CHM 311                         Biochemistry Lab                   Fall 2008

 

Instructor:        Dr. Matthew Junker    

314 Boehm Science Center

Phone:  610-683-4199      Email:  junker@kutztown.edu

Office hours:   Tues. 2-3pm;  Wed. 2-5pm;  Fri. 10-11am

Lab location:  Boehm Science Center, room 207 (2nd floor)

Lab times:       Section 011     Monday, 2:00-4:50 pm

                        Section 312     Tuesday, 6:00-8:50 pm

Textbook:        Biochemistry Laboratory: Modern Theory and Techniques by Rodney Boyer,

                        Benjamin Cummings, 2006, ISBN: 0-8053-4613-9.

Notebook:        A bound notebook is required.  Spiral notebooks are acceptable.  Entries

                        must be made with ink (not pencil). 

Co-requisite:  CHM 310  Biochemistry I

 

Grading:          The total final score for this laboratory will be comprised by:

                                    average of all prelab assignments      5%

                                    average notebook grade                     10%

                                    average of all worksheets                   20%

                                    average of all reports                          65%

                        This total final score will count 15% towards your grade in Biochemistry.

 

Course structure:

Each section meets once a week for a 3 hour lab.  All glassware and equipment must be cleaned and stored by the end of each laboratory session.  Handouts with instructions for each lab will be distributed during a CHM 310 lecture during the preceding week.  Students are responsible for reading the handouts and assigned sections of the textbook before coming to lab.

 

Course objectives:  Upon successful completion of this course, a student will be able to:

            - Use traditional and modern techniques of protein biochemistry

            - Explain the concepts on which the laboratory experiments are based

            - Write scientific reports, keep a laboratory notebook, and interpret laboratory data

 

Graded assignments:

1.  Beginning with the 2nd lab, a written pre-lab is to be brought to each lab.  The pre-lab includes an Introduction and Experimental section with a flowchart.  The pre-lab format is described on page 7 (and Figure 1.4) in the Boyer textbook.  For the experimental section, you only need to make a flow chart.  The pre-lab can be hand-written.  (Pre-labs 5% of grade)

 

2.  Periodically throughout the semester, and again at the end, lab notebooks will be collected and graded.  They will be graded for organization, clarity, and content.  The first notebook grading will be “free” (the score will not count).  Proper notebook organization will be discussed in lab today, and is also covered in Boyer on pg. 5-7.  (Notebooks 10% of grade)

 

3.  For some labs, the report that will be handed in will be in the form of “worksheets” with answers to specific questions.  These may be hand-written.  (20% of grade)

 

4.  For some labs, formal lab reports will be handed in.  The format of the reports is described on pg. 7-8 of Boyer.  THE REPORTS MUST BE TYPED.  Due dates will be specified in the lab handouts (typically one week after the lab session).  (65% of grade)

 

Important notes on grading: 

1.  Getting experiments to work is always great, but the main emphasis of this course is learning the basic principles of experimental biochemistry, including how to trouble-shoot when things don’t “go right.”  Consequently, the grading of all reports and worksheets will be heavily weighted by demonstrated comprehension, as well as clarity, organization, and thoughtfulness. 

 

2.  The worksheets and reports will also be graded for the quality of writing: organization and logical flow, grammar and punctuation, and spelling.  Use complete sentences, proper paragraph construction, etc.

 

3.  You will work in teams of 2-3 people for many of the experiments.  However, all handed-in written assignments are to be your own work only, without collaboration with other students.  You may come to me for help (office hours, pre-arranged times, or email) as often as you like.

 

ADA Notice:  Any student who needs accommodation for a disability should contact me for assistance early in the semester.  Students should also contact KU Disability Resources and Services at 610-683-4108 or in Stratton 215. 

 

Expected schedule of experiments:

 

Dates

 

Topic

Type of

report

 

 

 

Aug. 26, Sept. 2

Pipetting and solution preparation

worksheet

Sept. 8, 9

Acid/base chemistry and pH

report

Sept. 15, 16

Assaying a phosphatase I

 

Sept. 22, 23

Assaying a phosphatase II

report

Sept. 29, 30

Molecular graphics visualization of proteins

worksheet

Oct. 6, 7

Lysozyme I:  preparation

worksheet

Oct. 13, 14

Linear regression (No Lab meeting)

worksheet

Oct. 20, 21

Lysozyme II:  purification by chromatography

worksheet

Oct. 27, 28

Lysozyme III:  Protein concentration assay

worksheet

Nov. 3, 4

Lysozyme IV:  SDS-PAGE

report

Nov. 10, 11

Lysozyme V:  enzyme kinetics- specific activity

worksheet

Nov. 17, 18

Lysozyme VI:  enzyme kinetics- data analysis

report

Nov. 24, 25

PCR and DNA electrophoresis I

worksheet

Dec. 1, 2

PCR and DNA electrophoresis II

report