Download CHEM 341-01 Syllabus Spring 2017 FINAL

CHEM 341: Biochemistry II
Course Syllabus, Spring 2017
San Francisco State University
(As the learning facilitator, I reserve the right to make announced changes to the syllabus, if necessary)
Learning Facilitator Information
Class Meeting
Facilitator
Teaster Baird, Jr., Ph.D.
Office/Office Hrs.
Email
Phone
TH 805 (Inside TH 806)
Mondays
2:00 p.m. - 4:00 p.m.
[email protected]
415.405.0935
Course and Text Information
Class Time
11:10 - 12:00 MWF
Class Location TH 429
Required Item
iClicker 2
New: $56, Used: $42, Semester Rental: $27.97
(SFSU Bookstore Prices)
Optional Items
Textbook
I am not requiring a specific textbook for the course this semester. The course
content will be driven by the in-class lectures, discussions, group work and
homework. However, you should consider procuring a textbook to assist your
work flow and understanding. I have suggested some textbooks below. All are
available from a number of sources. The publishers offer more economical etext options.
Text
Recommended
Texts
Potential Source(s)
Lehninger: Principles of
Biochemistry, 5th or 6th
Editions, by Nelson and Cox
• Amazon.com (5th and 6th Editions)
• Textbooks.com (5th and 6th Editions)
• Direct from publisher: (6th Edition) http://
www.whfreeman.com/Catalog/product/
lehningerprinciplesofbiochemistrysixthedition-nelson
Fundamentals of
Biochemistry: Life at the
Molecular Level, 3rd and 4th
Editions, by Voet, Voet and
Pratt
• Amazon.com (3rd and 4th Editions)
• Textbooks.com (3rd and 4th Editions)
• Direct from publisher (4th Edition): http://
www.wiley.com/WileyCDA/WileyTitle/
productCd-EHEP002174.html?
filter=TEXTBOOK
Biochemistry, 4th and 5th
Editions, by Garrett and
Grisham
• Amazon.com (4th and 5th Editions)
• Textbooks.com (4th and 5th Editions)
• Direct from publisher (5th Edition): http://
www.cengagebrain.com/shop/search/
9781133106296
Class/Course Information and Policies
Pre-requisites:
CHEM 340 (Biochemistry I) or equivalent with a grade of C (not C-) or better. I will drop registered
students who have not taken the pre-requisite course or have not completed it with the appropriate
grade. Students who have completed the pre-requisite at other institutions will be required to show me
proof before I allow them to remain in or to add the course.
Add Policy:
I will take attendance take during the first three class meetings. Registered students who are not in
attendance on the first day of class will be dropped unless prior agreement has been made with me. If
room is available, students who have not registered for the course, but have attended the first three
meetings and have satisfied all pre-requisites will be allowed to add the course until the class has
reached its capacity. Priority will be given to those students in the following order (to be considered for
adding based on priority assumes that pre-requisites have been satisfied):
Priority
Classification
1
2
3
SFSU Undergrad
Major
Other Criteria
Graduating BIOCHEM major
Proof of commitment to
graduation in spring 2017 must
be provided
Graduating BIOL major
Proof of commitment to
graduation in spring 2017 must
be provided
Graduating senior of any
other major
4
BIOCHEM
5
BIOL (all concentrations)
6
CHEM
7
All others
Proof of commitment to
graduation in spring 2017 must
be provided
Not graduating in spring 2017
semester
and 1st time enrollment
8
SFSU Grad
CHEM/BIOCHEM/BIOL
9
Open University
All
Please note that the official registration wait list is only valid up until registration concludes. After that
point, the wait list content or order is irrelevant as it is up to my discretion to add students as I deem fit.
Attendance Expectations:
As mentioned in the previous subsection, I will take attendance during the first three class meetings.
Afterwards, I may record attendance intermittently, but you are expected to attend class regularly.
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Course Description: (3 units) The focus of Biochemistry II is metabolism. Many metabolic pathways will be
covered with the intent of understanding how the pathways are organized, regulated, and integrated to
maintain and sustain cellular and organismal life. Whereas metabolism that was in Biochemistry I
focused on carbohydrate catabolism, in Biochemistry II, catabolism and anabolism of all 4
classifications of biomolecules will be considered.
Required Background Knowledge: In taking this course, I assume that the you have a comfortable working
knowledge and understanding of the following topics from Biochemistry I:
• the structures and properties of the 20 standard amino acids
• structural features of proteins
• basic structure-function relationships in proteins
• drawing and interpreting enzyme mechanisms
• basic enzyme kinetics for both Michaelis-Menten and regulatory enzymes
• the principles of biothermodynamics and bioenergetics
• redox chemistry
• general features of metabolic pathways
• central metabolism (glycolysis, citric acid cycle, electron transport and oxidative phosphorylation)
There will be no review of these topics
Course Structure: The course is broken into 4 separate modules and each module will cover certain
metabolic pathways. Class meetings will be a mixture of lecture and small-group, POGIL-like sessions.
My goal is to use lectures and podcasts to provide you an overview of the pathways that will be covered
in the module and to use the small-group sessions to analyze and understand the pathways. The
assignments will not be graded based on content but will be counted for completion as long as the
answers suggest that you have made a sincere effort to answer the questions. In other words, if you do
the assignment before the deadline, you will get credit for it even if all your answers are incorrect, but
not if your answers are gibberish, “I don’t know,” totally unrelated to the topic, etc.
Course Objectives and Learning Goals: Metabolism is a broad topic that encompasses many aspects of
biochemistry. Consequently, how it is taught can vary widely depending on the instructor’s goals. My
goals are for you, at the end of the semester, to be able to leave the course with:
1. an appreciation of how chemistry at the cellular level relates to health, disease and other macro
level phenomena.
2. a level of understanding such that you feel confident in explaining similar things to a general
audience that may have very little science background.
3. a fundamental understanding of metabolism that allows you to make reasonable predictions
about other metabolic pathways
Therefore, my approach in teaching metabolism will be largely on metabolic regulation, integration, and
how the chemistry that occurs in the cell (micro level) leads to physiological observations (macro level).
In short, the overall goal of the course is for you to understand how metabolic pathways and processes
are organized, regulated and integrated in order to maintain cellular and organismal life.
Your focus should not be on memorizing pathways per se, but understanding and appreciating how
each metabolic pathway contributes to homeostasis and how each may be affected by local and distal
perturbations in the cell and organism. For each metabolic pathway or process, you should:
1. be able to explain why the pathway or process exists at all;
2. understand the regulatory mechanisms of the pathway and why those particular regulatory
mechanisms may have evolved for that pathway as opposed to other regulatory mechanisms
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3. be able to predict how certain perturbations will affect the pathway and how those perturbations
may affect the cell and organism;
4. be able to discuss how perturbations that directly affect one pathway can directly or indirectly
affect other pathways because of how the pathways are integrated;
5. be able to correlate certain metabolic malfunctions to health and disease.
CHEM 341 on the Web at SFSU:
Other learning aids and materials will not be handed out in class but will be posted on the web through
iLearn. If you are registered for the class, you already have access to the iLearn website for this course.
The iLearn site will also be used to post announcements for the course. You should check the
announcements regularly to ensure that you are kept up to date on postings of lecture notes and other
materials. If I need to contact you, I will use your SFSU email address. San Francisco State University
requires that all registered students have an “@mail.sfsu.edu” address. You may have email forwarded to
you from your SFSU address to another address that you check more frequently. It is not my
responsibility to make sure that a you have received an email if you use a bad or non-functional email
address.
iLearn
Course materials and announcements will be posted on the University’s iLearn site at http://
ilearn.sfsu.edu (details are below)
1. Direct your browser to http://ilearn.sfsu.edu.
2. Login.
3. Select CHEM 0341-01 BIOCHEMISTRY I Spring 2017 from your course list.
How to Study for This Course:
1. STUDY AND REVIEW FREQUENTLY!
2. DO NOT GET BEHIND! Doing so can put you in a situation from which it is nearly impossible to
recover.
3. Work hard and diligently to thoroughly understand the core concepts and principles in each section.
Subsequent topics will be built on these core concepts and principles.
4. Try to understand as opposed to memorize. Some memorization will be required, but try not to
make that your primary approach to the course material.
5. Do the pre-class assignments. The primary intent of the pre-class assignments is to get you focused
and ready for the small-group sessions.
6. Look for the logic. Everything should make sense. If it doesn’t, try to find out if you are
misunderstanding a concept or if a topic was not explained clearly.
7. Use all your resources. The lectures, podcasts and in-class materials will be the primary source of
information for the course, but you should find a textbook that will describe details for you. Use the
internet and other people as well, but with caution. For example, Wikipedia is a good starting point,
but don’t let it be your sole source of information.
8. Study with classmates. Science is best learned and understood through collaboration.
9. If you are having difficulty understanding some material, seek help early. There isn’t a TA for this
course, so try come by my office or make an appointment with me if you can’t make it during the
listed office hours.
Dropping/Withdrawing From the Course:
The last day to drop from the course without receiving a “W” is Thursday, February 9th. After the 9th of
February, withdrawal from a course will result in a “W” grade and will count as having taken the course
once. Because the course is overly impacted, I will only issue withdrawals after February 9th for serious,
compelling and documented reasons in accordance with the university withdrawal policy. Note that
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“because I’m not passing the course,” or any similar reason is NOT considered a serious or compelling
reason.
Grading
In-Class Exercises
We will be using the iClicker in-class response system (clickers). Clicker questions will be
presented during class at random times throughout the semester but may not be used in every class
meeting. The clicker sessions will primarily be used as a means to assess your understanding of the
material, but credit will be given for participation as well (see “Calculation of Final Grade,” below). Each
clicker question will count for 1 pt. if correctly answered and 0.25 pt if answered incorrectly. Therefore, it
is to your advantage to answer every clicker question, even if you are not sure of the answer. You will also
receive 1 participation point for answering at least 75% of that session’s questions. Each session will be
normalized to 100%, regardless of the number of questions in the session. For example, answering 3
questions correctly in a 6 question session is worth the same as answering 10 questions correctly in a 20
question session (i.e., each is 50%).
We also will be doing small-group Biochemistry In-Class Group Activity (BIGA) exercises based on
the POGIL (Process Oriented Guided Inquiry Learning) approach throughout the semester. At this point,
the number of sessions is not set, but the dates of the BIGAs sessions will be announced beforehand. The
BIGA sessions are designed to promote and develop critical and logical thinking skills about the subject
matter as well as discussion and communication skills between students. Similar to the clicker sessions,
the BIGA sessions will not be graded individually but will be used primarily as an assessment tool. To
receive credit for the BIGA sessions, each student will have to: 1) be in attendance on the date(s) of the
BIGA session; 2) actively participate in the BIGA session; and 3) submit any required documentation.
Exams
There will be four (4) semester exams (tentative exam schedule is at the end of the syllabus). The
format of each exam will generally be a combination of multiple choice, problem solving and short
answer/essay questions. Each of the semester exams will be after we have finished a module and will
cover material that was in that module. The exams will not be comprehensive. The letter grades of each
exam (and the final grade for the course) will be determined by the point scale outlined in the following
table.
Grade Point Distribution and Grading Scale
Percentage
Letter
Grade
90.0 – 100
A
65.0 – 69.9
C-
86.0 – 89.9
A-
60.0 – 64.9
D+
83.0 – 85.9
B+
55.0 – 59.9
D
80.0 – 82.9
B
50.0 – 54.9
D-
76.0 – 79.9
B-
0.0 – 49.9
F
73.0 – 75.9
C+
70.0 – 72.9
C
Percentage
5
Letter
Grade
Calculation of Final Grade
The final grade will be calculated as follows:
1. The in-class exercises (clickers and small-group work) will each count for 10% of the final grade.
2. The highest score of the four semester exam grades will count for 30% of the final grade.
3. The second highest score will cost for 20% of the final grade
4. The remaining exam scores will each count for 15% of the final grade
The final grade will be calculated based on the formula below:
(Clicker Scores x 0.10)
+ (Group Work x 0.10)
+ (Highest Exam Percentage x 0.30)
+ (2nd Highest Exam Percentage x 0.20)
+ (3rd Highest Exam Percentage x 0.15)
+ (4th Highest Exam Percentage x 0.15)
= Final Grade Percentage
Extra Credit
There are currently no provisions for extra course credit, so please don’t ask. If extra credit
opportunities arise, I will notify you of them. Otherwise, the final grade will be determined only from the
formula above.
Examination Materials
The exams will be administered in class. You are allowed to have a stand-alone calculator, writing
utensils, erasers and nothing else. The calculator function on a cell phone is not allowed. No other
electronic materials are allowed to be out during examination as well. You may also be required to bring a
coin to the exams for the multiple-choice components.
Missed Exams:
If a you miss any exam, you will receive a “0” score for that exam. As policy, no make-up exams
will be given. However, extreme or unusual circumstances may be considered on a case-by-case basis.
Disputing Grades:
You have 7 calendar days from the date that you receive the graded exam to bring to my attention
any perceived errors in grading. However, doing so also gives the me the right to re-check the entire exam
and adjust the grade accordingly, whether it is to your advantage or disadvantage. Only one re-grade per
exam is allowed and the score assigned after a re-grade is final. To request a re-grade, you should follow
the instructions that in the Grade Dispute form on the iLearn website. Regrades for an exam will NOT be
considered after the 7-day period, so it is to your benefit to examine the graded exam soon after receiving
it.
(NOTE: Periodically, I make errors in adding up points. Submitting an exam for a correction of this type
will not count as a regrade, so the exam will not be checked otherwise.)
General Class Issues:
I expect you to attend class regularly and exhibit considerate classroom behavior. Please silence
your cell phone before class begins. If you enter the classroom late, please do so quietly and discreetly as
noisy entrances may disrupt the learning process for your classmates. Once you have entered the
classroom, please remain for the entire class period. If you know beforehand that you must leave early for
some reason, please seat yourself near the exit to minimize any disturbance your exit may cause.
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Students with Disabilities:
Students with disabilities who need reasonable accommodations are encouraged to contact me. The
Disability Programs and Resource Center (DPRC) is available to facilitate the reasonable
accommodations process. The DPRC is located in the Student Service Building and can be reached by
telephone (voice/TTY 415-338-2472) or by email ([email protected]).” (http://www.sfsu.edu/~dprc/
index.html)
Student Disclosure of Sexual Violence:
SF State fosters a campus free of sexual violence including sexual harassment, domestic violence, dating
violence, stalking, and/or any form of sex or gender discrimination. If you disclose a personal experience
as an SF State student, the course instructor is required to notify the Dean of Students. To disclose any
such violence confidentially, contact:
The SAFE Place - (415) 338-2208; http://www.sfsu.edu/~safe_plc/
Counseling and Psychological Services Center - (415) 338-2208; http://psyservs.sfsu.edu/
For more information on your rights and available resources: [http://titleix.sfsu.edu]
Course Outline
(The content for each module will be selected from the given topics; it is
possible that not all topics will be covered)
MODULE 1. CARBOHYDRATE METABOLISM
Segment
Topic(s)
1
Course Overview
Metabolic Principles (Refresher)
Central Metabolism (Continued from fall 2015)
2
Carbohydrate Metabolism, Concluded (Fermentation and the Pentose
Phosphate Pathway)
3
Citric Acid Cycle
4
Electron Transport and Oxidative Phosphorylation
MODULE 2. MEMBRANES AND LIPID METABOLISM
Segment
Topic(s)
5
Fatty Acids and Triacylglycerols
6
β-oxidation
7
Ketone Bodies
8
Membrane Composition/Architecture
9
Membrane Dynamics/Transporters
10
Cholesterol and Lipoproteins
7
MODULE 3. AMINO ACID METABOLISM
Segment
Topic(s)
11
Nitrogen Metabolism
12
Fates of Amino Groups/Glutamine Synthesis
13
The Urea Cycle
14
Protein Degradation
15
Amino Acid Catabolism
16
Amino Acid Biosynthesis
17
Amino Acid Derivatives
MODULE 4-NUCLEOTIDE METABOLISM
Segment
Topic(s)
18
Nucleotides
19
Nucleotide Degradation
20
Nucleotide Biosynthesis
21
Deoxyribonucleotide Biosynthesis
If time permits, the topics below will be covered
22
Nucleic Acid Structures
23
Nucleic Acid Chemistry
Tentative Exam Schedule
(All exams will be given in TH 429. Exams 1-3 will be administered during the scheduled class time. Exam 4 will
be administered during the time scheduled for the final exam by the University)
Exam
Exam Type
Day/Date
Topics
1
Semester
Wed/February 22
Module I
2
Semester
Wed/April 5
Module II
3
Semester
Wed/May 3
Module III
4
Semester
Wed/May 24
Module IV
341.01: 10:45 a.m. – 1:15 p.m.
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