*Syllabus Only*
BIOC 4025
“Laboratory Methods in Biochemistry Manual”
January 20, 2015 – May 6, 2015
Lab: Tues or Thurs, 8:15am, 1:15pm, or 5:20pm
2-126 MCB, Minneapolis Campus
Lecture: Monday 4:40 pm
Room: 3-120 MCB
Instructor: Professor Alex J. Lange, Department of Biochemistry,
Molecular Biology and Biophysics. Lange024@umn.edu, Tel. 6-4502
BioC 4025
BIOCHEMISTRY LABORATORY
BIOC 4025
Spring Semester 2015
Professor Alex Lange
INSTRUCTOR
Instructor:
Professor Alex Lange
Dept. of Biochemistry, Molecular Biology and Biophysics
e-mail: lange024@umn.edu
7-136 MCB Building, Minneapolis
Teaching Assistants:
Aaron Edmund edmun043@umn.edu
Chao Li-13 lixx2518@umn.edu
Sujin Yeom yeomx010@umn.edu
REQUIRED BOOK:
Laboratory Methods in Biochemistry Manual This course packet is available
weekly on Moodle. You are advised to download and compile the weekly
installments. We are in the continual process of editing this manual, and will try
to stay a few weeks ahead of you in making edits. Suggestions on how to
improve the manual are welcome, if constructive.
Supplementary reference (several are available in the Lab):

Lehninger - Principles of Biochemistry: Nelson and Cox, Worth Publishing
(6th edition is the newest) Or any other biochemistry textbook
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Syllabus: BioC 4025: Laboratory in Biochemistry
Spring 2015
Course Goals: Laboratory experience in protein expression, purification and
characterization; an appreciation for the role of protein expression and purification in
modern (G4) life.
Topics: Buffers and solutions, protein (lactate dehydrogenase) purification, protein
electrophoresis, protein expression using recombinant technology, enzyme
characterization using kinetic and immunochemical methods.
Instructor:
Alex Lange, e-mail: lange024@umn.edu, phone: 612-626-4502. Office location: MCB 7136. Office hrs: Will be available Mondays before lecture in the Molecular and Cellular
Biology (MCB) Bldg. outside of the class room 3-120.
Teaching Assistants:
TA Name
Email address
Chao Li
Office Hours
Section
Times
9:30- 10:30 am
Friday
MCB 2-126
5&7
Thurs 1:15pm
Thurs 5:20pm
10-11 am
Monday
MCB 2-126
11:30-12:30
Wednesday
240H Gortner
Hall (St. Paul)
3&6
Tues 1:15pm
Tues 5:20pm
2&4
Tues 8:15am
Thurs 8:15am
lixx2518@umn.edu
Aaron Edmond
edmun043@umn.edu
Sujin Yeom
yeomx010@umn.edu
Section
Section
Section
Section
Section
Section
Section
1
2
3
4
5
6
7
Monday (Lecture) All students
Tues 8:15 am 16 students (max)
Tues 1:15 pm 16 students (max)
Thurs 8:15 am 16 students (max)
Thurs 1:15 pm 16 students (max)
Tues 5:20 pm 16 students (max)
Thurs 5:20 pm 16 students (max)
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Check with TA to confirm office hours. You ca go to any TA for help.
Laboratory coordinator:
Barbara Pinch, Room 2-132 MCB (office/prep room), e-mail: pinch001@umn.edu,
phone: 612-625-4282.
Prerequisites: BioC 3021 (Biochemistry) or BioC 4331 (Biochemistry I) or Biol 3021
(Biochemistry). Contact instructor for exceptions.
Text (Lab manual): A Laboratory Manual (Laboratory Methods in Biochemistry
Manual) will be provided on MOODLE on a weekly basis. The course is keyed to the
week number (WEEK 1, WEEK 2, etc.) Week number matches Lab number.
Supplement: Supplementary materials will be distributed as needed. Since we are
editing manual, hopefully there will not be a great deal of supplemental material.
Laboratory Notebook: A bound, graph-ruled laboratory notebook is required.
Examples are U of MN No. 20775 (96 pp.) or Dennison 73333 53110 (96 pp). No
loose-leaf or spiral bound notebooks.
Course web site: login via MOODLE: syllabus, schedule, Lab Manual, lecture slides,
example exams, current grades, and additional materials as needed. No handouts
will be given out for lectures. Students are advised to print out the posted lab
manual and lecture handouts from the web site.
Lectures: (Section 1, all students) Mondays at 3:35-4:25 pm in MCB 3-120. These
are important because they will cover what you are doing that week in the lab.
Laboratory: Tuesday and Thursday in MCB 2-126. Laboratory start times are shown
in the table above. There are 6 lab sections. Tues morning, section 2; Tues
afternoon, section 3; Tues evening, section 6; Thurs morning, section 4; Thurs
afternoon, section 5; and Thurs evening, section 7. The lecture is section 1 (all
students).
Grading Scheme:
Points
Lecture
Quizzes (LecQ, best 5 out of 6, 10 pts each)
50
Midterm & final exams (MTE-80 pts., FE-80-pts.)
160 (27%)
Biochem Q and A (BQA - weekly ½ page referenced
reports on biochemical question of your choosing
(Ex. How does aspirin work, biochemical mechanism?)
4
(8.3%)
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BIOCHEMISTRY LABORATORY
(BQA1[4 ]-20 pts., BQA2 [4]-20 pts.)
40
(6.7%)
_________
Lecture Subtotal
250 (42%)
Laboratory
Prelab quest., notebook (PreLab, best 10 out of 11)
75
(12.5%)
Punctual arrival, cooperation & cleanup (PACC)
25
(4.2%)
Lab reports & questions (LabR, best 12 out of 13,
150 (25%)
12.5 pts. each)
Large lab report (LLR)
100 (16.7%)
___________
Laboratory Subtotal
350 (58%)
_______________________________________________________
Grand Total
600 (100%)
COURSE DESCRIPTION
This biochemistry laboratory course is designed to give students hands-on
experience performing common strategies and techniques used in modern
biochemistry, as well as the background information needed to understand what
kind of information can be obtained by using them. Because of the dual nature of
this course, a portion of the laboratory time will be spent on lectures explaining
the theory behind the techniques being used as well as practical aspects of
experimental design. In addition, readings will be assigned that explain the
history and principles behind some of the techniques used.
COURSE OBJECTIVES

Students will be able to successfully perform some basic techniques used in
modern biochemistry.

Students will be able to interpret data from their experiments.

Students will be able to design protein purification and characterization
experiments using the techniques learned in the lab.

Students will be able to use computer-based sequence analysis software and
to find nucleic acid and protein sequence information using the Internet.
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Learning Goals
1. Foundational Knowledge
Be able to explain and discuss key ideas regarding pH and buffers, strategies
in protein purification and characterization, different types of chromatography
and electrophoresis methods. Be able to identify unsolved scientific problems
related to protein purification and characterization.
2. Application Goals
Be able to critically evaluate a protein purification – does it achieve its goals
of purity, cost, safety? Be able to critically evaluate a protein characterization
– does it establish the purity and identity of the protein? Be able to evaluate
a proposed experimental procedure for safety issues. Be able to work safely
in a laboratory
3. Integration
Be able to identify where proteins and protein purification affect our daily life.
Be able to identify current society issues involving protein purification and
characterization. Be able to identify where advances in protein purification
and characterization have created business opportunities. Be able to identify
ethical issues created by protein purification and characterization
technologies.
Grading Guidelines and Course Policies
In lecture quizzes (50 pts., best 5 out of 6, 10 pts. each)
Random lecture classes will include a quiz. The possible grades are 0-10 for
each. The best 5 quizzes will go toward your grade. There is no opportunity to
make these up if you miss them. The quiz will test your understanding of
assigned reading material, laboratory experiments, and lecture material.
In lecture midterm exam (March 9, 2015) and final exam (May 4, 2015) (50
min for each, 80 pts. each, 160 pts. total)
These closed book exams consist of multiple choice, short answers, and simple
problems that cover understanding of the laboratory experiments and lecture
material. Calculators may be used. If you miss an exam and have an excused
absence, then you must make arrangements with the instructor to take a
make-up exam. The makeup exam may have a different format (e.g. all
essay). Alternately, for an excused absence you may be able to take midterm
exam early. Final exams may not be taken early. All exam time/date changes
must be in writing (e-mail OK). Calculators may be used, however no external
communication is allowed during the examinations.
Biochem Q and As (first 4 [20 pts.], second 4 [20 pts.] = 40 pts. total)
A Biochem Q and A is a written record of your reflections on how biochemistry
relates to things of interest to you. Can you relate what you are learning to the
world you live in? Pose a question on something related to biochemistry that
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you don’t understand and try to find the answer to it from the literature search
you do. You can take things from current events of the day. All sources are
allowed, but put your reports in your own words. Primary sources can be used
to back up web sources. Cite your sources.
Part 1. Write a weekly short report, starting in week 2, you must write at least
a single spaced ½ page report every week. The first 4 BQ&As will be turned in
on March 2nd, 2015, before or after lecture.
Part 2. Continue weekly reports as above. The second 4 entries will be turned
on April 20th, 2015, before or after lecture.
These will be assessed based on the student asking questions for which
biochemistry knowledge will give him/her a better understanding of how things
work (or don’t work) in the world.
A reference for each report will be required.
Prelab (75 pts, best 10 out of 11 labs at 7.5 pts each excluding the first one)
The prelab has three components that are listed below:
All three of these components must be completed before you come to lab.
Component 1: Assigned prelab questions (2.5 pts.)
These are at the beginning of the lab procedures for each week, must be
answered in your notebook. You may photocopy the questions from the lab
manual and paste them into your notebook (ANSWERS MUST BE WRITTEN
IN YOUR LAB NOTEBOOK).
Component 2: Your planned experimental procedure in your notebook (2.5
pts)
1. Title of the experiment and the date on a new page.
2. Objective: One or two sentences stating the purpose of the experiment.
3. Materials: any reagents, chemicals, equipment, etc. for the experiment. The
composition of all buffers should be included or a page number given for a
notebook entry that contains the buffer composition and the calculations made
in preparing solutions.
4. Procedures: outline or flow sheet of the procedure based on the lab manual.
Tables are also useful for experiments with multiple variables. A checklist of
things to add/complete is useful. You may not tape photocopies of procedure
overheads into your notebook. You must make a plan for yourself so you know
what you are doing.
Component 3: Lab notebook entries below (5.
conclusion/summary.) from the previous week). (2.5 pts)
results
and
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5. Results: Record all data taken, gel photos, printouts, etc., all calculations,
analyzed data, and remarks about how the experiments proceed. Note any
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deviations of the actual procedure from the preliminary protocol. A lab book
should provide all the information needed for someone to repeat your methods
and results.
6. Conclusions/Summary: briefly summarize your results and state your conclusions. If the
experiment didn’t work, hypothesize what went wrong and what will you do next time to try
to trouble shoot?
Note: 3 parts to the prelab, 2.5 pts each
Punctual arrival to laboratory, co-operation & clean up (everyone starts with 25 pts)
Failure to do these things will result in an erosion of these points. Also, you must be dressed in
long pants with closed-toe shoes.
During lab:
Clean up any spills or broken glass (broken should be put in the “Broken Glass”
disposal box.).
Missing a lab (only with a written, valid excuse, e.g., illness, grad school
interview):
Check with the TA for another section and get permission to attend and do the lab in
another section. It must be in the same week as the lab set up will be different the
next week. You are allowed only one excused lab.
You cannot switch labs without a valid reason.
Switching sections – It is difficult to switch sections, but if the excusable occasion
arises, you will be allowed to switch only once.
Missing 2 unexcused labs will result in being dropped from the course.
The best thing you can do is be there for all the labs. The lab experiments are
sequential and if interrupted, you do not have what you need to go forward. Also, if
you are not conscientious, your lab partner will suffer, remember, you are a team.
Lab reports and assigned questions (150 pts, best 12 out of 13)
General:
Write your answers using a computer and hand in paper copies. Check with
your TAs for any changes in format.
Numbers without units are incorrect (unless it is a unitless number, e.g. pH,
absorbance).
All graphs must have axis labels with units and scales.
Show your work for all calculations.
Your teaching assistant will provide detailed grading criteria.
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Large lab report (to be turned in at the end of the semester): This is a
cumulative report where you report your semester’s work, which involves the
isolation, expression, purification and characterization of the enzyme LDH. It is
worth 100 pts., or 1/6 of your grade. You will be given more information and
instructions on the large lab report during the course.
General Policies
Late work policy: loss of 10% of max score per 24 h or part thereof including
weekends and holidays. Example: Five points will be deducted from an assignment
worth 50 points that is 12 h late.
Basis for an incomplete: If you miss three or more labs due to documented illness or
extraordinary circumstances, you will get a grade of "I” or Incomplete. Incompletes
are not given because a student is earning a low grade. Before an ‘I’ grade is given,
the instructor and student must fill out an Incomplete Contract. To complete the
course, the entire course must be repeated.
(http://www.cbs.umn.edu/studentservices/policies.html), which outlines the
conditions for making up the missed laboratories and other work. "I" grades
automatically lapse to ‘F’s at the end of the next semester of a student's registration,
unless an instructor submits a change of grade.
Changes of grade: Only requests in writing (e-mail OK) will be considered within two
weeks of the grade return date. State the reasons that your grade should be
changed. The instructor or TA will consider your request, its fairness to the other
members in the class, and give an answer in two days. If you are not satisfied, you
may then contact the Student Dispute Resolution Center (SDRC) in 107 Eddy Hall
(625-5900) for assistance.
Extra work: Students are not permitted to submit extra work to raise their grade.
Scholastic misconduct is broadly defined as "any act that violates the right of another
student in academic work or that involves misrepresentation of your own work.
Scholastic dishonesty includes, (but is not necessarily limited to): cheating on
assignments or examinations; plagiarizing, which means misrepresenting as your
own work any part of work done by another; submitting the same paper, or
substantially similar papers, to meet the requirements of more than one course
without the approval and consent of all instructors concerned; depriving another
student of necessary course materials; or interfering with another student's work." If
you are not sure, ask your instructor or TA or check the student code at:
http://www1.umn.edu/regents/policies/academic/StudentConductCode.html.
Suspected scholastic misconduct will be dealt with through university procedures for
academic dishonesty (http://www.sja.umn.edu/conduct.html). Plagiarism also
includes copying directly without attribution from a book, journal article, the lab
manual or the internet. Discussing ideas, procedures, and interpretations is
encouraged. You must write your own lab reports and Q&As. Info on
distinguishing between plagiarism and legitimate use and citation of someone else's
work: http://CISW.cla.umn.edu/ugradinfo.html.
E-mail course notices: Course information will occasionally be sent out by email to your
assigned “___@umn.edu” address. Please check your umn.edu mailbox daily. Don’t
forward your umn.edu mail to another account (e.g. hotmail or yahoo), as these
accounts can fill up and reject important messages.
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Accommodations for student with disabilities: If you have a disability that might hinder
full participation class activities, contact the instructor. Additional information is
available from Disability Services in 230 Gateway (V/TTY) 624-4037.
How to get an “A” in this course
A = 93 to 100, A- = 90-92. The course will not be curved.
1. Keep up with the course schedule.
Attend each class and lab and arrive on time, or it will cost you
points.
Arrive prepared: reading completed, prelab questions done, lab
notebook filled out for the last week’s experiment and for the current
experiment.
Clean up after yourself in the lab.
Hand in your lab reports and learning profiles on time.
2. Think about the course and its implications on society.
Think while you work in the lab. Why are you doing each step? What
do you expect to happen? What could go wrong? On the molecular
level, what is happening at each step?
Make entries in your learning portfolio each week. Think about how
proteins influence your life and society. Notice protein issues in the
news.
Take notes in class. Clarify things you are not sure about by asking
questions.
3. Write excellent lab reports.
Reports should be clearly written and demonstrate that you
understand not only what you did and why, but also the implications
of the experiments in other situations. It is not essential that the lab
experiments succeed to get a good grade, but it is essential that you
demonstrate mastery of the concepts and implication of the
experiment.
4. Do well (≥90%) on the midterm and final exam.
If you are not on track to get the grade you expect in within the first three weeks, you
must change your approach to the course. Contact your TA or the instructor. Student
Expectations: As a student in this course, you are expected to take an active role in your
learning.





You are expected to attend every class, and to arrive on time and not leave early.
You should be prepared for each lecture by reading the assigned material. You
should take good lecture notes and use them to make sure you understand all of the
concepts covered in class.
You should ask questions in lecture to help clarify concepts.
You should participate actively in the discussion sessions.
You should adhere to the University of Minnesota Student Conduct Code found at:
http://www1.umn.edu/regents/policies/academic/Student_Conduct_Code.html.
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The university policies and where to find them on the web follows:
The University utilizes plus and minus grading on a 4.000 cumulative grade point scale in
accordance with the following:
A 4.0 - Represents achievement that is outstanding relative to the level necessary to meet course
requirements
B 3.0 - Represents achievement that is significantly above the level necessary to meet course
requirements
C 2.0 - Represents achievement that meets the course requirements in every respect
D 1.0 - Represents achievement that is worthy of credit even though it fails to meet fully the course
requirements
S Represents achievement that is satisfactory, which is equivalent to a C- or better.
For additional information, please refer to:
http://policy.umn.edu/Policies/Education/Education/GRADINGTRANSCRIPTS.html
Regrades: Any errors or problems with grading should be brought to the instructor's
attention within a week of return of the graded item. No adjustments to the grade on that
item will be made after one week.
Make up Exams: Requests for make-up exams must be supported by documentation (e.g.,
letters from university offices, doctors, police reports). A note saying you were seen at
Boynton is not sufficient, you must have a note from a doctor saying you were sick. You
must contact the instructor either before the exam or in a timeframe after the exam that is
consistent with the reason for missing the exam.
Electronic Devices : No electronic devices, including iPods, and cell phones, may be
used during any examinations. We do allow calculators during exams. Use of a
prohibited device during an examination is considered Scholastic Dishonesty and falls
under the University Student Conduct Code.
Academic Misconduct: Cheating during an exam and altering an exam prior to
submission for regarding are examples of academic misconduct. Violations of acceptable
academic conduct will elicit penalties commensurate with the offense. Penalties can
include assignment of a failing grade for an examination or a failing grade for the entire
course, depending upon the nature and severity of the infraction. Although collaboration
during examinations is strictly forbidden, students may work together on problem sets if
the instructor gives explicit permission. See the “scholastic dishonesty” section of the
Student Conduct Code at:
http://www1.umn.edu/regents/policies/academic/Student_Conduct_Code.html.
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Academic Integrity: The grade in a course is intended to be a reflection of what you have
learned in the course. Any instances of plagiarism (presenting someone else's work as your
own) will be dealt with through university procedures for academic dishonesty (see The
Office for Student Conduct and Academic Integrity for more information:
http://www1.umn.edu/oscai/index.html ). If you need assistance in distinguishing between
plagiarism and legitimate use and citation of someone else's work, please refer to the Center
for Student Writing Support at: http://writing.umn.edu/sws/quick_help/online_resources.htm
- plagiarism .
Use of Personal Electronic Devices in the Classroom: Using personal electronic
devices in the classroom setting can hinder instruction and learning, not only for the
student using the device but also for other students in the class. To this end, the
University establishes the right of each faculty member to determine if and how personal
electronic devices are allowed to be used in the classroom. For complete information,
please reference:
http://www.policy.umn.edu/Policies/Education/Education/CLASSROOMPED.html.
Appropriate Student Use of Class Notes and Course Materials: Taking notes is a
means of recording information but more importantly of personally absorbing and
integrating the educational experience. However, broadly disseminating class notes
beyond the classroom community or accepting compensation for taking and distributing
classroom notes undermines instructor interests in their intellectual work product while
not substantially furthering instructor and student interests in effective learning. Such
actions violate shared norms and standards of the academic community. For additional
information, please see:
http://policy.umn.edu/Policies/Education/Education/CLASSNOTESSTUDENTS.html.
Disability Accommodations: The University is committed to providing quality
education to all students regardless of ability. Determining appropriate disability
accommodations is a collaborative process. You as a student must register with Disability
Services and provide documentation of your disability. The course instructor must
provide information regarding a course's content, methods, and essential components.
The combination of this information will be used by Disability Services to determine
appropriate accommodations for a particular student in a particular course. For more
information, please reference Disability Services: http://ds.umn.edu/.
Mental Health Services: As a student you may experience a range of issues that can
cause barriers to learning, such as strained relationships, increased anxiety, alcohol/drug
problems, feeling down, difficulty concentrating and/or lack of motivation. These mental
health concerns or stressful events may lead to diminished academic performance and
may reduce your ability to participate in daily activities. University of Minnesota services
are available to assist you. You can learn more about the broad range of confidential
mental health services available on campus via the Student Mental Health Website:
http://www.mentalhealth.umn.edu/.
Consolidated course policies are found at
http://www.policy.umn.edu/Policies/Education/Education/SYLLABUSREQUIREMENT
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S_APPA.html
Problems in the course? For any concerns, contact the instructor.
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