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369L_sp10_syllabus

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					                                    CH 369L
                  Biochemistry Laboratory/Biochemical Techniques
                                   Spring 2010


Instructor: Dr. Gene McDonald
Office: WEL 3.270C
Office Hours: MWF 9:30 – 10:30 am or by appointment
Email: gmcdonald@cm.utexas.edu

Lectures: MW 12-1 pm, WEL 2.308

Labs: Section 1 (53565), MW 1 – 4:30 pm, WEL 3.268
      Section 2 (53560), TTh 9 am – 12:30 pm, WEL 3.268
      Section 3 (53570), TTh, 2 – 5:30 pm, WEL 3.268

Course web page: http://courses.cm.utexas.edu/gmcdonald/ch369l/
Lecture slides available on Blackboard

The prerequisites for this course are completion of CH339K and completion or
concurrent registration in CH339L.

In this course you should learn:
    • Common biochemical laboratory methods
    • Good basic biochemical laboratory technique
    • Ability to choose appropriate method to answer a given question

The lab manual for this course is required, and is available from the copy center in Welch
2.228. You will need a bound laboratory notebook, preferably one with carbon duplicate
pages. Both the copy center and the American Chemical Society Student Affiliate sell
acceptable lab notebooks. Spiral notebooks and loose paper are unacceptable. There are
also several texts available on the shelves in the Chemistry Library that may be useful as
background references. They include:

Boyer, R., Modern Experimental Biochemistry
Holme, D. J. and Peck, H., Analytical Biochemistry
Holtzhauer, M., Basic Methods for the Biochemical Lab
Mikkelsen, S. R. and Corton, E., Bioanalytical Chemistry
Robyt, J. F. and White, B. J., Biochemical Techniques: Theory and Practice
Switzer, R. and Garrity, L., Experimental Biochemistry


The University of Texas at Austin provides upon request appropriate academic
accommodations for qualified students with disabilities. For more information, contact
Services for Students with Disabilities at 471-6259 (voice) or 232-2937 (video phone).




                                            1
Schedules (tentative and subject to change if conditions warrant)

Lab schedule

Dates                Lab
25/26 Jan.           Experiment 1, Buffers and pH
27/28 Jan.           Experiment 2a, Native ultraviolet absorbance of biomolecules
1/2 Feb.             Experiment 2b, Protein fluorescence spectroscopy
                     Experiment 2c, Bradford protein concentration assay
3/4 Feb.             Experiment 3a, Enzyme kinetics
8/9 Feb.             Experiment 3b, Assays using NAD-dependent enzymes
10/11 Feb.           Experiment 4, Polyacrylamide gel electrophoresis (PAGE)
15/16 Feb .          makeup lab
17/18 Feb.           Experiment 5, Restriction digest, ligation, and agarose gel
                           electrophoresis of bacteriophage  DNA
22/23 Feb.           Experiment 6a, Isolation and PCR of plasmid DNA
24/25 Feb.           Experiment 6b, Agarose Gel Analysis of Plasmid Prep and PCR
                           Products
1/2 Mar.             Experiment 6c, PCR-based forensic analysis of human DNA
3/4 Mar.             Experiment 6d, Agarose Gel Analysis of Human PCR
8/9 Mar.             Experiment 7a, Transformation and Plating of E. coli
10/11 Mar.           Experiment 7b, Examination of Transformed Cell Cultures
22/23 Mar.           Experiment 7c, Purification of a Cloned Protein
24/25 Mar.           makeup lab
29/30 Mar.           Experiment 8a, Enzyme-linked immunosorbent assay (ELISA)
31 Mar./1 Apr.       Experiment 8b, Western Blot (1): PAGE gel and blotting
5/6 Apr.             Experiment 8c, Western Blot (2): Probing the membrane
7/8 Apr.             Experiment 9a, Isolation of Acid Phosphatase from Wheat Germ
12/13 Apr.           Experiment 9b, Gel Filtration (1): Pouring and Calibration of
                           Sephadex G75 Column
14/15 Apr.           Experiment 9c, Gel Filtration (2): Sephadex G75
                           Chromatography
19/20 Apr.           Experiment 9d, Ion Exchange Chromatography
                     Experiment 9e, Bradford assay of purified protein fractions;
                           Purification table calculations
21/22 Apr.           makeup lab
26/27 Apr.           Experiment 10a, Crystallization of a Protein
28/29 Apr.           Experiment 10b, Examination of Protein Crystals




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Lecture schedule

20 Jan.            Introduction
25 Jan.            Buffers and pH
27 Jan.            Ultraviolet absorbance of biomolecules; Bradford assay
1 Feb.             Protein fluorescence spectroscopy
3 Feb.             Enzyme kinetics
8 Feb.             Assays using NAD-dependent enzymes
10 Feb.            Polyacrylamide gel electrophoresis (PAGE)
15 Feb.            Quiz 1
17 Feb.            Restriction digest, ligation, and agarose gel electrophoresis
22 Feb.            Isolation and PCR of plasmid DNA
24 Feb.            PCR-based forensic analysis of human DNA
1 Mar.             Transformation and Plating of E. coli
3 Mar.             Genomics and Proteomics
8 Mar.             Quiz 2
10 Mar.            Sequencing of Proteins and DNA
22 Mar.            Protein Expression
24 Mar.            Enzyme-linked immunosorbent assay (ELISA)
29 Mar.            Western Blot
31 Mar.            Quiz 3
5 Apr.             Isolation of Acid Phosphatase from Wheat Germ
7 Apr.             Gel Filtration Chromatography
12 Apr.            Ion Exchange Chromatography; Purification table calculations
14 Apr.            Other Protein Chromatographic Methods
19 Apr.            Protein Structure Analysis
21 Apr.            Quiz 4




                                        3
Grading

       Your overall course grade will be determined by lab report average (65%), lecture
quiz average (27.5%), and evaluation (7.5%).


Lab Report Due Dates and Contribution to Report Grade Average

Report                Due date                   Percent of Avg.
1                     1/2 Feb.                        8%
2                     8/9 Feb.                        8%
3                     15/16 Feb.                      12%
4                     22/23 Feb.                      10%
5                     1/2 Mar.                        10%
6                     8/9 Mar.                        10%
7                     29/30 Mar.                      10%
8                     12/13 Apr.                      12%
9                     26/27 Apr.                      15%
10                    3/4 May.                        5%


Lab Report Guidelines

        Due dates for lab reports will be posted on the course web site and in the lab. Lab
reports are due at the beginning of the lab period on the posted date. Late lab reports will
be subject to a 10-point deduction for each day late. Requests for regrades of lab reports
must be made to the TA within one week of when the report is returned. Requests must
include valid reasons why you believe regarding is warranted.
        Lab reports must be typed or printed from computer. Computer labs are available
on the 2nd floor of Welch Hall and at other campus locations. The computers and printers
in the CH369L/369T labs are not to be used for the preparation of lab reports.
        Plagiarism on lab reports or any other form of academic dishonesty will not be
tolerated. Lab partners can confer on general aspects of data interpretation, but each
student must write his/her own lab report independently. Plagiarism also includes
copying text or figures verbatim from any published source, including web pages,
without proper attribution. Violations will be reported to the Dean of Students in
accordance with University policy. Policies and standards regarding academic
dishonesty can be found at the Student Judicial Services web site,
http://deanofstudents.utexas.edu/sjs/.

University of Texas Honor Code
The core values of The University of Texas at Austin are learning, discovery, freedom,
leadership, individual opportunity, and responsibility. Each member of the university is
expected to uphold these values through integrity, honesty, trust, fairness, and respect
toward peers and community.



                                             4
    This course is listed as a Significant Writing Component course. As such, you will be
expected to write and turn in lab reports that conform to established guidelines for proper
writing, both general rules and specific ones for scientific writing. Your writing will be
expected to demonstrate the following proficiencies:

   1.   No run-ons, comma splices, or inappropriate fragments.
   2.   A lean, efficient style.
   3.   No offensive or inappropriate language.
   4.   No subject/verb agreement errors.
   5.   No pronoun agreement errors.
   6.   No pronoun reference problems.
   7.   No misused, dangling, or misplaced modifiers.
   8.   Commas used correctly.
   9.   No spelling errors

Vocabulary used should be appropriate for a practicing scientist; appropriate technical
terms for equipment, reagents, measurement variables, etc. should be used. First-person
voice is acceptable provided the overall tone of the report is professional. The course
web site (http://courses.cm.utexas.edu/gmcdonald/ch369l/) will link to some online
resources for scientific writers.
        In addition, your lab reports will be expected to follow the format given below.
Failure to do so will result in significant deductions from your grade on each lab report.


Lab Report Format


Introduction – 25%
     State a concise objective for the experiment
     Explain theory and methods directly applicable to the experiments done in the lab
     Identify any reagents, apparatus, etc., that are new to this experiment, and the
       reason for their use

Data and Observations – 25%
    Present all raw data in appropriate format
           Tables for numerical data (e.g., absorbance readings, pH values)
           Pictures of gels, blotted membranes, etc. with labels for lanes, bands, etc.
           Copies of instrument-printed data (e.g., spectra)
    Label all data appropriately
           Descriptive titles for tables
           Lane numbers for gel pictures
    Describe any observations made while performing the experiment
    Describe any procedural changes from the lab manual




                                            5
Results and Discussion – 35%
    Report reduced data (calculated values derived from raw data)
    Present any graphs or plots of reduced data
            Include the individual data points, not just the curve
            For a linear regression, include equation and correlation coefficient (R2)
            Label all graphs and plots with title and axis units
    State and justify any conclusions reached from analysis of data
    Discuss probable sources of error (specific to each lab and based on your actual
       data and observations)
    Discuss specific topics listed in the lab manual at the end of each experiment

Appendix – 5%
    Show example calculations (typed)
    List literature references (including lecture notes) for any quoted text or figures
      used
    Attach carbon or Xerox copies of lab notebook

Spelling/Grammar/Writing Style – 10%
    Use correct spelling and grammar (caution: spell check software does not always
       correct scientific terminology properly)
    Always use complete sentences and paragraphs (no bulleted lists)
    Reference any figures or text not made or written by you
    Write clearly and concisely
    Use an overall professional tone


Lecture quizzes

        There will be 4 quizzes given during the lecture portion of the course. Each quiz
will cover the material associated with 2-3 experiments, e.g., spectroscopy, buffers,
electrophoresis. Calculations and data analysis of a similar nature to those you have done
for your lab report may also be included. There will also be two short take-home
exercises assigned. Your quiz grades plus the take-home exercise grades will be
combined to give your lecture quiz average.


Evaluation

        Your evaluation grade will be assigned by the TA and Dr. McDonald based on
lecture and lab attendance and/or tardiness, lab technique, attitude, lab notebook keeping
and pre-lab quizzes. You are responsible for reading and understanding the lab procedure
and the lecture notes relevant to each lab exercise, and doing any preliminary calculations
and other notebook preparation, before coming to lab. Pre-lab quizzes may be given in
each lab section at various times to assure adequate preparation for lab. Points will be
deducted from your evaluation grade for the following reasons: Unexcused absences,




                                            6
excessive tardiness, failure to follow lab manual procedure or TA instructions, improper
notebook keeping, failure to keep lab working areas clean and orderly.


Attendance

        You must carry out a lab exercise to receive credit for it. Attendance at lecture
and lab is mandatory; absences will only be excused for documented medical or other
unavoidable reasons. Unexcused absence from either lecture or lab will result in loss of
points on your lab report and/or your evaluation grade. You will be expected to arrive in
lab at or before the scheduled starting time; tardiness will be penalized by deductions to
the evaluation grade. At the discretion of the TA, a student that is excessively late to a
lab session may be denied entry to the lab and required to make up that lab exercise at
another time.

Lab Notebooks

       You must turn in the carbon copies (or you can use a copier to make copies) with
your lab reports. Before each lab period you will be expected to prepare your notebook.
This includes stating a concise objective, and doing any calculations required for the
experiment. The TA will check lab notebooks during each lab. Note any changes to the
lab manual procedure and record data and observations. Proper notebook upkeep will be
a part of your evaluation grade; the lab notebook does not have to be pristine and
beautiful, but it must be organized and legible.




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