 %
20 %
20 %
20 %
8%
100 %
Individual quizzes and exams will be marked on varying numbers of points. For example a quiz worth 3%
of the final course grade may be marked out of a total of 10 points, where as an exam worth 20% of the final
course grade may be out of a total of 50 points. When you keep track of progress, please make certain you
are tracking your total earned course percentage, not points or average letter grades. Throughout the
semester, I will report your current standing, as a percentage and letter grade, based on the total course
percent that has been evaluated.
Participation: (9%) Participation will be based on your inside and outside of class involvement and
observation of all class requirements (see below), which includes the following areas: lecture attendance,
email communication, in-class attitude, in-class questions or answers, looking at microbiology news on the
web, and being conscientious regarding your course performance (i.e. seeking help when grades slip). Your
participation evaluation will be based on a weekly self-evaluation and the instructor’s independent record.
Your weekly self-evaluation sheet must be submitted at the end of Friday lecture. Attach to your weekly
self-evaluation a printed copy of any microbiology news you have read that week and the source website
URL. Suggested URLs to try can be found on the course website.
Quizzes: (8%; 2% each) There is one quiz prior to each exam, for a total of 4 quizzes during the
semester. Quizzes are unannounced on a Monday at the start of class. You need to keep up on the
textbook reading and review notes on a weekly bases for success in the course. The intent of Monday
quizzes is to help you keep up with course materials. A weekly review sheet of major concepts and terms is
submitted at the end of each Friday lecture. A Monday quiz is based on the previous Friday’s weekly review
sheet content. Content covered on a quiz does not influence the content of the next exam, i.e. question
content on a quiz could appear on the exam.
Exams: Course content for each exam is given in the lecture schedule (below). Questions are largely
derived from lecture material, but may include content covered in assigned chapter readings. Use the weekly
review sheets as a study guide. Exams 1-3 will be administered during the normal scheduled lecture period
and location. Students are provided a minimum of 50 minutes for each of these exams. Date, time and
location of Exam 4 will be scheduled for sometime during finals week. Although the last exam during finals
week is not cumulative in regard to details from earlier course content, students are expected to master core
concepts and vocabulary presented earlier in the course, as these are required to understand later content. I
advise that you review earlier course content, particularly problem topics, when preparing for the final.
Bad Bug Talks: Pairs of students will present a 10 to 15 minute presentation on a specific pathogen.
More details on this assignment and my expectations will be discussed in lecture and presented as a handout.
MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
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Grades:
Letter grades are based on the total percentage of course marks accumulated as indicated below. Plus (+) or
minus (-) designations will be assigned only at final grade submission, and will be based on the distribution
of marks, i.e. "the curve", within each posted letter grade range. [E.g.: total course marks equal to or above
89, the A-range, will always be either an A-, A, or A+; which +/- designation received within the A-range
will depend on the distribution and number of students within the A-range.
A
B
C
D
F
89 - 100 %
77 - 88 %
65 - 76 %
53 - 64 %
< 52 %
"Make-Up" and Testing Policy:
Missed exams, quizzes, labs, or assignments can only be made-up, or waived, by prior arrangement and/or
with proof of an excusable absence (e.g., documented medical reason, sanctioned University function). A
different set of questions may be used for any make-up assignments or exams.
Exams and quizzes will be administered at the beginning of class on their scheduled dates. Late arrival to
class on a quiz or exam day is extremely disruptive and inconsiderate to your other classmates. You also
run the risk of not being allowed to take the exam. If any student completes and submits the exam prior to
your arrival in class, you will not be permitted to take the quiz or exam, and you will forfeit your grade
(receive a 0%). Please show up on time!
Lecture Topic Syllabus and Reading Assignments:
Lecture # Dates
Topic*
1
2
3
4
5
6
7
8
9
10
11
Jan 13
Jan 15
Jan 17
Jan 20
Jan 22
Jan 24
Jan 29
Jan 31
Feb 3
Feb 5
Feb 7
EXAM 1
Monday, Feb 10
Assigned Reading
Course Introduction
Microscopy
Chemistry Primer
Major Biomolecules
Anatomy of Organisms I
Anatomy of Organisms II
Anatomy of Organisms III
Metabolism I
Metabolism II
Metabolism III
Microbial Growth & Its Control
Ch 1
Ch 3
Ch 2
Ch 2
Ch 4
Ch 4
Ch 4
Ch 5
Ch 5
Ch 5
Parts of Ch 6 & 7
Covers content of Jan 13 through Feb 5.
MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
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12
13
14
15
16
17
18
19
20
21
Feb 12
Feb 14
Feb 17
Feb 19
Feb 21
Feb 24
Feb 26
Feb 28
Mar 3
Mar 5
Genetics I
Ch 8
Genetics II
Ch 8
Genetics III
Ch 8
Biotechnology I
Ch 9
Biotechnology II
Ch 9
Microbial Taxonomy
Ch 10
Bacteria Diversity
Ch 11
Archaea Diversity
Ch 11
Microbial Eukaryote Diversity
Ch 12
Microbial Diversity Review (Extra Credit)
EXAM 2
Friday, Mar 7
Mar 10-14
Covers the content of Feb 7 through Mar 3.
SPRING BREAK WEEK
22
23
24
25
26
27
28
29
30
31
Mar 17
Mar 19
Mar 21
Mar 24
Mar 26
Mar 28
Mar 31
Apr 2
Apr 4
Apr 7
EXAM 3
Wednesday, Apr 9
33
34
35
36
37
38
39
40
41
42
Apr 11
Apr 14
Apr 16
Apr 18
Apr 21
Apr 23
Apr 25
Apr 28
Apr 30
May 2
EXAM 4
Finals Week
Viruses I
Viruses II
Viruses III
Infectious Disease
Epidemiology
Pathogenicity I
Pathogenicity II
Host Defense: Non-specific Resistance
Host Defense: Non-specific Resistance
Host Defense: Immunity I
Ch 13
Ch 13
Ch 13
Ch 14
Ch 14
Ch 15
Ch 15
Ch 16
Ch 16
Ch 17
Covers content of Mar 17 through Apr 4.
Host Defense: Immunity II
Immune System Disorders
Antibiotics I
Antibiotics II
Medical Microbiology I
Medical Microbiology II
Medical Microbiology III
Bad Bug Talks (Pairs # 1 – 3)
Bad Bug Talks (Pairs # 4 – 6)
Bad Bug Talks (Pairs # 7 – 11)‡
Ch 17
Ch 19
Ch 20
Ch 20
Parts of Ch 21-26
Parts of Ch 21-26
Parts of Ch 21-26
Parts of Ch 21-26
Parts of Ch 21-26
Parts of Ch 21-26
Covers content of Apr 7 through May 2.
* Presentation dates for specific topics may change during the semester. Please be advised that all updates
of the syllabus will be posted on the course website (www.yk.psu.edu/~mph13/)
‡ Scheduled laboratory time for MICRB 107 will be used for the last pairs of speakers.
Snow Closure Policy:
We are expected to have a snowy winter this semester, and cancellation of class meetings is very likely.
Please be advised that the “course” will not be cancelled in the case of such a snow closure. Yes, this is to
say you will be responsible for topics or assignments covered on cancelled days. How to approach this
MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
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situation will be at the instructor’s discretion, and you will be notified via email to your PSU account. Such
approaches may include rescheduling the lost class meeting(s) at another time (possibly during weekends or
evenings) or giving you an “at-home” assignment.
Course Requirements:
1. Observe all class guidelines (see below) and bring your most positive attitude.
2. A PSU Access Account. Go to IST Rm 106 and make the request for your user-ID and password.
It will take about 24 hours for activation, at which time I recommend you change your password.
3. A single Email address. I will send all course announcements and notes to your PSU user-ID
address. This is also the easiest address for other PSU students to use in reaching you, as it is on
the PSU Directory. I suggest you use the PSU Webmail, which can be accessed from your home
4. You will keep in touch with me and other students in the class by Email. Check your Email
frequently (i.e. daily) so you don’t miss important announcements.
5. The ability to save computer work to permanent space on the network, a diskette, CD-R, or zipdisk. You will have to supply the disc or CD-R.
Class Guidelines:
I would like everyone to participate in making our class times a nice comfortable place to learn throughout
the next fifteen weeks. To this end, please, let us all adopt the following guidelines on appropriate and
considerate behavior.
 Unless you are waiting for an organ transplant, or a birth is imminent, please turn off all electronic
devices (e.g. cell phones, pagers, etc) that could generate distracting noises prior to entering class.

I encourage you to fill the room with questions and discussion on the topic at hand. Please ask questions
freely, and if not in class then out of class, either verbally or via Email. When others ask, or answer,
questions in class, please give them your full attention and respect.

If you have a comment or complaint regarding any aspect of the course other than the course content or
activity being discussed, please wait to speak with me until after class, outside of class, or by Email.
This saves valuable class time and is much more discrete, particular on issues of grade disputes or any
other potential misunderstanding.

Please don’t study or read other course material in class. If you find yourself in a time management
crises come see me before class instead.

Also, refer to “Promoting a Vibrant Learning Culture” at www.psu.edu/oue/vibrant.html.
MICRB 106: Elementary Microbiology
PSU-York (Spring 2003)
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Academic Integrity:
Academic dishonesty, aka cheating, is not something you want on your record, nor do you want to lower
your grade or fail the course. This first year of university is a time to focus on developing study skills and
learning your strengths and weaknesses. Students that cheat are not challenging themselves, and such
cowardly behavior now, will leave them even more ill prepared for their future. If you ever feel the urge to
cheat in any form, that is your signal to seek help from your peers, instructor, and/or the learning center.
Faculty will have great respect for the hard working honest student that has learned something regardless of
grade outcome. Preservation of a high standard of academic integrity is, for many individuals, a source of
self-confidence and pride.
To possess academic integrity means you don’t cheat. So what is cheating?
 Copying someone else’s assignment or/and submitting it as yours.
 Referring to another student or sources during a quiz or exam.
 Falsifying participation sheets.
It is NOT cheating to work with other students while studying for quizzes and exams. It is NOT cheating to
seek assistance from another student, a tutor, or your instructor, in order to understand an in-class activity or
out-of-class assignment.
If the instructor suspects you of cheating, they will immediately notify you to meet informally after class or
at some other time outside of class. At that time, the instructor will inform the student of the accusation and
its circumstances, and the student will have the opportunity to explain their view point or situation. The
instructor will then decide whether to proceed with a formal academic sanction. Notification of an academic
sanction will involve a formal meeting between accused student and instructor. At this formal meeting, the
student will be presented with an academic sanction form that explains the accusation and the sanctions, such
as a failing grade on an assignment, quiz, or exam. The formal meeting will be arranged by e-mail or phone
call. The student may agree and sign the form or contest the allegations through the university authorities. If
a student is absent from the formal meeting time, they will be given three additional days to contact and meet
with the instructor. Failure to formally meet with the instructor will be deemed as the student's acceptance of
academic sanction, and waives the student's right to contest the allegations of academic dishonesty. Note,
that any student(s) assisting or facilitating others in cheating will be subject to equal penalty and treated
according to these same guidelines The official guideline on this policy can be found in the Academic
Administrative Policies Manual, which is available on the PSU website under item “G9” at
www.psu.edu/dept/oue/aappm/.
Disability Statement:
Please see me immediately after the first class if you have a documented disability that may require
special accommodations for this course. I will do all I can to accommodate your needs and/or arrange to get
you any additional required assistance.