CHE 360 Proteins Spring
2006
Instructor: Jeff Dahlseid, Ph.D. Office:
Nobel 221C, Phone: x6129
E-mail: dahlseid@gustavus.edu Classroom: Nobel 222
Office hours: M 9, F 1:30 or by appointment Laboratory: Nobel 207
Class URL: www.gustavus.edu/~dahlseid/CHE360/index.html Class:
MWRF 12:30-1:30
Texts: Proteins: Structures and Molecular Properties,
Creighton, 2nd Ed., 1993, Freeman, NY, NY and Lehninger
Principles of Biochemistry, Nelson & Cox, 4th Ed., 2005,
Freeman, NY, NY
Course
Description/Theme:
Biochemists
study all aspects of the various molecules found in living systems, including
their structures, synthesis, degradation, physical interactions, cellular
localization, reactivities, and biological functions. Yet biochemistry is more than that. Nelson and Cox write that biochemistryÕs Òultimate concern
is with the wonder of life itself.Ó (pp. 3, Lehninger Principles of
Biochemistry) This course will
focus principally upon proteins and will attempt to give balanced and
integrated consideration to both the various aspects of these molecules and the
wonder underlying their study.
Course Objectives:
Biochemistry
is an enormous subject, and much is lost in attempts to provide exposure to all
aspects of the discipline in two semesters. Thus, we will use protein molecules as a focus and a vehicle
to achieve the objectives of this course.
The central objectives for this course are that you will broaden and
deepen knowledge and understanding of biochemistry and biochemical
principles, develop independent and critical thinking skills, strengthen communication skills,
cultivate and mature collaborative skills, and grow in independence as a
scientist and a ÒlearnerÓ. I hope
that you also experience the excitement of discovery and come to appreciate how
biochemistry and the related biomolecular science fields influence and permeate
one another. Specifically, my
objectives are that you:
¥ add
breadth and depth to your knowledge/understanding of protein biochemistry
¥ learn
to read and critically evaluate the primary literature in the biochemical and
related biomolecular science fields
¥ increase proficiency in communicating your scientific ideas clearly in oral and written form through discussing, presenting, planning, coordinating, executing, recording, reporting, and proposing experimental science
¥ develop
skill at cooperating with a team to achieve progress toward a shared goal
¥ mature
your ability to work independently in a field of experimental science
¥ develop
proficiency at applying your knowledge, the primary literature, biochemical
principles, and experimental approaches to testing hypotheses, both
conceptually and experimentally
Teaching approach:
Your
experience in this course will most likely be different from experiences you
have had in other science courses.
This course is structured particularly to reflect the process of
science. The course
objectives give you some idea of what this is going to look like, especially
the emphasis placed upon increasing your independence as a scientist. In addition, what follows is intended
to give you some idea of how we will spend our time this semester, with the aim
of achieving the course objectives.
Additional descriptions of the major vehicles for achieving these
objectives follow in the syllabus.
We
will use our time together in the classroom a number of
different ways this semester. On
Thursdays we will utilize this as part of laboratory, including having
occasional progress updates as needed (see below). We will regularly use class time for a Journal Club, focused
on presentation and discussion of the primary literature. If properly embraced, these meetings
have great potential to add to the depth of your training in science. Because the research proposal
assignment will likely be new to you, we will periodically focus class toward
the Ôhow toÕ of this endeavor. The
remaining time will be used to review, initially, and then cover new and
advanced topics concerning proteins, through interactive lecture and class
discussion. For this, we will draw
upon multiple sources, including the two texts for the course (both Creighton
and Nelson & Cox - see above) as well as the primary literature and other
sources. I welcome and encourage
your participation in all classroom learning.
We
will use scheduled laboratory time to engage in hands-on, investigative
projects that are aimed toward publication. This will be a lot of fun, and will serve as one vehicle for
cultivating independence through experimental biochemical research. The success of your group will depend
heavily upon careful preparation and planning, and probably will require some
time outside of scheduled laboratory.
To help cultivate the skills necessary, we will have research team
presentations during laboratory to engage in reporting research progress,
trouble-shooting, and planning activity.
This is an opportunity to gain help from your peers and I. Again, I welcome and encourage
your participation.
Because
biochemistry is a challenging discipline, you should prepare in advance for
each meeting and participate in order to gain the most from this class. This includes reading or reviewing
relevant material, preparing questions, identifying points for clarification,
or noting ideas for discussion in class.
Should your participation be lacking in class activities, I reserve the
right to reduce your final grade to reflect this (note participation/attendance
points).
You
are required to attend all scheduled course meetings, both physically and
mentally, to give yourself every opportunity to learn the discipline. If you anticipate a valid reason for
being absent, please see me. I
will try to work with you to make arrangements for acceptable reasons. However, should you miss a class, you
are responsible for understanding the material from class, laboratory
meetings, etc., including handouts.
Note that absences for Journal Club are not permitted due to the
discussion format. If you expect
an unavoidable conflict, notify me immediately to permit rescheduling.
I
welcome and encourage your participation in learning, whether in the classroom
or laboratory. Biochemistry is a
rigorous discipline and I expect hard work, but if you are having problems with
the course please let me know. I
am here to help you learn.
Course Activities
and Requirements:
¥ Content
Summaries: Typically,
preparation for an exam involves cognitive rehearsal of course material,
resulting in learning and retention.
In this class, other means will be use to achieve this outcome. You will prepare summaries of the
content from some of the six units of material covered by the recommend
readings and class lecture and discussion. Typically, these will be due one week after completing a
particular topic. An additional
handout describing the summary is posted and due dates can be found on the
course schedule (see course URL).
¥ Research
Proposal: You will be asked this semester to prepare a comprehensive
research proposal on a topic in the biomolecular sciences. We will be using resource material from
the National Science Foundation and the National Institutes of Health to aid
you in this endeavor, and the proposal will be prepared according to the
National Science Foundation guidelines, modified as appropriate. Deadline for topic selection is February
20th. To help prepare you
for writing the proposal, you will compile an annotated bibliography of the
necessary references from the primary literature (due March 6th). The report itself will be turned in
twice. First you will turn in the
introductory background for the proposal, itself in final form, including
references. Near the end of the
semester you will turn in the entire proposal, including the experimental
section and a revised version of the introductory background. See the course schedule for due dates. You will need to use the search tools
Medline and/or SciFinder, the Gustavus library (and ILL), as well as a larger
regional library (Mayo or U of MN) to identify and obtain the necessary
research articles to complete this assignment. It is recommended that you consider using bibliographic
software, such as Endnote or ReferenceManager. A software option called ProCite is available through the
Gustavus library at no charge. An
additional handout describing the details and information about topic selection
is posted (see course web page).
¥ Journal
Club: Reading,
critically evaluating, discussing and applying the scientific literature are
related and valuable skills. A
common activity where you might employ all of these skills is known as a
journal club. Although this
activity takes many forms, in this class we will be meeting regularly (see
schedule) to critically discuss pre-assigned papers of relevance to the
course. Your full participation
will require that you prepare in advance for these discussions by reading the
papers carefully (and probably repeatedly). Also, for each meeting a group of you will prepare beyond
that of others to be a resource for questions that might arise during the
discussion, i.e. to serve as resident experts on that paper. The structure of this activity aims to
promote participation by all. The
class Journal Club is intended to give you experience with the journal club
format as well as provide an opportunity for you to develop the skills of
independent and critical thinking.
Evaluation will be based on your participation and the quality of your
contributions as an expert group member and as a participant. An additional handout describing the
assignment information and detail is posted (see course web page).
¥ Laboratory
notebooks: Keeping a careful record of your work is a critical component to
laboratory investigation. A
hallmark of scientific credibility is reproducibility, and reproducibility is
favored by a detailed record of work completed. Your project this semester will be investigative, with the
aim of obtaining a publishable (see poster) outcome, so it will be valuable (to
you and to me) to have a clear record of your work. As you will be working with others, I want you to keep a
single notebook for your group. It
will take vigilance to make sure everyone is recording their work, but you can
check each other on this. The
notebooks are to be left in the laboratory, with the exception that they may be
taken out for short periods (30 minutes) for photocopying. However, your group must set up a sign
out procedure even for this, and the notebooks must not leave Nobel Hall. Notebooks will be evaluated during the
semester. Records must be dated,
pages numbered, and detailed enough to repeat.
¥ Progress
summaries: In order to assist you in your project and help you evaluate the
state of your notebooks, each member of your laboratory group will take a turn
at preparing a progress summaries during the semester. As a group, you should compile a
schedule for these and share it with me.
I will expect your group to meet this schedule. Each summary should be done
individually, though you must have your group acknowledge reading of the final
drafts. An additional handout with
details and information is posted (see course web page).
¥ Laboratory
poster: For laboratory, your laboratory group, together, will prepare a
poster and present the outcome of your groupÕs project to the Gustavus
community at semesterÕs end. See
course schedule for the due date for draft presentation and for the final
poster presentation. We will be
spending some class time on the subject of how to prepare posters, and
additional resources will be noted.
An assignment page describing the evaluation criteria for posters will
be made available on the course web site, as the time draws near.
¥ Participation:
Participation
is an important part of learning in this class. It has been intentionally designed into the course
activities through various forms of group work. Thus, it will also be assessed. Part of this assessment will come from me, but I will also
be providing self- and peer-assessment tools for group work.
Grading breakdown:
Content summaries 140
Annotated
bibliography 40
Research proposal
part I & II - 100 pt @ 200
Journal Club
Activities 100
Laboratory notebooks
100
Progress summaries 40
Laboratory Poster
100
Total 850
¥ Final
grades
will be assigned according to a straight percentage scale. The following percentage scale will
serve as a guideline for letter grade assignment:
90-100% = A
80 - 89% = B
70 - 79% = C
60 - 69% = D
Academic
honesty: It is my expectation
and policy that you will participate in this class in an honest and honorable
way. This means that, while I
encourage you to work together to learn protein biochemistry, the work you
submit on behalf of an assignment must be your own. I will not tolerate academic dishonesty. Dishonesty includes plagiarism, which
is presenting some else's ideas or words as your own. Thus, it is your responsibility in written work to credit
sources from which you draw ideas and language (quotes are rare here) with
proper referencing. Gustavus
Adolphus College has an Honor Code, and you will be asked to print and sign the
following statement at the end of major assignments: ÒOn my honor, I pledge
that I have not given, received, nor tolerated othersÕ use of unauthorized aid
in completing this work.Ó
Honorable work is assumed for ALL assignments. If you have questions
about academic dishonesty, please see me.
Documented dishonesty can result in failure of the course and will be
reported to the DeanÕs office.
Class e-mail
policy: I use e-mail to help manage and field questions about the course,
so I require all that you use your Gustavus e-mail account. The advantages to this system include
speed, avoided trips to Nobel Hall for simple questions, and a generally
smoother running course. HereÕs
the protocol. When you have
questions, e-mail them to me.
If your question is very specific, I will reply directly. If the question seems potentially
interesting to the entire class, I will forward the question (anonymously) and
my reply to the class. I will
assume you do not object to sharing your question unless you specifically state
so. I also encourage you to use
the class (s-che-360-all) and lab (s-che-360-003) aliases to ask each other
questions. As I may refer to
e-mail questions in class and I use e-mail for general class announcements, I
encourage you to check your e-mail before class. Campus rules for alias use apply and
abuse will not be tolerated.
Feedback: I am very
enthusiastic about being and becoming an outstanding educator, both for you and
future students. I welcome
constructive suggestions about how to improve class, my teaching, and the
course. I expect to learn from you
this semester how I might teach better.
I invite you to discuss your suggestions with me in my office at any
time.
Students with
disabilities: Appropriate accommodations will be made for students with
specific, documented disabilities of a physical, psychiatric or learning
nature. Related information will
be kept strictly confidential.
Please contact either me or Laurie Bickett (x6286) in Academic
Advising if this applies to you.
Note this syllabus
and schedule are subject to change at the instructorÕs discretion.