CHE 255
Biochemistry
Fall 2005
Instructor: Jeff Dahlseid, Ph.D.
Class: MTWF 11:30-12:20
Office: Nobel 221C, Phone: x6129
Classroom: Nobel 222
E-mail: dahlseid@gustavus.edu
Laboratory: Nobel 207
Class URL: www.gustavus.edu/~dahlseid/CHE255/
Office hours: M 2:30, W 9:00, F 1:30
Texts: Chemistry 255 - Biochemistry Lab Manual
Lehninger Principles of Biochemistry, Nelson & Cox, 4th
Ed., 2005, Freeman, NY, NY
Description and Course Outline:
Biochemists study the molecular
basis for the functioning of living systems, including the structures,
chemical properties, physical interactions, and biological functions of
biochemicals. Yet biochemistry is more than that. Authors of our
textbook write that biochemistry's "ultimate concern is with the wonder
of life itself." (pp. 3) Biochemistry is surely an exciting and integrative
field of study. The four types of macromolecules central to biochemistry
are called proteins, nucleic acids, lipids, and carbohydrates. This semester
you will discover these and a host of other biomolecules, be exposured
to techniques and principles for biochemical investigation, and gain insight
into the significance of biochemistry as part of our effort to understand
the living world.
In this course, we will
study proteins, their building blocks, structure, and folding. We will
learn about nucleic acids, their structure, building blocks, and how these
molecules store genetic information. A case study of the proteins involved
in oxygen binding and transport, including their physiological context,
will serve to illustrate the relationship between protein structure and
function. We will extend these ideas by considering enzymatic catalysis
and kinetics of biochemical reactions. We will study lipids and the associations
that give rise to membranes, the principal biological barrier. Consideration
of biosignaling processes will help us appreciate the control of the metabolic
processes we will study. An introduction to bioenergetics and carbohydrates
will precede a study of energy metabolism including glycolysis, the citric
acid cycle, and oxidative phosphorylation. Examples of the mechanisms of
protein catalysis and of the mechanisms regulating protein function will
be integrated into the material.
Course Objectives:
This course aims to integrate
class and laboratory learning of biochemistry. Although a course in biochemistry
necessarily involves learning new facts and laboratory techniques, my goal
for this course is that you will come to appreciate the breadth
of biochemistry and develop a solid background its fundamental principles
and practices. Specifically, my objectives regarding content are that you:
-
develop a knowledge of biochemical building blocks and how their structures
and assembly mediate their biological functions
-
appreciate nucleic acid structure and its informational role in genetics
-
understand and apply principles of enzyme kinetics to biochemical problems
-
appreciate the structures of lipids and the interactions that contribute
to the formation and maintenance of membranes
-
develop a knowledge of the events and principles of signal transduction
-
comprehend the principles of bioenergetics and how the reactions and events
of catabolism, the citric acid cycle, and oxidative phosphorylation produce
energy
-
appreciate the relationship between the structure and function of biomolecules
-
illustrate mechanisms of protein catalysis and regulation
Laboratory is an integral part
of this course. Our hands-on learning about biochemical investigations
will focus upon protein enzymes and their activities, properties, and kinetics.
Laboratory will also have an emphasis on scientific writing. For laboratory,
my objectives are that you:
-
understand and use many of the techniques and tools of biochemistry
-
comprehend fundamental principles of biochemical experimentation and research
-
communicate research results accurately and effectively in written form
Teaching approach:
We will primarily use class
time to engage in learning course material, and it is my hope that together
we can cultivate an environment of active learning (including real discussion).
Because of this approach and the challenging nature of the subject, you
should expect effective learning to come from reading the text material
for each class meeting ahead of time and preparing questions, points
for clarification, or ideas for discussion in class. You are required
to
attend class, both physically and mentally, to give yourself every opportunity
to learn the material. Repeated unexcused absences will be sufficient basis
for a lower course grade. If you anticipate a valid excuse for being absent,
please see me about being excused. In the event that you miss a class,
you are responsible for understanding the material from class, including
handouts, etc.
We will use scheduled laboratory
time to engage in hands-on learning about biochemical techniques and principles
as well as to focus upon scientific writing. Coming prepared, as for class,
is highly recommended. I believe this is so important that we will hold
pre-laboratory meetings before each scheduled exercise. You are
required
to attend laboratory, both physically and mentally. Failure to do so will
result in failure of this portion of the course. If your attendance is
challenged by a crisis or emergency, please contact me as soon as possible.
Arrangements will be made for valid circumstances.
I welcome and encourage
your participation in classroom and laboratory learning. Biochemistry is
a rigorous topic and I expect everyone to work hard, but if you are having
problems with the course please let me know. I am here to help you learn.
Academic honesty:
It is my expectation and
policy that you will participate in this class in an honest and honorable
way; I will not tolerate academic dishonesty. While I encourage you to
work together to learn biochemistry, the work you submit on behalf of an
assignment or exam must be your own. Dishonesty includes plagiarism, which
is presenting someone else's ideas or words as your own. It is your responsibility
in all written work to credit sources from which you draw ideas and language
(quotes are rare here) with proper referencing. Dishonesty also includes
cheating on exams. Gustavus has an Honor Code and, by virtue of being a
student here (as well as your signed agreement from course registration),
you have agreed to uphold the Honor Code. In this course, you are required
to sign the following statement for papers and exams (though it applies
to all of your work): "On my honor, I pledge that I have not given, received,
nor tolerated others' use of unauthorized aid in completing this work."
Central to the code is non-tolerance for violations. Though you are not
expected to police others' actions, under the code (and in this class),
failure to report a violation of which you are aware also constitutes an
honor code violation. Documented violations will result in a zero for the
assignment in question, will be reported to the Dean's office, and may
result in failure of the course. If you have questions concerning particulars
of academic honesty, please see me.
Course Activities and Requirements:
-
Research Article Summaries: Throughout the semester, you must use
the search tools Medline or SciFinder Scholar and the Library (and ILL)
to identify and obtain a copy of a research article on a biochemical topic
(NOT a review) of interest to you. You will be required to read the article
and write a two-page summary addressing a series of provided questions.
Due dates are on the schedule. See course web page for details.
-
Protein Explorer (PE) Exercises: This assignment will require you
to do three things: 1) learn how to use a tool for the graphic display
of molecular structures called Protein Explorer, 2) use Protein Explorer
to explore the structures of biomacromolecules (proteins mostly) and capture
a graphical image of your molecule, 3) record your observations from your
exploration of molecular structure. Due dates are below. See course web
page for details.
-
Exams: During the semester you will be required to take four mid-term
exams and a final exam. The mid-term exams will cover new material and
concepts covered in class, laboratory material, and assigned readings through
the test date. The final exam will be comprehensive, so it will be important
to integrate your learning of material from throughout the course. All
exams will assess your cumulative learning of biochemical principles, problem
solving skills, and critical thinking skills. They will require some level
of synthesis and include questions requiring recall (facts, names and structures)
and short answers.
The mid-term examss and
comprehensive final exam will be given at the times indicated on the schedule.
Exam
attendance is mandatory, and exams cannot be made up except for a crisis
or emergency. For a crisis, you must talk with me personally
in advance to arrange for a make-up exam. In an emergency, contact me by
phone, voice-mail or e-mail, or, if you are unable to reach me, Nadine
Zuhlsdorf (x7320) in the Chemistry office or the Dean's office (x7526).
IF I am properly notified AND your emergency is valid, a make-up exam will
be arranged. All students must take the final exam as scheduled.
-
Laboratory reports: For laboratory, you will write two short reports
and a initial and final draft of a full report as part of an integrated
series of activities intended to promote good scientific writing. Both
report types will be formal. The short format allows an early focus on
the writing of methods and results. The full report is designed to provide
significant feedback on a complete report. See the lab manual for scheduled
due dates and assignment details. Note that the Writing Cener (x6027 for
appointments) is available to you for help with your writing.
-
Peer evaluations of laboratory reports: You will evaluate the initial
draft formal report of one of your peers. Additional detail will be available
as the time nears.
-
Data analysis and questions (DAQs): You will complete and
hand in your data analysis and answers to provided questions for three
laboratory exercises. These assignments are aimed at assessing your ability
to perform technically in laboratory, to acquire good data, and to meaningfully
analyze and present it.
-
Experimental investigation: This multi-week experience will
proposing, planning and implementing an original biochemical investigation.
Stay tuned for details.
-
Laboratory notebooks: Keeping a careful record of your work is a
most
important component of laboratory investigations. You must
keep
a laboratory notebook for biochemistry laboratory. The notebooks will be
collected twice during the semester for evaluation (see schedule). Note
that although notebooks receive their own point score (see below), I will
make substantial penalty point reductions for laboratory reports that are
inadequately supported by a laboratory notebook record.
Grading breakdown:
Article summaries (2 @ 30 pts)
60
PE exercises (2 @ 20 pts)
40
Midterm Exams (4 @ 100 pts)
400
Comprehensive final exam
100
Laboratory reports
Short reports (2 @ 20 pts)
40
First draft full report
25
Final draft full report
75
Peer evaluation
30
Experimental investigation
70
DAQs (3 @ 10 pts)
30
Laboratory Notebooks (2 @ 20 pts)
40
Total 910
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
Class e-mail policy: I use e-mail to help manage the course and
field questions about the material, so I require 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.
Here's 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 f-che-255 class alias 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 (x7027) in Academic
Advising if this applies to you.
Note this syllabus and schedule are subject to change at the instructor's
discretion.