Xavier University, CHEM 4140: Metabolism, Spring 2014
Syllabus
Metabolism (CHEM 4140)
MWF 10:00 – 10:50 am (3 credit hours)
NCF 115
Instructor: Dr. Kelly E. Johanson
Office phone: x 7610
Office: NCF 301H
Email: kjohanso@xula.edu
Office hours*: M:1:00-3:00 pm; W:1:00-4:00 pm; R: 11:00 am – 12:00 pm
*Please contact me if you need additional help outside of office hours or if these hours do not work with your schedule.
Required text:
Essential Biochemistry 3rd Edition, 2011, Charlotte W. Pratt and Kathleen Cornely
(You may use the 2nd edition but will need to check page numbers, etc. with the 3rd edition)
Course Outline and Objectives:
This course is a study of biochemical energetics and the many biochemical pathways of carbohydrate, lipid, protein, and
nucleic acid metabolism. The student will gain insight into the metabolism of biochemical substances on the molecular
level, and insight into the universal and integrated nature of metabolism. Prerequisite: C or better in CHEM 4130.
This course will cover key metabolic pathways such as glycolysis, glycogen metabolism, gluconeogenesis, the citric acid
cycle, electron transport, fatty acid metabolism, and amino acid metabolism. We will learn both the compounds involved in
these pathways as well as mechanisms of regulation and control of each pathway. We will also discuss one or more
enzymes from each pathway in detail. Students will be expected to learn the mechanisms of these enzymes and apply this
knowledge to other parts of the pathway. This course will enhance your knowledge of metabolism in preparation for
medical school, graduate school, and other pre-professional programs.
In the text, we will cover chapters 12-19 but will not cover them in numerical order. We will not be able to cover every
detail of each chapter in class. Unless otherwise noted, you are responsible for all material covered in the reading
assignments. You may need to read sections from more than one chapter to prepare for the days lecture. The purpose of
the lecture is to discuss the more difficult concepts and to draw connections between the different pathways. Lecture is not
intended to teach everything in the book nor is it designed to eliminate any need to read and review on your own. You are
expected to come to class prepared to discuss the material and ask questions about concepts that you do not understand.
You must be an active participant in this class in order to fully understand much of the material. It is impossible to learn
metabolism simply by reading a few pages of the text and sitting passively through lecture.
The schedule of topics and readings is provided at the end of the syllabus and is intended as a guide only. While all listed
topics will be covered, they may extend to the next day as needed. Conversely, if a chapter is finished quickly, we will
move on to the next topic.
Course Requirements:
1. Read all textbook chapters assigned.
2. Attend class regularly and take notes
3. Participate in class by asking questions and discussing questions asked by others (including your professor)
4. Complete all Sapling on-line homework on time
5. Turn in all advance work for group assignments, attend class on the day of the scheduled exercise, and turn in the
revised answers after class.
6. Turn in all assignments for project on time
7. Take at three quizzes
8. Take three exams (two during the semester and one final)
9. Read primary literature articles about an inborn error of metabolism and prepare a paper and oral presentation about
your research
Quizzes (150 pts):
There will be 2 scheduled quizzes given during the semester, each worth 50 points. Quiz dates will not be changed unless
there is a change in the University schedule and will start at 10:00 am on the date specified. Extra time will not be given
for late arrivals. If you know you will be absent on a quiz day due to a university-sponsored event, it may be possible to
arrange to take the quiz a day early. Please notify me at least one week in advance. If a quiz is missed due to illness or
other legitimate but unanticipated event, you may take a make-up on the date specified on the schedule as long as
documentation is provided at least one week after the missed quiz (note that the make up will not be the same quiz taken by
your classmates). If more than one quiz is missed, please see me to discuss your specific circumstances. Pop quizzes on
the reading assignments will be given at random throughout the semester. These quizzes will be given in the first 5 minutes
of class and will be worth 10 points each. Only the top 5 pop quiz scores will count toward your final grade. The total
number of quizzes given will be determined by the instructor but will be 7 or greater. Pop quizzes cannot be made up, if
you are absent or arrive late it will count as one of your dropped scores. You may only take the pop quiz if you are in the
classroom by 10:02 am.
Homework (150 pts):
There will be 10 homework assignments worth 15 points each given using the Sapling learning system. You may work on
these problems throughout the semester; but they must be completed by 11:00 pm on the due date. Late homework will not
be accepted. Please log in to the Sapling system for more information and for practice exercises. It is your responsibility to
keep track of due dates for each homework. There will be an opportunity in class to ask questions about homework
assignments (see schedule at the end). However, if less than 50% of the class has attempted the homework on the
scheduled question day, the homework will not be discussed. Questions about homework can be asked at any time during
office hours.
There is opportunity to earn bonus points by completing a Sapling practice exercise, a review on amino acid and sugars,
and a review of all chapters before the final exam. Sapling grades will be transferred to Blackboard at midterm and after
the final exam. At all other times, you may check your homework grade on the Sapling website.
CHEM 4140 Homework
In class Q's
24-Jan
29-Jan
7-Feb
12-Feb
21-Feb
26-Feb
12-Mar
21-Mar
7-Apr
26-Apr
Due Date
20 Jan
25 Jan
30 Jan
9 Feb
13 Feb
22 Feb
27 Feb
13 Mar
23 Mar
8 Apr
27 Apr
1 May
Topic
Amino acids and sugars
1 - Thermodynamics, free energy, enzyme classification
2 - Metabolic pathways, redox reactions
3 - Electron transport, chemiosmosis, ATP
4 - Citric acid cycle
5 - Glycolysis, lactate, fructose catabolism
6 - Gluconeogenesis, pentose phosphate pathway
7 - Glycogen, hormonal regulation of glucose metabolism
8 - Fatty acid metabolism
9 - Nitrogen metabolism, urea cycle
10 - Integration of metabolism, disorders of metabolism
Final exam review (all topics) - Grad seniors due 8:00 am 4/29
*Bonus
Points
*5
15
15
15
15
15
15
15
15
15
15
*10
To log into the Sapling system:
1. Go to http://saplinglearning.com
2a. If you already have a Sapling Learning account, log in and skip to step 3.
2b. If you have Facebook account, you can use it to quickly create a Sapling Learning account. Click the blue button with
the Facebook symbol on it (just to the left of the username field). The form will auto-fill with information from your
Facebook account (you may need to log into Facebook in the popup window first). Choose a password and timezone,
accept the site policy agreement, and click "Create my new account". You can then skip to step 3.
2c. Otherwise, click the "Create an Account" link. Supply the requested information and click "Create My Account". Check
your email (and spam filter) for a message from Sapling Learning and click on the link provided in that email.
3. Find your course in the list (listed by school, course, and instructor) and click the link.
4. Select your payment option and follow the remaining instructions. (Cost: $29.99 on-line; possibly cheaper if purchased
bundled with the text book in the bookstore). Once you register, you will have 2 weeks to complete the payment
information.) If you cannot afford the Sapling fee, please let me know ASAP. If I have not heard from you by the third
week of classes, financial difficulty will not be accepted as an excuse for failing to complete homework assignments.
Once you have registered and enrolled, you can log in at any time to complete or review your homework assignments.
If you have any technical problems or grading issues, send an email to support@saplinglearning.com explaining the issue.
The Sapling support team is almost always more able (and faster) to resolve issues than your instructor.
Group Exercises (150 pts):
There will be 4 group exercises each worth 50 pts (see schedule). These exercises will require you to work on an
assignment designed to connect the material from the textbook with data from primary literature articles. The assignment
will be available on Blackboard one week prior to the date listed on the schedule. You are required to answer the questions
using only your book and notes. You may not discuss the questions or answers with other students, faculty, or look up
information using the internet. Students found to violate this policy will receive a zero for the entire assignment and will be
reported for academic misconduct.
The grade for this assignment will be calculated based on work done before, during, and after class. Your answers to the
posted questions must be uploaded to Blackboard by 11:00 pm the day before the Group Exercise date listed on the
schedule (15 points). This first part will be graded primarily on effort, although the full 10 points cannot be earned unless
at least some of the answers are correct. Assignments turned in between 11:00 pm and 10:00 am will receive a 10% point
deduction. In class, you will be split into groups of 2-3 and given 10-15 minutes to compare and discuss your answers.
After that, we will have a class discussion of the answers with each group leading part of the discussion (30-40 minutes).
Your participation in the class discussion is worth 10 points; a rubric will be provided for the in class points so that you will
know what is expected during class. After class, you are expected to use the information from the class discussion to revise
your answers where necessary. The revised answers must be uploaded to Blackboard by 11:00 pm the day following the
Group Exercise date (25 points). Late revised assignments will not be accepted unless Blackboard is down for more than
12 hours.
If you turn in the first part of the assignment and are absent the next day for a legitimate reason (severe illness, university
sponsored event, etc.) you will still receive credit for the work turned in but and may able to make up the second part of the
assignment if documentation is provided for your absence. If you do not turn in the assignment before class, you will be
allowed to participate in the group discussion and turn in an assignment after class but will be docked 5 participation points
and will not be able to make up the points for the advance assignment. At the end of the semester, I will drop the lowest
Group Exercise grade; however, zeros due to missed assignments cannot be dropped. You should bring your text and all
notes to class on Group Exercise days.
Project (200 pts):
You will explore an inborn error of metabolism using primary literature articles. You will research the genetic cause of this
error and how it specifically affects at least one of the pathways we will study this semester. This project will be done in
groups of 2 (a group of 3 may be allowed if there are an odd number of students in the class). Each group member will
write their own paper focusing on one particular aspect or enzyme involved in the disorder. Papers from group members
can contain similar (but not identical) background information but should not be significantly similar in other areas of the
text. The same references may be used for both papers, although the reference list should not be identical. Each paper
should be 8-10 pages, double-spaced, with references cited in the text and is worth 150 points. Each group will combine
and present their findings to the class in a single 10 minute oral presentation (50 points) at the end of the semester (see
schedule). It will not be possible to discuss everything about your topic in 10 minutes; your group will need to decide what
information is most important and most interesting. Your paper and presentation must include information about the direct
connection between the disorder and a specific metabolic pathway discussed in class.
You will have several assignments due throughout the semester to help you prepare both assignments. These interim
assignments will count toward 10% of your final paper grade. The due dates for these interim assignments are given on the
schedule (all assignments are due by 11:00 pm on the due date). All assignments including the final paper draft will be
turned in using Blackboard; email or hard copies will not be accepted. Late assignments will receive feedback, but will not
receive any points. Your final paper is due the day of your presentation. Rubrics for both the paper and presentation will
be provided and discussed in class before the due date. A list of topics will be provided on a Google docs spreadsheet (link
on Blackboard) – please sign up ASAP. You may choose a topic not listed, but must obtain approval for this topic before
January 22.
CHEM 4140 Project - Interim assignments
22-Jan
17-Feb
24-Feb
13-Mar
27-Mar
Topic - Write a brief description of your topic. You must include the names of the enzymes that you
will explore in your papers/presentation and how the topic will be divided among group members (this
may change as you do more research about the topic). If your disease is not linked to specific
metabolic enzyme, include a brief explanation of the connection between this disease and metabolism.
Only one group member is required to turn in this assignment (2 points)
Annotated Bibliography - Write annotated entry for 7-8 primary sources. You may use one website as
a source, but it cannot be Wikipedia or any other general interest website. Each group member must
turn in their own annotated bibliography but it can contain some of the same references. The
annotations should be different for the majority of the shared sources (3 points).
Outline - Write an outline of your paper. There is no specific format or level of detail required, but the
more detail included the more specific the instructor can be with feedback. Each group member should
turn in their own outline (3 points).
Rough Draft - Turn in a complete draft of your paper. This draft will be reviewed by another student,
please do not include your name on the draft so that the peer review process can remain anonymous.
Annotations should not be included in reference list. Each group member should turn in their own
rough draft (5 points).
Peer Review Rough Draft - Complete a peer review for two other students. Rough drafts turned in
after the due date will not receive a peer review and you will not be allowed to complete a peer review.
Each group member will complete two reviews. You may review your partner’s paper (2 points).
Exams (300 pts):
Two 100-point exams will be given according to the schedule. Exam dates will not change unless the University schedule
is changed. A cumulative final exam (100 points) will be given on Friday, May 2 at 1:30 pm. If you miss an exam, you
may take an essay-format make-up exam on the date specified in the schedule or you may double your final exam grade.
Graduating seniors will take their final on the last day of class.
All quizzes, group exercises, exams, and homework assignments collected prior to March 17, 2014 will be used to calculate
your midterm grade. Low scores will not be dropped during calculation of the midterm grade.
The final grade will be determined as follows after the lowest pop quiz and group exercise scores have been dropped:
(Exam grades) + (Quiz grades) + (Homework) + (Bonus) + (Project) /950 = %
A 90% - 100%
B 80% - 89%
C 70% - 79%
D 60% - 69%
F below 60%
Course Policies:
1. Please silence all cell phones before class.
2. Please do not text during lecture. This is very disruptive to your instructor and to fellow students. We only have 50
minutes together each day, please spend that time actively engaged in the class.
3. Graded assignments will be returned in class or on Blackboard as soon as possible. Please ask if you do not know
how to view comments on a graded assignment in Blackboard. If you are not in class the day an assignment is
returned, please see the instructor to collect your assignment. If an assignment has not been picked up after one
week, it will be placed on a shelf outside of the instructor’s office for collection.
4. Grades on all work may be disputed up one week after being returned. Errors in adding up points can be brought to
my attention after class. Regrades must be requested in writing with the reason for the regrade. Regrades may
result in a grade higher or lower than the original grade.
Evacuation policy:
In the event that classes are cancelled due to a hurricane evacuation, assignments and course materials will be posted to
Blackboard. Please log on to the Blackboard site as soon as possible after the evacuation.
Academic Misconduct:
The CAS Academic Integrity Policy will be followed in this course. According to the policy, academic misconduct
includes, but is not limited to, the following:
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
Using unauthorized materials in completion of an exam, quiz, or assignment.
Assisting or gaining assistance from an unauthorized source during an exam, quiz, or
assignment.
Providing assistance to another student in a manner not authorized by the instructor.
Obtaining an examination or assignment in an unauthorized manner.
Using material from a source without giving proper citation.
Fabricating or altering data.
Submitting work to one class that is substantially similar to work submitted for another class
without prior approval from the instructors involved.
Submitting written work that is not completely one’s own or allowing others to submit one’s
work.
Destroying or altering the work of another student.
Committing any other violation of academic integrity as described in this syllabus.
Specific examples of academic misconduct in this class include:
•
•
•
•
•
•
the use of a cell phone during an exam or quiz for any reason (even as a calculator);
talking during an exam or quiz;
using anything other than explicitly authorized materials on a quiz or exam;
attempting to read from another student's quiz or exam;
copying class assignments
working with others on any assignments (in or out of class) when not authorized;
You are responsible for arriving on time for all quizzes or exams, as you will not be permitted to begin after any other
student has left the room. You are responsible for all written materials on, under, and near your seat during quizzes and
exams, so it is in your best interest to ensure that the desk surface is clear of writing and that no extraneous papers are
within your line of sight (both when you begin and finish). Cell phones should always be off and inside a bag during a quiz
or exam; your instructor will not give you the benefit of the doubt if a cell phone is used or visible. The CAS policy makes
no distinction between the person receiving unauthorized assistance (copying an assignment) and the person providing the
assistance (allowing work to be copied); both actions are academic misconduct.
All cases of academic misconduct will be reported to the CAS Dean's Office per Xavier's Academic Integrity Policy. Any
case of academic misconduct on assignments will result in a grade of zero for the assignment and may result in a grade of F
for the entire course. Premeditated academic misconduct during an exam (for example, using a cell phone to text or
preparing a “cheat sheet”) will result in the student being asked to leave immediately and in a failing grade for the course.
A grade of zero assigned for academic misconduct may not be counted as a drop score.
Date
13 Jan
15 Jan
17 Jan
20 Jan
22 Jan
24 Jan
27 Jan
29 Jan
31 Jan
3 Feb
5 Feb
7 Feb
10 Feb
12 Feb
14 Feb
17 Feb
19 Feb
21 Feb
24 Feb
26 Feb
28 Feb
3 Mar
5 Mar
7 Mar
10 Mar
12 Mar
14 Mar
17 Mar
19 Mar
21 Mar
24 Mar
26 Mar
28 Mar
31 Mar
2 Apr
4 Apr
7 Apr
9 Apr
11 Apr
14 Apr
16 Apr
18 Apr
22 Apr
24 Apr
26 Apr
28 Apr
2 May
Lecture Topic
Course Introduction/KnowledgeAssessment
Metabolism: substrates and products
Enzymes: Classes/Regulation
Martin Luthur King Jr. Holiday
Thermodnamics/free energy in biological systems
Metabolic pathways
Thermodynamics of Redox Reactions/ The mitochondrion
Electron Transport
Chemiosmosis/ATP Synthase
Group Exercise 1
Citric Acid Cycle Reactions/Regulation
Anabolic/Catabolic Functions of CAC, Quiz Review
Quiz 1, Glycolysis introduction/reactions
Glycolysis reactions/regulation
Pyruvate/Lactate/Cori cycle/
Catabolism of other sugars/alcohol
Group Exercise 2
Gluconeogenesis
Pentose phosphate pathway
Lecture as needed/Exam Review
Exam 1
Mardi Gras Holiday
Mardi Gras Holiday
Mardi Gras Holiday
Glycogen metabolism/Hormone regulation
Fatty acid transport/ oxidation
Fatty acid oxidation
Fatty acid synthesis,Ketone bodies
Group Exercise 3
Syntheis of other lipids
Nitrogen fixation/Transamination, Quiz Review
Quiz 2,Amino acid synthesis
Nucleotide synthesis/catabolism
Amino acid catabolism
urea cycle
Group Meetings (Project)
Group Exercise 4
Lecture as needed/Exam Review
Exam 2
Presentations
Presentations
Easter break
Integration of metabolism
Disorders of fuel metabolism
Final Exam Review/Make-ups
Final Exam ( GraduatingSeniors)
Final Exam
Reading
Syllabus
12-1
6-1, 6-2,7-1, 7-2(198-200),7-3
1-3, 12-3
12-2
15-1
15-2
15-3, 15-4
14-2
14-3
13-1
13-1
13-1, 14-1, 19-1
Box 13A, 13B
13-2
13-4
13-3, 19-2
17-1
17-1
17-2
17-3
18-1
18-2
18-3
18-4
18-5
19-1, 19-2
19-3