Biochemistry Lab

Course Details

Course Number: 4242  Section Number: 101

Fall 2014

Location: Bolin Hall

Classroom Number: 309/323

Days & Times:

Thursday 1:00-4:50pm



Course Attachments

Biochemistry Lab Syllabus Undergraduates F2014  F2014 Biochemistry Lab UGrad Syllabus Machunis Masuoka-20140821-121814.docx

Textbooks

MSU Faculty Member
Elizabeth Ann Machunis-Masuoka PhD   
view Profile »

Grading Standards

Grading

Grades are assigned based on lab reports, assignments, and participation (including the notebook, outlines, and lab etiquette). Students are expected to demonstrate their mastery of the material through the successful completion of all assignments.

 

On the first day of lab, you will be given a preliminary homework set dealing with math and graphing (dilutions, making solutions, and creating and interpreting standard curves). You should have seen this math before. If any of it is hazy, come see me. This assignment will be worth 50 points. The Assignment is due on September 4.

 

Over the course of the semester, you will turn in 5 formal lab reports as outlined below:

 

Report #

Content

Experiment #

Lab Report

Due Date

Points

1

Pipetting and Dilutions

1

Sep 18

50

2

LDH Purification and Enzymatic Analysis

2, 3, and 4

Oct 16

100

3

Characterization of LDH Using SDS-Page and Western Blotting

5 and 6

Nov 6

100

4

Enzyme Kinetics

7

Nov 13

100

5

Analysis of GMOs

8

TUES Nov 25

100

 

Experiment #9 will be turned in as a 50 point assignment, not as a lab report. It will be due December 4.

 

Lab Reports are worth a total of 550 points; participation is worth 100 points. The overall class is worth 650 points. Grades will be assigned on a strict 10% scale based on 650 pts (100-90% = A; 89-80% = B; 79-70% = C; 69-60% = D; 59% and below = F).

 


Submission Format PolicyNote: You may not submit a paper for a grade in this class that already has been (or will be) submitted for a grade in another course, unless you obtain the explicit written permission of me and the other instructor involved in advance.

Plagiarism Policy Plagiarism is the use of someone else's thoughts, words, ideas, or lines of argument in your own work without appropriate documentation (a parenthetical citation at the end and a listing in "Works Cited")-whether you use that material in a quote, paraphrase, or summary. It is a theft of intellectual property and will not be tolerated, whether intentional or not.

Student Honor Creed

As an MSU Student, I pledge not to lie, cheat, steal, or help anyone else do so."

As students at MSU, we recognize that any great society must be composed of empowered, responsible citizens. We also recognize universities play an important role in helping mold these responsible citizens. We believe students themselves play an important part in developing responsible citizenship by maintaining a community where integrity and honorable character are the norm, not the exception. Thus, We, the Students of Midwestern State University, resolve to uphold the honor of the University by affirming our commitment to complete academic honesty. We resolve not only to be honest but also to hold our peers accountable for complete honesty in all university matters. We consider it dishonest to ask for, give, or receive help in examinations or quizzes, to use any unauthorized material in examinations, or to present, as one's own, work or ideas which are not entirely one's own. We recognize that any instructor has the right to expect that all student work is honest, original work. We accept and acknowledge that responsibility for lying, cheating, stealing, plagiarism, and other forms of academic dishonesty fundamentally rests within each individual student. We expect of ourselves academic integrity, personal professionalism, and ethical character. We appreciate steps taken by University officials to protect the honor of the University against any who would disgrace the MSU student body by violating the spirit of this creed. Written and adopted by the 2002-2003 MSU Student Senate.

Students with Disabilities The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Disability Support Services in Room 168 of the Clark Student Center, 397-4140.

Safe Zones Statement The professor considers this classroom to be a place where you will be treated with respect as a human being - regardless of gender, race, ethnicity, national origin, religious affiliation, sexual orientation, political beliefs, age, or ability. Additionally, diversity of thought is appreciated and encouraged, provided you can agree to disagree. It is the professor's expectation that ALL students consider the classroom a safe environment.

Contacting your Instructor All instructors in the Department have voicemail in their offices and MWSU e-mail addresses. Make sure you add your instructor's phone number and e-mail address to both email and cell phone lists of contacts.

Attendance Requirements

Attendance Policy

Attendance of the lab is mandatory (this includes the pre-lab lecture and the lab itself). Lab meets once per week and labs build upon each other. Although you will be working in groups, it is not acceptable to miss class. Students are expected to have read all materials prior to class and to have formulated a flowchart or some sort of outline for the day’s work to make the course run more smoothly. If you have a dire excuse (extreme and verifiable illness, accident, or injury; extreme family emergency) and you have proof of this dire excuse (which must be provided to me), one lab may be missed without penalty. Missing more than one lab will result in an instructor drop with the grade of “F”. Please plan on being present the entire lab period as well; you may get out early, but you should not assume that you will.

 


Other Policies

Required Materials

  1. Biochemistry Laboratory: Modern Theory and Techniques, 2nd edition, R. Boyer (Prentice Hall), 2012 (REQUIRED – this is not optional). There is an eTextbook option for sale available at: http://www.coursesmart.com/biochemistry-laboratory-modern-theory-and/rodney-boyer/dp/9780321743237. There is also a pdf eTextbook that can be found by Googling the textbook’s title (this is free and searchable; or at least it was when I located it).
  2. Laboratory Notebook: quad-ruled composition book
  3. Scientific Calculator: bring every day unless you like doing math in your head
  4. Printed protocols and handouts: materials for each lab experiment will be posted on D2L or handed out in class/hung up outside my office door. You are responsible for downloading or retrieving these materials and going through them thoroughly prior to the start of lab lecture each Thursday. They should be brought with you to class.
  5. “Samples”: some labs will require you/your group to bring samples (generally grocery items) to lab to process; these are your responsibility to bring as I will not have extra samples. You will be told the week before such samples are required to bring them in (can be brought in early, we will stick them somewhere).

 

Suggested Materials

Writing Papers in the Biological Sciences, 3rd, 4th, or 5th edition, Victoria E. McMillan (Bedford/St. Martins). This text is useful for both biology and chemistry reports and papers. Older editions are dirt cheap and the information has not changed greatly, thus you do not need the newest edition.

 

Prerequisites

Credit or Concurrent Enrollment in CHEM4243

 

Attendance Policy

Attendance of the lab is mandatory (this includes the pre-lab lecture and the lab itself). Lab meets once per week and labs build upon each other. Although you will be working in groups, it is not acceptable to miss class. Students are expected to have read all materials prior to class and to have formulated a flowchart or some sort of outline for the day’s work to make the course run more smoothly. If you have a dire excuse (extreme and verifiable illness, accident, or injury; extreme family emergency) and you have proof of this dire excuse (which must be provided to me), one lab may be missed without penalty. Missing more than one lab will result in an instructor drop with the grade of “F”. Please plan on being present the entire lab period as well; you may get out early, but you should not assume that you will.

 

Laboratory Notebooks

Students are required to maintain a laboratory notebook for this class. You will use the notebook to record protocols and any changes made to those protocols, individual and class lab data, and all calculations made during the course of your experiments. You will then use your notebook to write your lab reports. Below are some guidelines for keeping a laboratory notebook. You should also read Boyer, Chapter 1, Section B for more information.

  1. Everything that you do must be recorded directly into your notebook and it must be recorded in pen. Mistakes should be neatly crossed out, initialed by you, and the correction written down next to the mistake. Never remove pages or obliterate mistakes.
  2. All calculations must be written down in your notebook (show your work; I can’t help you troubleshoot problems if I can’t see your math).
  3. All recorded measurements, pictures, computer printouts, computer rendered graphs, etc. (i.e., data) must be taped or written directly into your notebooks; they should not be left loose, nor placed in a separate binder or folder.
  4. Each new lab should start on a new page, and each experiment should have a title, date, and objective. Protocols should not be blindly copied into your notebook or taped in without annotation – you need to write down what was actually done, what was measured, what it looked like, whether accidents occurred, etc. Use subheadings to denote different parts of any given experiment (most experiments will run over at least 2 days).
  5. The dates should appear at the top of each page so you know exactly when you performed specific parts of each experiment.
  6. Never record information on loose sheets of paper, paper towels, etc. with the intent of copying material into your notebook later – everything must go directly into the notebook.
  7. Each time you record data (measurements, absorbencies, etc.), record a brief interpretation. For example, is a given measurement higher or lower than what you expected and what effect might that measurement have on the overall results? At the end of the experiment you should also include an overall interpretation/summary of your work that will help you write your lab report. Essentially, you need to ‘think out loud’ into your notebook.
  8. Record all mistakes or accidents and what you did or will do to try and fix them.
  9. Record any questions you have and the answers you receive – this can help with your interpretation later.
  10. If you look material up, you need to cite your sources using proper scientific citation style.
  11. Laboratory notebooks will be turned in at the end of the semester for a grade.

 

Laboratory Reports

You will be turning in 5 formal Lab Reports over the course of the semester as outlined in the Grading section of this syllabus. To help you write your lab reports, you will use LabWrite, a National Science Foundation (NSF) funded lab report writing tutorial system designed by NC State University. LabWrite is freely available at http://www.ncsu.edu/labwrite/index_labwrite.htm. LabWrite has many useful features and will help you to write a good lab report. You should also consult Boyer, Chapter 1, Section B. Lab reports must be typed in their entirety (including photo captions, tables, graphs, etc.). All 8 sections described in LabWrite (from title to references) must be included in each report. Reports will be held to the highest writing standards, so make sure you proofread your work before you turn it in! All reports are to be individually written, but you may talk with your lab partners and work together when discussing results. Below are some general notes to consider while writing your lab reports:

  1. As LabWrite suggests, you should not write your reports in the final order in which the report will appear (i.e., title first, references last). It is best to start with the core and work outward – follow the writing order suggested by LabWrite and your work should be easier and better.
  2. Do not be afraid to rewrite/rework various sections to make the reports coherent – you will get a higher grade the more work you put into the report. Do NOT wait until the night before to write your reports. Last minute work always receives a poorer grade.
  3. Please keep your Abstracts to between 150 – 200 words and remember that this is often the only part of the paper ever read – it needs to be concise, but informative. The overall conclusion must be stated here.
  4. Remember, “Lab Report X” is NOT at title!
  5. The Introduction and Discussion sections MUST include references to primary and secondary journal articles (while you may need to cite handouts and/or your textbooks, these are not journal articles and don’t count towards the required references). Lab Report #1 must have a minimum of 3 total journal references; Lab Reports #2 – 5 must have a minimum of 7 total journal references. References MUST pertain to the experiments at hand. For example, for Lab Report #1, a paper on the importance of calibration would be relevant, but a reference on the history of spectroscopy would not be. Please cite using the following format:
    1. Use bracketed numbers in the text (example: [1]) and number the references in the order of use; if the same reference is used more than once, always use the same original number assigned to it.
    2. List the references at the end in the References section in the order of usage by their assigned number (do not alphabetize).
    3. Use this citation format: Author Last Name, Author first initials. (Year) “Title of the Article”, Journal Title, Vol #(Issue#): page numbers. doi #.
    4. If in doubt, ask me.
  6. The Methods must appear in paragraph form as they do in normal journal articles – read the Methods sections of several primary journal articles to get a feel for this section.
  7. The Results section is ALWAYS a combination of text and figures/graphs, etc. and the text that is present explains the figures/graphs, etc. Each method usually has a result, which needs to be presented, and all methods/results together produce a final overall result of the experimental sequence. Make sure there is logic and cohesion to this section.
  8. The Discussion is not a rehash of the results, but rather summarizes the results and places them within a broader scientific context. Do not forget to give this context and a final conclusion. Additionally, the Discussion usually recommends further research or changes to the protocols used; you should include such a commentary.
  9. Figure legends need to be informative and figures/tables/graphs must be interpretable on their own. The reader should be able to tell from the combination of figure legend and figure what was done and why it mattered.
  10. If something in your report seems really off, I may ask to see your lab notebook to figure out what went wrong. It would be better, however, if you do the troubleshooting. If you have questions, ask me and I will help you (though I will not write your reports for you, nor proofread them prior to your turning them in).

 

Late Assignments

No late assignments will be accepted for any reason. This is a non-negotiable policy. Lab reports are due at the beginning of lab lecture on the days specified in the grading section.

 

Cell Phones in Lab

You should never make or receive phone calls or texts during lab. Phones are a distraction that can result in lab accidents that are harmful to you, your lab partners, and your experiments. If I catch you on your phones playing, you will lose 1% from your overall grade in the lab. An exception to the “no cell phones in lab policy” may on occasion be made for data collection purposes. Cell phones can be of surprising use in documenting data; HOWEVER, should you spill anything caustic on your phone or contaminate your phone with potentially hazardous or infectious materials, YOUR PHONE WILL BE CONFISCATED AND TREATED AS WASTE (i.e., it will be destroyed and you will NOT be reimbursed for your loss). Many phones will fit into a plastic baggie if you wish to protect your phone and use it in the lab. In all cases, cell phone use is to be limited and any loss of damage associated with cell phone use in the lab will be the fault of the student, not the department.

 

University Code of Conduct

For university standards of conduct please refer to the MSU Student Handbook. In general, students are to attend all meetings of all classes; instructors may drop students for excessive absences, indifference, disruptive behavior, or failure to complete class assignments; students are prohibited from cheating, plagiarizing, or colluding. Students are expected to have read the Student Handbook.

 

Academic Dishonesty

Cheating, plagiarism, and collusion (as well as several other forms of conduct) are all strictly prohibited at MSU. Please read the MSU Student Handbook definitions of cheating, plagiarism, and collusion and MAKE SURE that you do not engage in any of these behaviors. If you are unclear on what may count as cheating, plagiarism, or collusion, please see the instructor or the Dean of Students.

 

Instructor Drops

According to the 2012-2013 MSU Student Handbook, p. 47, “An instructor may drop a student any time during the semester for excessive absences, for consistently failing to meet class assignments, for an indifferent attitude, or for disruptive conduct.” For the purposes of this course, “consistently failing to meet class assignments” includes consistently not turning in assigned work or turning in work that consistently receives a failing grade.

 

Intellectual Property

By enrolling in this course, the student expressly grants MSU a “limited right” in all intellectual property created by the student for the purpose of this course. The “limited right” shall include but shall not be limited to the right to reproduce the student’s work product to verify originality and authenticity, and for educational purposes.

 


Writing Proficiency Requirement All students seeking a Bachelor's degree from Midwestern State University must satisfy a writing proficiency requirement once they've 1) passed English 1113 and English 1123 and 2) earned 60 hours. You may meet this requirement by passing either the Writing Proficiency Exam or English 2113. Please keep in mind that, once you've earned over 90 hours, you lose the opportunity to take the $25 exam and have no option but to enroll in the three-credit hour course. If you have any questions about the exam, visit the Writing Proficiency Office website at http://academics.mwsu.edu/wpr, or call 397-4131.