Biochemistry Lab

Bio 420/Chm 420

Department of Biology/Chemistry

Iona College

Fall 2008

 

Instructor:      Yourha Kang, PhD                             Meeting time: W 2:00-5:52

                        Cornelia 105                                        Meeting place: Cornelia 212                                                  633-2260

                         ykang@iona.edu

Office hours: M, W, F, 12 - 1 p.m.

Course website: www.iona.edu/faculty/ykang/index/bio420.htm

 

Course Description:  Welcome to a laboratory course designed to involve you in a number of biochemical techniques. The course will hopefully give you a broader understanding of what it is to be a biochemist, or more generally, a scientist.  The goal of the Biochemistry Laboratory is not only for you to learn how to physically perform techniques, but also for you to learn about the theory and relevance behind the techniques, and to understand how these techniques are used to answer biological questions.   

            This course is divided into three major projects, each delving into a particular set of biological questions, and utilizing specific biochemical methods that are being performed in research today.  In the first major project, you will learn to isolate, quantitate, and assay for the protein, a-amylase.  You will also learn how to separate proteins based on molecular weight using gel electrophoresis and to detect specific protein using the western blotting method.  In the second project, you will be performing an exercise in enzymology, where you will investigate the catalytic activity of the enzyme, tyrosinase, under varying conditions.  In between the second and third projects, we will have one lab devoted to using various computer resources that are available on the internet.  The third project will involve purification of a protein using various chromatographic techniques.

 

Course Objectives:  By the end of this course, students should be able to:

  1. make the connection between answering biological questions and using specific biochemical methods
  2. become familiar with a variety of biochemical techniques and internet resources
  3. understand the uses of the techniques and internet resources
  4. write a report in the style of a journal article

 

Lecture and Attendance: You are required to come to every class session.  If you are unable to come to class, you must inform me ahead of time and make up the lab during that week.  You are to come to class with a laboratory notebook and the handout of the lab to be performed that day (already read before class!).  Lab reports are ALWAYS to be in your own words and must be handed in on time.  Plagiarism (including sources from the internet!) will not be tolerated and will result in an automatic “F” for the report or assignment (you should know how to reference quotes and cite works by now).  Late lab reports results in a 10% deduction for every day that it is late.  I will accept reports as attachments as part of an e-mail message.

 

 

Grading:         20% Lab notebook, collected at the end of the semester

                        60% Lab reports (3 reports, 20% each)

                        10% Assignment

                        10% Participation

 

Lab notebooks:  A good lab notebook is essential to a scientist.  They are meant to be a complete and accurate description of what actually occurred during the course of an experiment.  This is so that the experiment may be repeated by another person or at a later time exactly (or not) as had been previously performed.  That is why it is crucial to leave in all relevant information (including mistakes!) in the lab notebook.  The notebook will not be judged by its neatness, but rather on its organization and its ability to describe your actions.

 

The lab notebook should be a bound notebook (no looseleaf paper), preferably a quadrille-ruled notebook.  The first page of the notebook should be a title page with your name, course, and semester.  That will identify the book.  The next three or four pages should have a table of contents (leave blank at the beginning and fill in as you go along), listing all the experiments that were performed.  The rest of the notebook will include all your experiments from the course.  Each project should be separate from one another with its own title and dates.  Each experiment in a project should have the following:

 

  1. Purpose of Experiment –What’s the use of performing an experiment if you don’t know why you’re doing it in the first place?  To be able to write down the purpose of an experiment in one or two sentences means that you have a good understanding of what’s really going on in terms of the biological questions that you are trying to answer.  You will appreciate the experiment more and the whole process will be made much easier.

 

  1. Materials and Methods – Since you will be given handouts, it is not necessary to copy the handouts into your book.  It is a waste of time and takes you away from the important things about the experiment.  You will only write in any changes from the handouts that you purposely or accidentally performed.  That way, you will have an accurate description of what you really did, as opposed to what should have been done.

 

  1. Data – This is probably the most important part of the notebook.  You should include every result that you get, and I mean everything.  All readings from instruments, graphs, calculations, observations, etc. should be included in this section.  It is also important to label everything you did.  Why keep a record if you won’t be able to understand it six months from now?

 

  1. Error Analysis – I consider this section to be the overall roundup of the experiment.  Were the results expected?  What are your thoughts about what happened?  What could have been done differently?  Here, you are starting to think about the data.

Lab Reports: A lab report should be a separate presentation, a compilation of all the important data in the notebook.  In other words, you will have teased out the pertinent information from the unnecessary stuff and all of the analysis should have already been performed.  A lab report not only informs the reader of what you did, how you did it, and what you got, it is there such that the reader will be able to repeat your experiment and hopefully get the same results.

Your lab reports are to be written in the format of a research journal article. It is to be typed (double-spaced, no less than 12 font) and should not include any raw data already in the notebook.  The report should be written at the level of a student who has just taken the course but is not familiar with these particular sets of experiments. You will be graded on three lab reports based on the three main projects.  Reports should have the following format:

1.      Abstract – This is a summary of the report.  It should not be more than a paragraph long.  The abstract should NOT be an introduction.  Information from ALL parts of the report (including the Results and Discussion sections) should be included in the abstract.  10 points

2.      Introduction - Here you will briefly state your objectives and the experiments that were performed to meet your objectives. You will also write in a few sentences (in your own words) why you did this experiment.  In a published journal article, the Introduction is used to provide background material for the reader in addition to the rationale behind performing the experiment.  In your reports, you will focus on just the rationale of the project.    I’ve given you the background; there is no need to regurgitate it.  20 points

3.      Materials and Methods -Like the notebook, you don't have to re-write the protocols.  Just mention the handout that was used and any changes that were made to the protocols, whether they were done on purpose or not. 5 points

4.      Results – This section is a presentation of important experimental data in tables and graphs with accompanying text stating what you obtained.  You want to be clear in your statements.  Just write what you got.  All tables and figures should have their own legends and you should refer to them in the written portion of your section.  Do NOT just put in the figures and tables.  They need to come with explanations.  Explain your results in a clear and concise manner.  The Results section, along with the Discussion, is the most important part of the report.  This is true here, as well as in published journal articles.  30 points

5.      Discussion and Conclusions - This is probably the hardest to write because here is where you interpret the data and explain the significance (if any) of your data.  Was it what you expected?  Did you fulfill your purpose?  Why?  Why not? What could be done to improve on the experiment?  Here is where the instructor determines whether or not you really understood the experiment. 30 points

6.     Works Cited - Be sure to cite any references that you used (including handouts, textbooks, and internet references) to write the report.  These not only include direct quotes, but information that you gathered form different sources.  5 points

Tentative Schedule

        Date                                            Topic                                                             

8/27/07                  Orientation, buffers, pH meter, use of micropipetter

 

Lab Project #1: a-Amylase Purification, Determination, Separation, and Detection

9/3/08                                a-Amylase purification and protein quantification

 

      9/10/08                              Activity determination

 

      9/17/08                              SDS-PAGE, membrane transfer

 

      9/24/08                              Immunostaining         

      Lab report #1 due 10/8/08

 

Lab Project #2: Tyrosinase Activity

10/1/08                              Tyrosinase extraction and protein determination

 

      10/08/08                            Determination of enzyme concentration, effects of stereochemistry

 

      10/15/08                            Determination of Vmax and Km

 

      10/22/08                            Effects of pH, inhibitors, and temperature on kinetics

      Lab report #2 due 11/05/08

 

Use of Computer Resources

      10/29/08                            Databases, Protein structure analysis

 

      Assignment #1 due 11/12/08

 

Lab Project #3:

 

      To be determined

 

Final lab report and lab notebook due 12/17/08