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Chem 108 Protein Biochemistry Laboratory Syllabus

Instructors: Dr. Anthony Mrse
Pac Hall 6140
Office Hours: by appointment

Dr. Xuemei Huang
NSB B005

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


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
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
Lab Attendance/Preparedness
(including Notebooks and prelabs)
2 Formal Lab Reports
Final Exam

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.

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

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. Still. Students must come to lab wearing proper attire dressed with long pants. They will also be required to get notes from another student in order to complete the formal lab reports. The topics given in the syllabus may vary to fit the lab experiments. Often only one lab partner will need to attend. Incomplete Grade Students seeking an I (incomplete) grade must file a petition with their instructor citing "unforeseeable. Late Assignment Policy: Any assignments turned in after the start of class on the due date will be deducted 10% per day (including weekends). Anyone with 2 or more unexcused lab absences may fail the course. and justifiable reasons. professional. Lab Tardiness and Attendance: Students are expected to be in lab and prepared at the start of class. 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. Please do not attend lab if you are ill. lab coat and closed toed shoes. Most important announcements will be posted online. ipods. however. 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 will not be allowed to eat or drink in the lab room. Students who miss a lecture will be required to obtain lecture notes from another student. Students will be required to read the Biochemistry Lab Safety information at the beginning of the lab manual. At times. and computers not directly used in lab experiments during lecture and lab time. 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. Lab Safety Lab Safety is a critical component of any lab course. Students are not to leave their lab partner to complete the experiment. No assignments will be accepted 1 week after the due date. Students will be asked to follow the safety guidelines outlined by the TAs and may be given a lab safety quiz. Electronic Devices: It is expected that students turn off cell phones. Students who arrive late will lose points. emergency. Suggested reading will be given and Power Points will be available on TritonEd ." Incomplete grades are rarely given out. students may be allowed to use their computers during the lab period. a student can make up a lab with a written medical. unless permission has been granted previously from the lab instructor or TA. if you miss a class you must check with another student to see if you missed any information.generally before the lecture is presented. If there is a long break in the experiment. please check with your TA or instructor. Preparation for experiments takes time and it is often not feasible to setup a lab for a single student. . Students who arrive after 12:15 may not be allowed to complete the lab.General Policies Lecture: Lecture will cover theory and background for the experiments compled in lab. 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. TAs will be giving students a safety orientation on the first day of lab.or they will not be allowed to participate in lab. having safety goggles (only prescription glasses is not satisfactory) . students will be allowed to leave for a longer period of time but must return at the time indicated by the TA. Students are responsible for all information given during lecture.

html). Copying directly from the lab manual. instructors reference database solely for the purpose of detecting plagiarism of such service is subject to the terms of use agreement posted on the Turnitin. Formal lab reports must be the student's own work. 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. In addition. For more information.4382 or by email at osd@ucsd. please contact the instructor as early as possible in the quarter to request accommodations. Students will not be allowed to use electronic devices other than a calculator on the exams.html.ucsd. All submitted papers will be included as source documents in the Turnitin. Students should read and understand UCSD's academic integrity policy at http://www. Formal Lab Reports will be monitored using Turnitin. all required papers will be subject to submission for textual similarity review to Turnitin. If you have a physical for evidence of plagiarism. labs and reports. Office for Students with Disabilities If you have a verifiable Use of the Turnitin. Students may be required to sign an academic integrity statement verifying that they have not used unauthorized assistance on the plagiarism or cheating may result in failure from the course and disciplinary action. Although it is expected that students will confer with each other while working on lab notebooks and reports.Academic Integrity Students are expected to do their own work on all exams. please contact the OSD at modifications may be made to the working for the detection of plagiarism. . textbook or other sources will result in a deduction of points on lab reports.534. however. Maintaining Academic Integrity: Students agree that by taking this course. all work must be completed.

steps 8-10) Section A2/B2: LDH Ex 5 Pt1: Ammonium Sulfate Precipitation May 2 LDH Ex 9: Run and stain SDSPAGE. steps 1-7) LDH Ex 6: Column purification of heart enzyme. 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. Run and Stain Native gels. 10: Complete Western Blot LDH Ex 10: Run SDS-PAGE and start transfer. 2016 Chem 108 Tentative Lab Schedule Week of March 28 Monday/Tuesday Lab Check in. Dialysis. steps 8-10) LDH Ex 5 Pt 2: Ammonium Sulfate Precipitation. Come in next day to harvest cells May 16 LuxG Ex. Come in next day to stop transfer and incubate in blocking solution. Assay activity in eluted fractions. San Diego Spring. 1:Lyse cells LuxG Ex 2: Nickel Chromatography. change buffer next day LDH Ex 7: Protein assay: Bradford assay.University of California. Ex. LuxG Ex 1: Induce protein expression and incubate overnight. and Spec20 spectrophotometer LDH Ex 2: Activity assays on extracts and controls. Lab Checkout Final Exam . Pour lower gel for native gel. Section A1/B1: LDH Ex 3: Kinetics (part 2. Pour gel for SDS-Page. LDH Ex 8: Pour upper native gel. 10 Pour lower gel for LDH May 9 LDH Ex. safety Ex 0: Pipet practice. 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.