Biochemical Pathways
Biology 361, Spring 2016
Instructor:
Office:
Office Time:
Email:
Lecture:
Text:
Lecture Notes:
Course Website:
Gregory Johnson, Ph.D.
Thompson 257d
M, 10-11 am; W, 11-12 pm; or by appointment
gregoryjohnson@pugetsound.edu
T&TH, 9:30-10:50 am, TH197
David L. Nelson and Michael M. Cox. Lehninger: Principles of
Biochemistry, 6th edition. W.H. Freeman and Company. 2013.
Provided online after class as a PDF on Moodle.
A Moodle site will be used to distribute lecture notes and other
materials. http://moodle.pugetsound.edu/
Class description
Biochemistry is a broad subject that has been touched upon in many of your prerequisite
courses. Between Bio 111, The Unity of Life; Bio 212, Cell Biology; and Bio 311, Genetics;
you have learned about carbon and water chemistry, biological molecules, conversion of
chemical energy to ATP, protein structure and synthesis, enzyme kinetics, nucleotide
structure, nucleic acid synthesis, and so on.
Biology 361 is a course designed for life-sciences students interested in furthering their
study of biochemistry, but who are not Biochemistry or MCB majors. Many of you are
interested in a career in the health professions and will need evidence of training in
biochemistry in order to proceed to post-graduate training. In order to make this course
most useful to you, we will not take a comprehensive approach in studying biochemistry.
Instead, in BIOL361, we will concentrate on the biochemistry topics that your prerequisite
courses did not cover in detail. Specifically, we will focus on metabolic pathways and their
regulation. Of course, since metabolic reactions do not happen in isolation, we will also
draw upon knowledge of cell biology and genetics from previous courses.
Course format
Lecture:
The lecture will include slides. These slides will be made available to you
after lecture. However, the slides alone do not constitute complete lecture
notes. You must attend class to get a complete picture of what has been
presented.
Reading:
We will use the text, Lehninger: Principles of Biochemistry, as the primary
supplement to topics presented in lecture.
Student Presentations:
Clear communication of technical information will be a vital skill
in your post-graduate lives. To hone this skill, you will have multiple
opportunities to present a topic related to biochemistry to your peers.
Assigned presentations include, but may not be limited to, a review
presentation at the beginning of this semester, metabolic pathway
presentation in the middle of the semester, and the literature review at the
end of the semester. Time requirements will vary for each presentation, but
will not exceed 45 minutes of in class presentation time.
Assessment
Your grade will be based on the following assignments:
Exams:
There will be three midterm exams. Exams will consist of short answer
questions covering material from the lectures, readings, AND student
presentations.
Presentations:
Your presentations will heavily influence your final grade. To promote
improvement in your presentation style, the first presentation will be worth
fewer points than your final presentation. A final poster presentation will
occur during the final exam time.
Writing:
For the final presentation project, you must write a mini-review paper
covering your chosen topic. This will be graded on its merit alone; the quality
of your presentation will not affect my assessment of your paper. Other brief
writing assignments will be due throughout the semester.
Participation and peer evaluations:
There will be many ways for you to participate in
our class. One of those ways is through participating in peer evaluations. You
will be asked to critique your peer’s class presentations. These critiques will
be summarized then relayed to the presenters to ensure anonymity. These
critiques are invaluable to the presenter as they can help to identify strengths
and weaknesses in their presentation skills.
Grading and other policies
Handing in assignments: If you need to turn something in, turn in a hard copy of the
assignment. You must have my permission to submit an assignment via
email. If handing in an assignment outside of class, you must either hand it
directly to me, or to Carol Curtin (Biology office: Thompson Hall room 223A).
Do not put homework assignments in my mailbox or slip them beneath my
door.
Disputing a test grade:
Return tests directly to me with a typed appeal attached to the
front of your test. This appeal should indicate (1) which question(s) you
would like re-graded and (2) why you are disputing the grade you received. I
will also check each exam to ensure that the point total was correctly
calculated. I will accept appeals up to one week from the date that the test
was returned to you.
Late assignments:
I expect assignments to be handed in on time. Coursework
handed in after its due date will be graded at a reduced rate; late
assignments will be docked 5% of the total points per day (including
weekends).
Academic Misconduct:
Cheating, plagiarism, and any other forms of academic
misconduct are serious offenses and will not be tolerated. You are
responsible for understanding what constitutes plagiarism. Refer to The
Logger (the university’s academic handbook) for definitions of, examples of,
and penalties for academic misconduct. At minimum you will receive a zero
for the assignment/exam/paper in question. At the discretion of the instructor
you may also be removed from the course.
Grades
Below is an approximate breakdown of how each type of assignment will contribute to your
final grade. This point distribution may change slightly.
Assessment
Review presentation
Exam 1
Exam 2
Exam 3
Final Presentation
Final Paper
Final Poster
Participation, brief presentations, short
writing assignments & critiques
Total:
Points
40 points
80 points
80 points
80 points
80 points
80 points
80 points
80 points
600 points
Letter grades will be assigned as follows:
Percentage
93-100
90-93
87-90
83-87
80-83
77-80
Letter Grade
A
AB+
B
BC+
Percentage
73-77
70-73
67-70
63-67
60-63
<60
Letter Grade
C
CD+
D
DF
Tentative Schedule of Course Content (subject to change)
The following is an outline of topics, associated chapters in Principles of Biochemistry and
student activities, presentations and due dates that we will occur this semester.
Student Presentation /
In Class Activities
Intended
Date
Chapters
1/19
1
1/21
2
Buffering
1/26
3
Enzyme Function and Kinetics
1/28
4
Enzyme kinetics and catalysis
mechanisms
Regulation of Enzyme Activity
3a
Chymotrypsin
Mechanism (In Class)
2/2
6
Enzyme regulation
Regulation of Enzyme Activity
3b
2/4
13
Principles of bioenergetics
The Logic of Signal
Transduction
HIV Protease Activity (In Class)
2/9
Topic/Activity
Introduction
Protein structure and folding
reviews; Buffering in biological
systems and Acidosis
Exam 1
2/11
Carbohydrate structure and function
Glycolysis and Fermentation
2/16
7
Glycolysis
Glycolysis Presentation by
Whole Class
2/18
14
Gluconeogenesis
The Citric Acid Cycle
2/23
Reciprocal Regulation of Glycolysis
and Gluconeogenesis
Electron Transport and
Oxidative Phosphorylation
2/25
Glycogenolysis and Glycogenesis
Diagram for Regulation of
Glycogenolysis; Diagram for
Regulation of Glycogenesis
3/1
Citric Acid Cycle; Glyoxylate Cycle
High-Fructose Corn Syrup
Papers (In Class Discussion)
3/3
Exam 2
Conferences in 257D (no lecture on
this day)
One page summary about
Metabolic Pathway Topic
3/8
3/10
15
16
Spring Break
3/15
Spring Break
3/17
Glycogenolysis and Glycogenesis
Diagram for Regulation of
Glycogenolysis; Diagram for
Regulation of Glycogenesis
3/22
17
Fatty Acid Catabolism
Trans Fat Activity (In Class)
3/24
21
3/29
18
3/31
22
Lipid Biosynthesis
Diagram for dietary proteins,
gastrointestinal track
Amino Acid Catabolism
Amino Acid Biosynthesis
4/5
Paper Due (Friday, 4/10 @
7:00 pm to Turnitin.com)
TBA
4/7
Exam 3
4/12
Presentations 1, 2 and 3
4/14
Presentations 4, 5 and 6
4/19
Presentations 7, 8 and 9
4/21
Presentations 10, 11 and 12
4/26
Presentations 13, 14 and 15
4/28
Final Day of Class
Final Poster Instructions
Provided
5/3
Final Exam, 5/10, 8:00-10:00 am
Final Poster Presentation
5/14