Dr. Fleming
Tentative Biology 412 Microbial Physiology syllabus
(Lecture/Laboratory/Discussion) Monday and Wednesdays from 1:00 to 4:50 pm in Holt 309.
Two themes will be explored in great detail.
1. The structure, function, and metabolism of microbes are modular and there are universal
properties that all microbes share.
2. Microbes respond to environmental changes by regulating their structure and metabolism
and do so in a manner that is relative to the threat or benefit of that environmental change.
1. Working with colleagues- you will work with your colleagues this semester, you will
be expected to behave respectfully towards others and work together productively. Sexist
or suggestive comments, and pet names (whether invited or otherwise) will not be
tolerated. Please behave accordingly. If you become uncomfortable please make an
appointment with me. You should note the new Title IX reporting requirements.
2. Confidentiality and Mandatory Reporting
As an instructor, one of my responsibilities is to help create a safe learning environment on our
campus. I also have a mandatory reporting responsibility related to my role as an instructor. I
am required to share information regarding sexual misconduct with the University. Students may
speak to someone confidentially by contacting the Counseling and Wellness Center (898-6345)
or Safe Place (898-3030). Information on campus reporting obligations and other
Title IX related resources are available here: www.csuchico.edu/title-ix
3. Academic Honesty and Professional Ethics. The students, faculty, administrators,
and staff of CSU, Chico are committed to a culture of honesty in which members of the
community accept responsibility to uphold academic integrity in all they say, write, and
create.
4. Fair access. If you need course adaptations or accommodations because of a disability or
illness, you need to make special arrangements in case the building must be evacuated, you are a
first generation student, have specific learning challenges, or struggle with English as a second
language, please contact me as soon as possible to set up an appointment.
5. Attendance & Sickness
Class begins promptly at 1 pm on M and W. It is NOT possible to make up any labs and you will
still be held responsible for any labs you have missed and incur a loss of points for missed labs.
However, if you have a fever, vomiting, or diarrhea, DO NOT come to school but do send me an
e-mail as soon as possible. You must be free of any one of these conditions for at least 24 hrs
before you come in contact with others. The impacts on your grade will be determined on a case
by case basis. Be aware you may have to come in before class or stay after class to complete
work.
6. Prerequisites: 1. basic microbiology (BIOL371), 2. general genetics (BIOL360), 3. general
chemistry, 4. math background should include knowledge of scientific notation, logarithms, and
basic algebra. Knowledge of Basic biochemistry and quantitative chemistry helped previous
students.
Spring 2016
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Dr. Fleming
7. Contacting me:
1) turn in assignments via Blackboard and
2) send messages to me via my e-mail address ([email protected]).
3) My office hours are T 1-3 pm, R 9:30-11, or by appointment, and are held in Holt Hall, Room
328.
8. Course description: This course is upper division class focused on: bacterial structure and
function, modes of metabolism, regulatory responses to environmental change and stress, and
microbial aspects of nutrition and growth.
9. Class format: I teach in a non-traditional manner with group work and discussions during
lecture that rely on you being prepared for class. Please come to class ready to actively
participate.
10. Course Learning outcomes:
1. Link basic microbial structure, function, and metabolism
2. Describe and site examples how microbes regulate their structure and metabolism in
response to environmental stimuli.
3. Perform and report on lab experiments focused on microbial metabolism and regulation.
4. Identify and characterize the basic genomic elements that code for central metabolic
proteins.
12. Texts used in this course
1. (Required) Neidhardt, F. C., Ingraham, J. L., and Schaechter, M. “Physiology of the
Bacterial Cell: a Molecular Approach”. (1990). Order a used copy on Amazon.
2. (Required) Snyder, L., Peters, J. E., Henkin, T.M., and Champness, W. “ Molecular Genetics
of Bacteria”. ASM Press (2010).
3. (Required) 10 sheets of semi-log graph paper. (can be printed here) http://
www.physics.utah.edu/~gernot/elem_labs/SL3.pdf
4. A fine point White Board Pen.
Additional texts referred to in this course.
1. *Reddy, C.A, Beveridge, T.J., Breznak, J.A., Marzluf, G., Methods for General and
Molecular Microbiology. ASM Press (2007).
2. *Michal, G. and Schomburg, D. “Biochemical Pathways: an Atlas of Biochemistry and
Molecular Biology” (2013)
3. Harold, F.M. “The Vital Force: A Study of Bioenergetics” (1986)
4. *Gottschalk…
5. *White, D., Drummond, J. T., and Fuqua, C. “The Physiology and Biochemistry of
Prokaryotes” (2012)
*On reserve at the library
†I will bring a copy to class and/or a copy is present in my office
Spring 2016
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Dr. Fleming
13. Assignments. Table 1 displays the 4 different categories and the grade percentage for each
category. Failing to participate or turn in an assignment will severely impact your grade.
Table 1. Grade break down for BIOL412
Category
Exams (30%)
Assignments
Exam 1 (in class)
Exam 2 (take home)
Exam 3 (take home)
Labs (30%)
Metabolism & Growth Labs (Lab 1)
Comparative Genomics Labs (Lab 2)
Chemotaxis Lab (Lab 3)
Anaerobiosis Lab (Lab 4)
Diauxic Growth Lab (Lab 5)
Assignments (30%)
Peer-review assignment
Oral presentation of gene
Quizes and Homework
Attendance &
Team work (10%)
Attendance and Timeliness
Metabolic performance
Team work
% of final
grade
10
10
10
6
6
6
6
6
15*
7.5
7.5
6
2
2
Grading: A=90-100%; B=80-90%; C=70-80%; D=60-70%. No extra credit.
* Peer Review assignment- All components must be turned in on time or this assignment
will not work. So if you are late then I will make it a 0.
1. You will first make a table from the first half of the Metabolism and growth lab (Quizzes and
Homework). Give you extensive feed-back on this Table and provide you with an example
of an excellent table and a poorly made table.
2. You will also perform a peer-review of a poorly made table. I will give you guidelines and
will give you extensive feed-back on this peer-review (again Quizzes and Homework).
3. You will make a clean table from the glucose & malate experiment.
4. Your table will be subjected to a peer-review by a classmate (each peer-review is 45 points;
peer-review assignment)
5. I will grade the initial table based on my assessment and the peer-review (45 points; possible
grades are 45, 30, 15, or 0; peer-review assignment).
6. You will need to address the reviewer’s criticism, my comments, additional modifications, in
a point by point disposition and your initial grade will be reconsidered based on both the
extent that you modify the table AND that you address all of the reviewers comments.
(possibility to earn a portion of the original points back)
Spring 2016
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Dr. Fleming
Assignments
Grouping
of total %
Due date
1 Entry assignment & quiza
Quiz/Home
0.75
1/25
2 Draw the biochemical pathways
Quiz/Home
0.75
2/03
3 Make a table of the conversion between
Klett, CFU, & OD, with your data & with
the class data
Quiz/Home
4 Review a poorly made table
Quiz/Home
0.75
2/10
Exam 1
10
2/22
Lab 1
6
2/24
Peer-rev
6.75
2/24
5 Exam 1
6 Results from metabolism & growth Lab
7 Glucose vs Malate figure
8 In class table give example from the
previous day
0.75
Quiz/Home
9 Peer-evaluation of Glucose/Malate figure
2/03
0.75
3/07
Peer-rev
6.75
3/09
Quiz/Home
0.75
3/21
11 Point by point disposition of reviewers
comments
Peer-rev
1.5 +
(6.75%)
3/30
12 Exam 2
Exam 2
10
3/30-4/06
Quiz/Home
0.75
4/04
14 Chemotaxis Lab
Lab 3
6
4/11
15 Computer lab exersizes
Lab 2
6
4/18
16 Anaerobiosis
Lab 4
6
4/25
17 Quiz from article
Quiz/ Home
0.75
4/27
18 Diauxic Growth
Lab 5
6
5/09
19 Take home final
Exam 3
10
5/09-?
Quiz/ Home
1.5
?
10 Response regulators
13 In class presentation from reading
20 Additional assessment
Spring 2016
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BIOL412
Tentative BIOL 412 Calendar—Spring 2016—Dr. Fleming
Wk
Lec
1
Date
M
Laboratory exersize
Lab safety,
dilutions, &
1/25 spectrophotometry
Lab reading
Lecture topic
General methods in
Microbiology
Course introduction (the
three paths, to realize the
dream of the cell), in lab we
will measure cells performing
that dream
1
2
3
W
M
2
4
5
W
M
3
6
W
Dilutions &
General Methods in
measuring cell
Microbiology.
1/27
density with turbidity
PBC Ch 3
(62-67) / PBC
Ch 5
(biosynthesis)
Ch 1 Ch 2
Assimilatory metabolismHow to make a cell (1)
monomers and
Polymerization
PBC Ch 5 Ch 1,
Ch 2
Dry lab,
Understanding
growth curves +
2/3
how chemostats
work
PBC Ch 7 Ch 8
Assimilatory metabolismHow to make a cell (2)
PBC Ch 3/ Ch 5
Growth curve with
assigned C source
2/8 (Pt II), & harvest to
quantify using plate
counts
PBC Ch 7
II. Bioenergetics- the quest for PBC Ch 6
food (uptake)
174-183 *Fig 1
Measure the total C PBC Ch 7 (Growth
source used,
yield).
2/10 generate a standard
curve measure
unknown.
Item due
1. Entry assignment &
Quiz
I. Core paradigm for building
PBC Ch 5, Ch 1,
the microbial cell (modularity, Ch 2
all cells functionally the same,
12 precursors, monomers
PBC Ch 7
(Unrestricted
growth,
Measurement of
growth, Growth of
cultures)
2/1
Growth curve with
assigned carbon
source (Pt I)
Lecture reading
Cellular conversion of
electron donors and electron
acceptors (dissimilatory
reactions)
PBC Ch 5
(Generation of
ATP) + Gottshalk
1. Drawing of the
biochemical pathways
(assignment 1)
2.
Initial table of
conversions between
Klett, CFU, & OD600
1. Review a table.
Tentative BIOL 412 Calendar—Spring 2016—Dr. Fleming
Wk
Lec
Date
Laboratory exersize
Lab reading
Item due
7
M
8
W
2/17
PBC Ch 1,2, 3,
5, & 6 and
Gottshalk
Exam 1 (In class)
M
Exam 1 Lectures
2/22 1-8
Exam 1
9
Dry Lab, computer
lab discussion/
2/24 metabolic
performance
III. Putting it together 1-> 2
Polymerization. Cell division,
Cell wall, chromosome
replication,
PBC Ch 3 74-75
MGB Ch 14
(605- 618), MGB
CH 1 31-42,
50-53
1. Glucose vs Malate
figure.
2. Results
from Metabolism and
Growth Lab
Computer lab 1
5
10 W
11
M
MGB CH 2 Box 2.5
Cell cycle timing
(109-114), Additional
articles.
PBC Ch 5 +
Gottschalk
MGB Ch 1
43-45, PBC Ch
15
Computer Lab 2
Polymerization RNA synthesis MGB Ch2 67-74
* Fig 2.9; 82-84
*Fig 2.23;
Computer Lab 3
Polymerization Protein
synthesis
MGB CH 2
86-97 *Fig 2.28;
105-109, CH 2
117-120
2/29
6
Cellular conversion of
electron donors.
(Phototrophs/PS ball toss)
Lecture reading
Dry lab, calculate
the cost to grow on
2/15
varying sources of
C.
4
PBC Ch 7 (Growth
yield).
Lecture topic
12 W
3/2
Protein secretion
MGB Ch 14
595-605
1. In class table
13 M
computer lab
discussion/
3/7
metabolic
performance
Chemotaxis Assay
3/9 Part 1 Plate assay
Motility and Chemotaxis
PBC Ch 6
183-189 & MGB
____
1. Peer evaluation of
Glucose/ Malate figure
7
14 W
Tentative BIOL 412 Calendar—Spring 2016—Dr. Fleming
Wk
Lec
Date
15 M
3/21
16 W
3/23
Laboratory exersize
Lecture reading
Item due
1. Response regulators
due
Overview of mechanisms of
regulation 1. local protein
level
MGB Ch 13 525,
PBC Ch 11, PBC
Ch 13
Computer Lab 5
Bacterial sensing of the
environment 2. local level
transcriptional regulation
PBC Ch 12,
MGB Ch 12
Chemotaxis Assay
Part 2 Beta-Gal
assay
Bacterial sensing the
environment signal
transduction (signal
transduction) signal
transduction, sigma factors,
and regulatory RNAs
MGB Ch 13 Box
13.4, Box 13.5,
Box 13.6, PBC
Ch 13
Global responses
PBC Ch 13,
MGB Ch 13
525-526 * Table
13.1
1. Point by point
disposition of the
reviewers comments
(Computer Lab) 6
Example 1. Responses to
nutrient limitation
MGB Ch 13
626-547
1. In class presentation
CRP/CAP,
(Computer Lab) 7
Example 1. Responses to
nutrient limitation
MGB Ch 13
626-547
1. Exam 2 (take home
exam due)
Diauxic growth
MGB Ch 13 526-547 Example 2. Responses to
growth limitation
MGB Ch 13
547-554
1. Chemotaxis lab due
Diauxic growth
Example 2. Responses to
growth limitation
MGB Ch 13
547-554
17 M
3/28
18 W
computer lab
discussion/
3/30
metabolic
performance
9
19 M
4/4
20 W
4/6
21 M
4/11
22 W
4/13
23 M
Computer Lab
4/18 presentations
24 W
4/20 No lab.
11
Lecture topic
Computer Lab 4
8
10
Lab reading
1.Computer lab
presentations, 2.
Computer labs
12
Tentative no lecture
Tentative BIOL 412 Calendar—Spring 2016—Dr. Fleming
Wk
Lec
Date
25 M
4/25
26 W
4/27
27 M
5/2
28 W
5/4
29 M
5/9
30 W
5/11
Laboratory exersize
15
Lecture topic
Anaeroboisis
MGB Ch 13 547-554 Example 3. Responses to
stress
Anaeroboisis
Lecture reading
Item due
MGB Ch 13 554
2. Diauxic growth lab
due
Example 3. Responses to
stress
Article
interpretations
1. Quiz from article
Anaeroboisis
Example 4. Cell- Cell
communication
MGB Ch 14
(573-576)
Discussion of
Anaerobiosis data
Example 4. Cell- Cell
communication
13
14
Lab reading
1. Anaerobiosis Lab due
1. Take home final
assigned