In this course
you will participate in ongoing research in biochemistry and depending
upon the results of your lab exercises you may be asked to co-author a
scientific publication in a peer reviewed journal. Each experiment
plays a role in an overall project in the directed molecular evolution
of proteins with the alpha/beta barrel protein architecture. You will,
in effect, design a new protein with improved biochemical properties
while learning experimental techniques that are basic to biochemistry.
Material to be covered includes using a UV-Vis spectrophotometer,
kinetic analysis of enzymatic function, protein purification and
analysis but most importantly we will focus on your critical thinking
skills as they apply to experimental design and the interpretation of
results. Techniques include error and statistical analysis of
experimental data, colorimetric spectrophotometry, gel permeation
chromatography and electrophoretic techniques, and maintenance of a
scientific notebook in a professional fashion. You will learn to
write-up scientific experiments in the fashion of peer-reviewed
journals and learn to critically evaluate the experimental manuscripts
of others. The Laboratory section of CHEM 401 is worth 25% of your
overall grade in CHEM 401.
Course Outline
(Lab Schedule)
|
Week |
Topic |
Due date |
Point Value |
|
1 |
Safety Exam,
Notebook Instruction, Scientific Method
Project &
Course Overview
Homework
Assignments:
1. “Learning
Style Survey” & “Learning Style Survey Results Survey” (found
under “Assignments” in Blackboard)
2. Reading a
Scientific Paper Francis Arnold’s Directed Evolution Approaches to
Protein Design and participation in online discussion |
Same Day
Next lab
Next Lab |
10
10 |
|
2 |
Viewing
Protein Structure; Analysis of Architecture and Active Sites (SwissPDB
Viewer)
|
Next lab |
20 |
|
3
|
PCR
Techniques & Error Prone PCR
|
Next lab |
20 |
|
4
|
Restriction
Digest, Gel Electrophoresis, and Critical Analysis
Peer Scoring
of Lab Report 2 Due |
Next lab |
20
10 |
|
5 |
Ligations,
Transformations, & Selections
Peer Scoring
of Lab Report 3 Due |
Next lab |
20
10 |
|
6
|
Midterm |
|
80 |
|
7 |
Protein
Purification
IMAC
Chromatography, Anion Exchange FPLC, & Affinity C.
Peer Scoring
of Lab Report 4 Due |
Next lab |
20
10 |
|
8
|
Measurements
of Protein Concentration & Standard Curves
Read Paper:
Bradford, M. M. (1976) A Rapid and Sensitive Method for the
Quantitation of Microgram Quantities of Protein Utilizing the
Principle of Protein-Dye Binding. Anal. Biochem. 72:248-254 and 3.
Online Discussion
Peer Scoring
of Lab Report 5 Due |
Next lab |
20
10 |
|
9
|
SDS-PAGE
and critical analysis of 3 different methods of purification
Peer Scoring
of Lab Report 6 Due |
Next lab |
20
10 |
|
10 |
Enzyme
Kinetics
Peer Scoring
of Lab Report 7 Due |
Next lab |
20
10 |
|
11 |
Enzyme
Inhibition
Peer Scoring
of Lab Report 8 Due |
Next lab |
20
10 |
|
12
|
Methods in
Protein Stability Analysis (Micro-calorimetry)
Peer Scoring
of Lab Report 9 Due |
Next lab |
20
10 |
|
13 |
Measurement of
Dissociation Constants
Peer Scoring
of Lab Report 10 Due |
Next lab |
20
10 |
|
13 |
Final Exam
Peer Scoring
of Lab Report 11 Due |
|
100
10 |
All labs begin at 8:00 a.m. If you are late,
one letter grade will be deducted from your lab report.
- Expect a 15 minute quiz
at the beginning of each lab covering material addressed in the last
lab period. There are no make-ups so make sure to come to class on
time.
- Labs will be written in
Lab Report Format similar to a scientific paper (see handouts) and
must be handed in both in paper and electronic format at the
beginning of the next lab.
- You will participate in
peer scoring exercises for each lab. Scorings are due at the
beginning of the lab after it was first assigned
- There are no pre-lab
assignments
Below is the Syllabus and links to specific
content and course tools.
DIVISION OF NATURAL SCIENCES AND
MATHEMATICS
CLAFLIN UNIVERSITY
Instructor
Office Phone Email
Dr. Nicholas Panasik Jr.
JST 221 803.937.9600 npanasik@claflin.edu
Yahoo Messenger ID:
Protein_structure_lab
Office Hours & Consultation:
MW 10:00 a.m. – 11:30 a.m. & 1:30 p.m.
– 3:00 p.m.; R 1:30 p.m. – 3:30 p.m.
We can always set an appointment for
another time via email and I am also happy to answer questions via
email or through the Blackboard Discussion board.
You can drop by at other times but I
may be busy. Feel free to send a text message to my phone to see when
I am free, or to Instant Message with me using Yahoo Messenger with
screen name: protein_structure_lab
Laboratory (Dr.
Panasik): Lecture (Dr.
Peters):
L01, 8:00 -10:50 a.m. T, JST
129 10:00 – 10:50 a.m. MWF, JST Rm. 32
L02, 8:00 -10:50 a.m. R,
JST 129
Blackboard
There is a course module for this lab at
http://blackboard.claflin.edu
Sign in with your normal Claflin ID
and password
Expectations (of You):
1.
You are expected to attend Dr. Peter’s Lectures.
2.
You are expected to attend ALL lab sessions and be on time.
3.
You are expected to check your email regularly (daily) for
announcements, added instructions, or discussion.
4.
You are expected to use check Blackboard regularly (biweekly) for
course announcements, lab protocols, and for submission of lab reports
5.
You should understand the precise meanings of all chemical and
biochemical terms discussed in lab and used in the reading
assignments.
6.
All lab reports must be submitted electronically through Blackboard in
Microsoft Word format.
7.
All lab reports must be in the proper Biochemistry Lab Format; details
of which are posted on Blackboard.
8.
You are expected to follow the Claflin Honor Code and all Safety
rules.
Expectations (of Me):
1.
I
am expected to provide a rich, intellectually challenging, and useful
series of exercises to enhance your understanding of biochemistry.
2.
I
am expected to train you in hands-on biochemical techniques, and help
you to increase your critical thinking skills and ability to use the
Scientific Method.
3.
I
am expected to be available and accessible to answer questions, and
facilitate your understanding of course and laboratory material.
4.
I
am expected to return graded materials in a timely fashion.
5.
I
am expected to be fair and equal in grading and dealing with students.
Laboratory Manual & Additional
Materials:
Instructions for
Labs and additional materials including Useful Information, Code of
Honor, my Teaching Philosophy, the Learning Style Survey and other
materials can be found on Blackboard (http://blackboard.claflin.edu)
Laboratory Safety & Honor Code:
Safety goggles will be worn at all
times in the laboratory. They can be purchased from the Chemistry
main office for $5. All students will view and be tested on a safety
video. You must pass the safety quiz with 100%. A safety contract and
Honor Code will be reviewed and signed by students.
Course Prerequisites:
If you have not completed a full year
(8 semester hours) of Organic Chemistry (with a C or better)
then you are not qualified for this course. Drop-it immediately.
CHEM 231 and 232 and BIOL 121 or 122.
Textbook (required):
Horton, R.H.; Moran, L.A.; Ochs,R.S.;
Rawn, J.D.; and Scrimgeour, K.G. (2006). Principles of Biochemistry,
4th Edition. (New Jersey; Prentice Hall).
Homework Problems:
Homework problems will come in the
form of lab write-ups for each lab and some
exercises on Blackboard.
Attendance and
Test Policies:
Lecture attendance is strongly
recommended. Laboratory attendance is required. There are no make-up
exams or labs. If you have an “Official Absence” (one that comes
complete with a letter from a University Official such as an athletic
director) then a virtual lab will be assigned in place of the lab that
you missed. You may drop 1 lab. Do not ask for special testing
privileges; it is not fair to others.
IV.
Course Evaluation
This Lab Section forms
25% of your overall grade for Biochemistry I (CHEM 401)
You can drop ONE lab.
There are 300 total points for the lab course (after 1 lab is
dropped).
See course outline for
values of individual items.
V.
Grading Scale
A
= 90 to 100 B+ = 85 to 89
B = 80 to 84 C+ = 75
to 79
C = 70 to 74 D+ = 65
to 69
D = 60 to 64 F =
0 to 59
VI.
Collaborative
Group Learning
If the lecture class has a failing
rate of 40 % or higher after the first exam, we will use the
“Group-Collaborative Learning model”. All students will be placed
into study groups (cohorts) of 5-6. Groups will study Biochemistry
lecture and lab content. Prior to any exam, each group will receive
questions to present to the class. Many of these questions will be
placed on the exam. Extra credit will be given to groups for scoring
the highest.
VII.
Surviving
Biochemistry
This course is
challenging, exciting and full of information. You will be expected
to integrate large amounts of complex information that will be
essential throughout your professional life. Excellent study habits,
organizational skills and your ability to focus will play an important
part in your success in this class. You must prepare (read) prior to
every class or you will fail. It is recommended that, after taking
the Learning Style Survey (offered in Blackboard) that you adopt some
of the study methods recommended for your particular learning style.
By succeeding in this class, you will be prepared for graduate school,
a research career or a health related career. You will be tested on
material that will require you to think, and make an informed decision
based on what you have learned, not based on memorization. You must
interpret data and formulate explanations. The exams will incorporate
standardized questions from the American Chemical Society, old ETS
exit exams and old GRE tests. Yes, you will be just as prepared and
knowledgeable as students from Ivy League institutions when you leave
this course. You have access to Organic Chemists, use them, we have
the best in the state. Also, take advantage of the supplemental
materials on reserve in the library and use the expertise of Dr.’s
Bagasra, Dillard, Panasik, Harris, and Chen. My expectations are
high, the bar has been raised and we will not lower our standards
because you are not prepared.
VI.
DISABILITY SERVICES
Disability services at Claflin University
exist to enable individuals with disabilities to participate in the
full range of college experiences. Claflin University recognizes an
individual with a disability as anyone who (1) has a physical or
mental impairment that substantially limits one or more major life
activities (2) has a record of such impairment, or (3) is regarded as
having such impairment.
A “qualified person with a disability” is
defined as one who meets the academic and technical standards required
for admission or participation in the education program or activity.
Individuals requesting accommodations must
provide current documentation of their disability to the Counseling
and Disability Center, located in the Student Campus Center. Office
hours are Monday through Friday, 8:00 a.m.-5:00 p.m. Information
pertaining to disability services can also be found on the Claflin
website at
www.claflin.edu.
VIII. Claflin Honor Code
CODE
OF HONOR POLICY STATEMENT
Claflin University prohibits all forms of academic or
scholarly dishonesty,
including written or oral examinations,
term and research papers or theses,
modes of creative expression,
and computer-based work.
Scholarly dishonesty includes lying,
cheating,
plagiarism,
collusion,
and the falsification or misrepresentation of experimental data. (For
social behavior,
see
Claflin
University
Student Handbook: Code of Conduct,
and Code of Ethics).
CODE
OF HONOR PLEDGE
In my enrollment at
Claflin
University,
I do hereby solemnly pledge that I will adhere to the Code of Honor.
As a
Claflin
University
Student,
I do solemnly pledge to uphold the integrity of
Claflin
University.
I will not participate in nor tolerate dishonesty in any academic
endeavor.
CODE
OF HONOR DEFINITION OF VIOLATIONS
1. Academic Dishonesty – This includes any other act (not
specifically covered in previous provisions) that compromises the
integrity of a student or intrudes on,
violates,
or disturbs the academic environment of the University Community.
Examples include attempting or agreeing to commit,
or assisting or facilitating the commission of,
any scholastic dishonesty,
failing to appear or testify without good cause when requested by the
Council for the Code of Honor, failing to keep information about cases
confidential,
supplying false information to the Council for the Code of Honor and
accusing a student of a violation of this Code in bad faith.
2. Cheating – This act implies an intent to deceive. It
includes all actions,
electronic or other devices and deceptions used in the attempt to
commit this act. Examples include,
but are not limited to,
copying answers from another student’s exam and using a cheat sheet or
crib notes in an exam.
3. Collusion – This is the act of working together on an
academic undertaking for which a student is individually responsible.
Examples include,
but are not limited to,
sharing information in labs that are to be done individually.
4. Plagiarism – Plagiarism is representing the words or ideas
of someone else as one’s own. Examples include,
but are not limited to,
failing to properly cite direct quotes, the false utilization of
copyrighted material and the failure to give credit for someone else’s
ideas.
SANCTIONS
All
proven cases of academic dishonesty shall be penalized as appropriate
under the circumstances. The imposition of any sanction will include
a statement of reasons supporting its severity. Recommendation of
sanctions for cases of proven dishonesty will be forwarded by the
Council for the Code of Honor to the Vice
President
for Academic Affairs. All proven cases of academic dishonesty will
result in a grade of “XF” which shall remain on the student’s
transcript for a minimum of two years. After two years, the student
may petition the Vice
President
for Academic Affairs to have the “X” removed; however, the “F” will
remain. Other sanctions may include but are not limited to:
·
A
defined period of probation or suspension
with or without the attachment of conditions;
·
The
withdrawal of University funding;
·
Expulsion from the University.
I
___________________________, hereby agree to and accept the terms and
conditions of the
Claflin
U.
Honor Code and pledge to follow them. Signed:
_____________________________ Date: __________
An alternate syllabi exists for participating
IRACDA Scholars
