Biochemistry Laboratory I

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					Biochemistry Laboratory II                                                       Spring 2006
CHEM 320

Instructor:            Kelli M. Slunt
Office:                Jepson 341             654-1406                       kslunt@umw.edu
Office Hours:          1:00 – 2:00 pm M, W, R, and F               2:00 – 3:00 pm M
                       And by appointment

Meeting Time           9:30 am – 12:15 pm T, Jepson 310 and 311

Course Materials       course pack (same one as for CHEM 319)
                       approved safety goggles
                       laboratory notebook with carbonless duplication
                       scientific calculator

Course Description

       This laboratory course (along with CHEM 319) is designed to demonstrate and teach the
techniques utilized in the biochemical sciences. This semester will focus on experiments
involving identification of carbohydrates, partial purification of biological materials,
chromatography, enzyme kinetics, and DNA manipulation.

After completing the course, a student should be able to
         design and conduct a biochemical experiment
         conduct a literature search for an article pertaining to a biochemical topic
         interpret and begin to critique the biochemical literature
         work with peers to complete biochemical investigations

Grading

The grade in the course will be based on the following scale:
       Notebook grade                                       20%
       Reports                                              60%
       Prelaboratory assignments and data analysis          10%
       Final Assignment (Examination)                       10%

A mid-semester report of unsatisfactory (U) will be reported if you have a C- or below in the
course at the midpoint of the semester.

Assignments

There are several different assignments throughout the semester:

1) Prelaboratory assignment - prior to coming to lab on a given day, the students must prepare a
   plan for experimentation and this must be approved by Dr. Slunt. These plans are due
   electronically by 5 pm on the Monday before the lab day.
2) notebook - follow the guidelines in the course pack (chapter 1) and turn in the duplicate
   pages of your notebook upon completion of the experiment

3) Data analysis - after completing the experiment, the data should be analyzed and a results and
   discussion section of a report prepared and submitted to Dr. Slunt by Friday (by 5 pm) of the
   week in which the experiment was completed.

4) formal report - write a laboratory report for the experiment(s) following the guidelines in the
   course pack (chapter 1), those listed on the ACS website
   http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=education\cpt\ts_rrguide.html
   and in guidelines for authors information posted on blackboard. For each formal report, you
   must use and cite at least one literature reference not listed in the coursepack. This reference
   could be a background literature article or one related to the experimental procedures
   followed.

5) short report – a brief report about the experiment – it is intended to be shorter than the formal
   report (article). The short report would include an abstract, experimental procedures, results
   organized in tables, figures, etc. with labeled captions, answers to questions, and conclusions.

6) final assignment – due by May 4th at 11 am.

   The course is designated as writing intensive. It is important that students learn to
communicate in written fashion such that peers in the field can understand the scientific findings
and conclusions addressed in the paper. In the abovementioned assignments, you will be
expected to communicate in the same style used by biochemists in industry, academic, or
government settings.

During the course of the semester you must complete the following assignments:
- you are required to complete the prelaboratory assignment and the post-lab data analysis
- you must write a report for each experiment (this could be either a formal report or a short
   report)
- you are required to turn in the duplicate pages of the notebook for each experiment
- you must write at least two formal reports and two short reports during the semester
- if you do not complete all of the required assignments, you will be assessed a 100 point
   penalty

All assignments are due one week (by noon) after the completion of an experiment as
indicated on the tentative schedule. A late report will receive a grade of zero. Each student is
allowed a one week extension on one laboratory report (excluding the final assignment report)
provided that the student has submitted a written request for the extension by noon on the
original due date.

Formal reports will be graded for scientific content (50%) and writing quality (50%).    See the
course pack for further details about writing reports.
Honor System

     Any assignment for which you will receive a grade must be completed individually and
pledged as your own work. This includes notebook pages, laboratory reports, etc. The honor
pledge must be written in full: I hereby declare upon my word of honor that I have neither given
nor received unauthorized help on this work. (Signature)

       Alteration of data or copying data from another individual is an honor offense. You may
discuss how to do the calculations with other students or get help from the instructor, but your
final report must be your own work.

Class Attendance

        Class attendance and completion of the experiments is mandatory. Lateness to the pre-
laboratory lecture is distracting to others and students should attempt to be on time. The pre-lab
lectures cover important safety and procedural information. If an individual is repeatedly tardy,
a five point deduction will occur for each instance. You are responsible for all materials covered
in class during your absence.

       Please contact me as soon as possible if you are absent from the laboratory. Missed
experiments may be made up only in the case of an emergency. You need to notify me
immediately of such an emergency.

         You should complete as much of the work and planning of your experiments as
possible during the assigned laboratory time. No unauthorized access to the laboratory is
permitted.

Important Registrar Dates:

The last day to add a class is January 20, 2006, and the last day to drop without a grade of W is
February 3rd. For more details about the academic calendar, please consult the following
website, http://www.umw.edu/calendar/cas_mwc/default.php.

Office of Disability Services

The Office of Disability Services has been designated by the University as the primary office to
guide, counsel, and assist students with disabilities. If you receive services through that office
and require accommodations for this class, please make an appointment with me as soon as
possible to discuss your approved accommodation needs. Bring your accommodation letter with
you to the appointment. I will hold any information you share with me in the strictest confidence
unless you give me permission to do otherwise. If you need accommodations, (note taking
assistance, extended time for tests, etc.), I would be happy to refer you to the Office of Disability
Services. They will require appropriate documentation of a disability. Their phone number
is 540-654-1266.
Tentative Laboratory Schedule
Assignments are due one week after the completion of the laboratory work is completed.

Date              Laboratory Topic
1/17              Course introduction
1/24              Experiment – Identification of Carbohydrates
                  Due – Identification of Carbohydrate Report
1/31              Experiment 18 – Kinetic Studies of the Enzyme Alkaline Phosphatase
2/7               Experiment 19 - Inhibition of Alkaline Phosphatase Activity
                  Due – Report for Experiments 18-19 (one combined report)
2/14              Experiment 12 - Salting Out of Proteins
2/21              Experiment 12 – Salting Out of Proteins
                  Due – Report for Experiments 12
2/28              Experiment 13 - Extraction and Characterization of Bacterial DNA
3/7               Spring Break
3/14              Experiments 5 – Thermal Denaturation Curve of DNA
                  Due Report for Experiments 13 and 5 (one combined report)
3/21              Experiment 15 - Gel-Filtration Chromatography of Proteins
                  Due Report for Experiment 15
                  Experiment 17 - Separation and Identification of Fatty Acids in
3/28              Commercial Oils
                  Due – Report for Experiment 17
4/4               Experiment 20 - Analysis of DNA Restriction Fragments
                  Due – Report for Experiment 20
4/11              Experiment 21. Visualization of DNA Topological Changes
4/18              Experiment 22. Effect of Drugs on DNA Topoisomerases
                  Due – Report for Experiment 21 and 22 (one combined report)
                  Experiment 23. Use of Commercially Available Kits for PCR
4/25              Amplification
5/4               FINAL ASSIGNMENT due by 11 am