Chem 108 Protein Biochemistry Laboratory Syllabus

Instructors: Dr. Anthony Mrse

Office:
Pac Hall 6140
Email:
amrse@ucsd.edu
Office Hours: by appointment
Website:
https://tritoned.ucsd.edu/

Dr. Xuemei Huang

NSB B005
xhuang@ucsd.edu

Course TritonEd: http://tritioned.ucsd.edu. Students will be required to access important course documents
and submit Formal Lab Reports through TritonEd.
Class Meeting: Section A
Section B

Lecture
Lab
Lecture
Lab

M: 9:00 - 9:50 a.m. Solis 104

M&W: 12:00-4:50 p.m. A01: NSB 1103; A02: NSB 1111
M: 9:00 - 9:50 a.m. Solis 104
T&Th: 12:00-4:50 p.m. A03: NSB 1103; A04: NSB 1111

Texts & Supplies:

Required: Lab manual: Techniques in Protein Chemistry: An Introduction (available at AS Soft
Reserves), lab notebook, lab coat, safety goggles (available in the Chemistry Stockroom or Price
Center Bookstore.)

Important Course Information

Course Summary: Students will understand and practice techniques used to study protein structure and
function, including electrophoresis, protein purification, column chromatography, enzyme kinetics, and
immunochemistry.
Prerequisites: Chem. 143A, Chem.114A.
Important Dates: Students must drop the course by the start of the second lab period.
Midterm: May 2, 9-9:50am
Final Exam: June 1st and 2nd during last lab periods

Course Grading
Midterm
Lab Attendance/Preparedness
(including Notebooks and prelabs)
Postlabs
2 Formal Lab Reports
Final Exam
Total

60 pts
65 pts
255 pts
200 pts
120 pts
700 pts

Lab Attendance/Preparedness: Points will be awarded based upon attendance in lab section,
completeness of written prelab, and ability to complete the lab in a timely fashion.
o Notebook checks may be conducted at random. Notebooks should contain a detailed prelab
write-up consisting of a detailed protocol and calculations.
The final course grade will be based on a total of all points and grades will be assigned based on
performance to the cumulative mean score.

Course Work
Lab Notebooks: Lab notebooks are important for maintaining records of what was done for the
experimenters and anyone who wishes to replicate the experiment at a later time. They should serve as a
single resource for record keeping. Additionally, lab experiments for this course involve multiple steps over
multiple lab periods. It is very important that students are prepared for lab each day to prevent experiments
running late and avoidable errors. At the start of each exercise/experiment, students must provide in their lab
notebook the following (Prelab):
A brief introduction to experiment (define the experimental goals and outline the techniques to be
used to orient the reader about the experiment.)
Notes on safety precautions and waste guidelines.
List of materials.
A numbered, step by step procedure and methods section written in the students own words.
Be sure to leave extra space in the procedure for making corrections, calculations, and
recordings.
At the TA/instructors discretion, students who are not prepared - do not have a procedure, safety guidelines,
etc.; in the lab notebook may not be allowed to participate in the experiment. During the lab session,
students will be required to take notes on the experiments including recording data and observations.
Students will be allowed to process data for some experiments on a computer. Copies of any photos should
be taped into the lab notebook. Calculations should be in the lab notebook and those done with EXCEL
should be transcribed or else printed and taped into the notebook. For this class, it is a good idea to generate
2 copies of experimental results (e.g. photographic records or images of experimental results). One copy
should be taped into the lab notebook, and the second copy may be included in the formal lab report.
Postlab Assignments: A postlab write-up is expected for each experiment unless otherwise mentioned by
the instructors. The postlab for each experiment is due at the beginning of the following lab period.
Submitted postlabs should contain:
Calculations including any figures or photos
Conclusion section summarizing work performed and results
Answers to assigned postlab questions
It is important that students do all their own work - you may not simply turn in a copy of your lab partners
calculations. If you turn in an EXCEL sheet with calculations, you should perform and understand all
steps/calculations yourself and include all necessary calculations with your postlab submission.
Final Exam: The final exam will be cumulative and will cover the material in lecture, lab and any assigned
reading. All students must take the final exam at the assigned time.
Formal Lab Reports: There will be two formal lab reports assigned this quarter. Each report will cover
several experiments and will be submitted through TritonEd and in print. The postlab assignments will have
content that can be used for the Formal Lab Reports. Once graded, any corrections made in the postlabs
should be incorporated into the formal report.
The formal report due dates and topics are given below:
Formal Report 1: LDH Experiments
Formal Report 2: LuxG Experiments

General Policies
Lecture: Lecture will cover theory and background for the experiments compled in lab. Students who miss a
lecture will be required to obtain lecture notes from another student. Students are responsible for all
information given during lecture. Most important announcements will be posted online, however, if you miss
a class you must check with another student to see if you missed any information. Suggested reading will be
given and Power Points will be available on TritonEd - generally before the lecture is presented. The topics
given in the syllabus may vary to fit the lab experiments.
Lab Tardiness and Attendance: Students are expected to be in lab and prepared at the start of class.
Students who arrive late will lose points. Students who arrive after 12:15 may not be allowed to complete the
lab, unless permission has been granted previously from the lab instructor or TA. The lab period is long and
students will be allowed to take a short (<15 min) break to eat outside the lab if they inform the TA and their
experiment does not need their attention. Students are not to leave their lab partner to complete the
experiment. If there is a long break in the experiment, students will be allowed to leave for a longer period of
time but must return at the time indicated by the TA. The nature of the experiments will require that lab will
on some days may start early or run late and there are times when students will be asked to come back to lab
at a later time or date outside the lab period. Often only one lab partner will need to attend.
Please do not attend lab if you are ill. Preparation for experiments takes time and it is often not feasible to
setup a lab for a single student. Still, a student can make up a lab with a written medical, professional, or
emergency excuse given either before or within 24 hrs after the absence if approved by the instructor AND if
accommodations can be made. Students who miss a lab can turn in prelab work (summary and procedure)
and postlab calculations and discussion if they obtain the results from their lab partner. They will also be
required to get notes from another student in order to complete the formal lab reports. Anyone with 2 or
more unexcused lab absences may fail the course.
Late Assignment Policy: Any assignments turned in after the start of class on the due date will be deducted
10% per day (including weekends). No assignments will be accepted 1 week after the due date.
Incomplete Grade Students seeking an I (incomplete) grade must file a petition with their instructor citing
"unforeseeable, emergency, and justifiable reasons." Incomplete grades are rarely given out.
Electronic Devices: It is expected that students turn off cell phones, ipods, and computers not directly used
in lab experiments during lecture and lab time. At times, students may be allowed to use their computers
during the lab period, please check with your TA or instructor.

Lab Safety
Lab Safety is a critical component of any lab course. Students must come to lab wearing proper attire dressed with long pants, lab coat and closed toed shoes, having safety goggles (only prescription glasses is
not satisfactory) - or they will not be allowed to participate in lab. Students will not be allowed to eat or
drink in the lab room. Students who do not comply with safety policies will have a deduction in their lab
preparedness grade and may be asked to leave the class.
TAs will be giving students a safety orientation on the first day of lab. Students will be required to read the
Biochemistry Lab Safety information at the beginning of the lab manual. Students will be asked to follow the
safety guidelines outlined by the TAs and may be given a lab safety quiz.

Academic Integrity
Students are expected to do their own work on all exams, labs and reports. Students should read and
understand UCSD's academic integrity policy at http://www.ucsd.edu/current-students/academics/academicintegrity/index.html. Students may be required to sign an academic integrity statement verifying that they
have not used unauthorized assistance on the exam. Students will not be allowed to use electronic devices
other than a calculator on the exams.
Although it is expected that students will confer with each other while working on lab notebooks and reports,
Formal lab reports must be the student's own work. Formal Lab Reports will be monitored using
Turnitin.com for evidence of plagiarism. Copying directly from the lab manual, instructors notes, textbook or
other sources will result in a deduction of points on lab reports. In addition, plagiarism or cheating may result
in failure from the course and disciplinary action.
Maintaining Academic Integrity: Students agree that by taking this course, all required papers will be
subject to submission for textual similarity review to Turnitin.com for the detection of plagiarism. All
submitted papers will be included as source documents in the Turnitin.com reference database solely for the
purpose of detecting plagiarism of such papers. Use of the Turnitin.com service is subject to the terms of use
agreement posted on the Turnitin.com site.

Office for Students with Disabilities

If you have a verifiable disability, please contact the instructor as early as possible in the quarter to request
accommodations. If you have a physical disability, modifications may be made to the working environment,
however, all work must be completed. Students who will need extra time to complete written work such as
exams and quizzes must be certified by the Office for Students with Disabilities
(http://disabilities.ucsd.edu/about/index.html). For more information, please contact the OSD at
858.534.4382 or by email at osd@ucsd.edu.

University of California, San Diego

Spring, 2016

Chem 108 Tentative Lab Schedule

Week of
March 28

Monday/Tuesday Lab
Check in, safety
Ex 0: Pipet practice, and
Spec20 spectrophotometer
LDH Ex 2: Activity assays on
extracts and controls.

Wednesday/Thursday Lab
LDH Ex 1: Isolate and freeze bovine
tissue extracts

Section A1/B1: LDH Ex 5 Pt1:

Ammonium Sulfate
Precipitation
Section A1/B1: LDH Ex 3:
Kinetics (part 2, steps 8-10)
LDH Ex 5 Pt 2: Ammonium
Sulfate Precipitation.
Dialysis, change buffer next day
LDH Ex 7: Protein assay:
Bradford assay.
Pour lower gel for native gel.

Section A1/B1: LDH Ex 3: Kinetics

(part 2, steps 8-10)
Section A2/B2: LDH Ex 5 Pt1:
Ammonium Sulfate Precipitation

May 2

LDH Ex 9: Run and stain SDSPAGE.

Ex. 10 Pour lower gel for LDH

May 9

LDH Ex. 10: Complete Western

Blot

LDH Ex 10: Run SDS-PAGE and start

transfer. Come in next day to stop
transfer and incubate in blocking
solution.
LuxG Ex 1: Induce protein expression
and incubate overnight. Come in next
day to harvest cells

May 16

LuxG Ex. 1:Lyse cells

LuxG Ex 2: Nickel Chromatography;

Pour gels for SDS-PAGE

May 23

LuxG Ex 3: SDS-PAGE on
LuxG
Memorial holiday

LuxG Ex 4: Enzyme assay

April 4
April 11

April 18

April 25

May 30

LDH Ex 3: Kinetics (part 1, steps 1-7)

LDH Ex 6: Column purification of

heart enzyme. Assay activity in eluted
fractions.
LDH Ex 8: Pour upper native gel.
Run and Stain Native gels.
Pour gel for SDS-Page.

Lab Checkout
Final Exam