Syllabus Chem. 317L Biochemistry Lab - Fall 2008

Credit Hours: 1 - 3 hours laboratory each week. Students must also enroll for Chem 315 (3 hours lecture per week; 3 credit hours)
Course Description: Application of the general principles of biochemistry in the laboratory. 

Prof.: John C Freeman Ph.D.
Office: 222 Scitech  Office phone: 570-422-3446
Office Hours:  T 9:30-10:30; W8:30-11:30 Th 9:30-10:30; or by appointment
I will generally be not be available on Fridays;   I will be available via email: jfreeman@po-box.esu.edu

Laboratory meets: T 11:00-2:00W 1:00-4:00, Th 2:00- 5:00 362 Scitech

Text - Biochemical Techniques, Robyt and White,Waveland Press, ISBN 0-88133-556-8 (REQUIRED)
Additional Required Materials:  Laboratory safety glasses or goggles, Closed Toed Shoes.  Bound notebook with numbered carbon duplicated pages (if carbon pages are not present be willing to photocopy experiments weekly at your own expense)
Suggested Materials: Lab coat or apron, or old clothing

Course Objectives:

1. To obtain an understanding of the basic laboratory techniques used in the field of biochemistry.
2. To relate topics discussed in the lecture course to real applications in the laboratory.
3. To improve problem solving and data analysis skills.
4. To write effective reports presenting laboratory results clearly and succinctly.
5. To develop the ability to investigate chemical literature.
6. To present laboratory results orally.
7. To learn to use chemicals and equipment in a safe manner.

Course Content: Schedule is Tentative. Times or experiments may change at the discression of the instructor.
I am deeply indebted to Dr Jones-Wilson for the materials found on this web site.
 

Week # Start Date	Laboratory	Pts.	Preparation (lab text) Web Links
Week 1 30 Aug	Check-in; notebook discussion; calculations assignment	50	calculations
Week 2   7 Sept; Labor Day Week now runs Tues to Monday	Use of micropipets- calibration -data handling  report help	50	Notebook -  pipets prelab
Week 3 - 14 Sept	Writing reports; presenting data; evaluating reports	20	Bring a paper to lab -  reports prelab
Week 4 21 Sept	Titration and buffer properties of Amino Acids	100	Short Report Amino Acid prelab
Week 5  28 Sept	Separation of Amino Acids by Ion Exchange Chromatography	100	Short Report -  Ion Exchange Prelab
Week 6  5 Oct	Separation of Proteins by Gel filtration Chromatography (Paper chromatography of AA)	100	Abstract Report -  Gel Filtration Prelab
Week 7  12 Oct Switch day week Monday on  Tuesday lab will need to work independently or meet thanksgiving week.	Rasmol (no formal meeting - work independently) (Paper chromatography of AA)	100	No Report/data sheets - prelab
Week 8 19  Oct	Carbohydrates/Nelson’s test Standard curves Nice site on Beers Law.	100	carbohydrates prelab
Week 9 - 26 Oct	Molecular Modeling	100	Abstract Report -  No prelab prep CAChe lab
Week 10-13 2  Nov 9 Nov 16 Nov	Oral Report Grading rubric for presentation. (delivered week of 11/16)  kinetics prelab   Same Nice site on Beers Law to remind you. Paper selection during final  week of kinetics (individual meeting)	250	Oral Report Grading rubric for presentation. (delivered week of 11/16)  kinetics prelabNice site on Beers Law.  Paper selection prelab
Week 13a 23 Nov	If Tuesday rasmol catch up if needed Wed, Thurs No Laboratory - Kill a Turkey in the name of a holiday		Thanksgiving Break
Week 13 30 Nov	Oral Report Enzyme Kinetics al	100
Week 14 - 7 Dec	Paper presentations	150	Oral report
The Week 15	FINAL EXAM - take homePosted Dec 7 Due noon Dec 12	200	Final Exam

Laboratory notebooks:
A laboratory notebook MUST be kept. This notebook should have a permanent binding with numbered pages and carbon copies (if not already numbered, you may do so in ink). Three ring binders or spiral notebooks are not acceptable. If you are unsure whether a book is appropriate, show it to me BEFORE using it. A table of contents MUST be included; keep the table of contents current. Use pen only to write in your notebook. Never enter anything in pencil. Never erase or scribble out any entry your notebook. If an error is made simply cross out using a SINGLE line through the error and write the correction above, below or to the right of the error. The error MUST be visible even after correction. Use of a felt tipped marker is not recommended. You laboratory notebook will probably get wet at least once this semester. Marker ink runs and smears when wet. NEVER enter your laboratory data on a separate sheet for later entry in the notebook. Data MUST be entered in the notebook directly. If I see you doing this I might just pick up your scrap of paper and destroy it and then you will be dataless and unable to complete your laboratory report.  Notebooks may be collected at random during the semester and checked for completeness. The grade will be based on organization and completeness. Notebooks should be readable; however, as this is a working document, I realize that it will not be as neat as a handed in assignment.All calculations which are part of the laboratory book MUST be included in your notebook.Incomplete notebooks will be severely penalized.

Do not leave the laboratory without a complete record of your data. Do not rely on a laboratory partner to keep the data or provide data later. Lack of data or problems with a lab partner are not valid excuses for late or incomplete assignments.

Preparation for Lab:
YOU MUST COME TO LAB PREPARED. This includes reading, studying and preparing the prelab assignment in your notebook. Completing these labs in the time required will be challenging. If you are unprepared, it will be impossible. "Extra" time will not be granted. If you are unprepared you will be excused from lab for that day and a grade of 0 will be recorded for that laboratory assignment, NO EXCEPTIONS. 

Prelab Assignments: DUE THE Night Before By 4:00 PM (yes Mondays lab will be due on Friday afternoon)
You are required to develop a procedure (in your own words) for each laboratory. This procedure should be included in your laboratory notebook in the format suggested. The procedure should be in your own words, not copied directly from the text/web. You may bring your handouts and text to lab for reference; however, you should follow the procedure as directed in your notebook. In addition to the procedure, prelab questions should be completed in your notebook. Carbon copies (or photo copies) of the prelab procedures and questions will be collected and graded. Prelaboratory assignments will be worth 30% of each laboratory. 

Laboratory Quizzes:
Quizzes may be given at my discretion. Short quizzes at the beginning of the laboratory period will be designed if students begin to come unprepared for lab. These quizzes will be open notebook (not open book or handout), to reward those who come prepared. 

Laboratory Reports and Due Dates:

Each laboratory report will be worth 60 % of the points for a given assignment. Laboratory preparedness as judged by the prelab will be worth 30 % of the points; post lab questions will comprise the remaining 10%. Laboratory reports must be typed. They WILL NOT be accepted hand written.Post laboratory questions should be answered in the notebook and the carbon copies attached to the typed laboratory report. Laboratory report instructions specific to each assignment will be accessible on the web page in the course schedule section of the syllabus.  Of course proper spelling and grammar is required.  Papers with more than 4 grammar/spelling errors per page will be automatically failed. 

Final Exam:
A take home final exam will be given. You must work independently on this assignment in accordance with the academic integrity policy you sign as a part of this class. You may use any written reference source. You may not consult any other person, including but not limited to students or other faculty. You may ask me for clarification of a question only. You may not ask another student. The assignment will be available on the web (linked to course schedule) on the specified date. It is due by 2:00 PM on the date noted. 

Due Dates:
Laboratory report due dates are generally two weeks after completion of the laboratory, allowing ample time to complete the assignment. Laboratory reports are due at the BEGINNING of the laboratory period or if we do not meet on a particular due date by 3:00 PM. Reports turned in after this time will be docked 10 points for each 24 hour period late. After 3 days (Saturday and Sunday are two days!), a late report will not be accepted and a grade of 0 will be entered for the assignment. The last written report is due on the first day of 15th week by 3:00 PM.

Laboratory Reports will take several different formats. Guidelines are provided for each report.
Abbreviated Formal Report (Short report)

Abstract Report (1/2 page abstract)
Oral Report

Grading:
Grading Scale:
Course total - 1470 + points depending on number of quizes given at 10 points each.

90%-100% A
80%-89% B
70%-79% C
55%-69% D
<55% F 

Grading Philosophy:
A - Student demonstrates an ability to understand the course material and to apply the material to new problems and situations. Student understands the connections between this course and other science courses and how the material relates to the world today.
B - Student demonstrates an ability to understand the course material. Student is able to apply the material to new problems and situations to a limited extent.
C - Student demonstrates an ability to understand facts relative to course material.
D - Student demonstrates a partial ability to understand facts relative to course
material.
F - Unacceptable Work.  Office Hours:
I will maintain an open door policy. This means that I am available for help with problems and with lecture notes when needed. If I am unavailable when you stop by I will make an appointment to speak with you at a later time. If I am not in my office please leave me a note with a number where you can be reached. You may occasionally see a Do Not Disturb, Come Back After...... sign on the door. Please respect this. You can always reach me by e-mail and will probably get the fastest response via that route. I will not be in my office on Mondays.

Email and Web Page
Material for this course including the syllabus are posted on the web. Updates and changes to the course schedule as the semester progresses will be posted and students will be notified via email. Email will also be used to communicate with the class concerning important events related to the class.It is your responsibility to provide me with a current email address.Each student must email me atjfreeman@po-box.esu.edu within the first few days of class so that I may collect the addresses in a class distribution list. You must do this separately for lab and class.  It is also your responsibility to check your email for information. Each email will include the course number in the title for identification. Failure to provide an email address or check email will mean that you will often be uninformed. In the case of changed scheduling of assignments, missing a notified change because you didn't check your email will not be a valid excuse. Each enrolled student can obtain an ESU email account free of charge by visiting academic computing. In addition, many free sites provide email (example yahoo). I do not care what server you use, just that you use one. 

Regrades:
I will be happy to regrade any assignment where I have marked a question incorrect in error. However, in the case of partial credit, I reserve the right to make all judgments about the quantity of points awarded. If you submit an assignment for partial credit regrade please be aware that I reserve the right to regrade the entire assignment. 

Extra Credit:
NO EXTRA CREDIT WILL BE AVAILABLE. 

Laboratory safety:
SAFETY GLASSES OR GOGGLES ARE REQUIRED AT ALL TIMES IN THE LABORATORY. Appropriate behavior in laboratory is essential to maintaining a safe environment. Being prepared is the best way to operate safely. Anyone operating in an unsafe manner will be excused from laboratory and a grade of 0 will be entered for that assignment. Two safety strikes and you are out of the course permanently. Please wear old clothing to lab or use an apron or lab coat. Individuals with long hair must tie back their hair before entering lab. You may not wear open toed shoes, shorts or half shirts which expose the stomach. Pay attention to specific instructions given at the start of each laboratory. You may feel that you are a careful worker and bad things won't happen to you. However, you cannot guarantee that the worker across the bench is as careful !

Chemical handling:
Required chemicals will generally be provided in small bottles in the fume hoods or on the bench. NEVER pour chemicals from the supply bottles inside the fume hood outside of the fume hood. Take your container to the hood and dispense the needed amount in the hood. Follow any other specific instructions provided with each laboratory. Material Safety Data Sheets are available for each chemical used. You may request a sheet from me or from the Stock Room Manager. If you are pregnant please inform the instructor.

Chemical disposal:
Many of the chemicals that you will be using cannot be disposed of in the trash or down the drain. Special waste containers will be provided. Use these as instructed. Please record this information in your notebook. 

Promptness:
DO NOT SHOW UP LATE FOR LAB! Important instructions will be given at the beginning of each lab. If you are late for lab you may be asked to leave. A grade of 0 will be entered for the assignment. 

Absence:
Attendance in lab is MANDATORY. There are VERY few excuses for missing lab. Labs generally cannot be made up. Exceptions including severe illness (you must be dying), death in the immediate family or athletic event absence should be cleared in advance whenever possible. Absences will be dealt with on a case by case basis. Documentation will be required. 

Special needs:
For students who have specific physical, psychiatric or learning disabilities and require accommodations, please let me know early in the semester so that your learning needs can be appropriately met. I will not discriminate against those with special needs. It is your responsibility to provide documentation of your disability to the Student Services office. All information and conversations concerning any accommodation will be kept strictly confidential. 

Academic Integrity: Absolute academic integrity is expected. Science requiresabsolute integrity. Penalties for copying, plagiarism, data fabrication or other types of cheating will be dealt with severely. My policy requires reporting of any and all violations of academic integrity. I will do this without hesitation. Any student guilty of academic dishonesty will be dismissed from the course and a failing grade will be recorded. Each student enrolled in my class is required to read and sign an academic integrity policy . Take this seriously - I do! 

Class Cancellation: Should class be cancelled due to weather or other emergency by the University, any assignments due during the cancelled class meeting will be due by 3:00 PM the next day that classes are in session or at the next class meeting, whichever occurs first.

Retention of Graded Assignments:I will retain graded assignments for this course for pickup by students until two weeks
into the next semester. After that time, any unclaimed assignments will be disposed of. 

Withdraw Policy: Please check the university calendar for appropriate dates for withdraw options. I will never tell a student to withdraw from a course. That is the individual students decision. I will however, provide information about progress in the course and scores needed for success (success is an individual definition; for some it is an A B or C, for some simply passing). Should a student decide to withdraw from the course it is the student's responsibility to make sure that he/she will still carry enough credits to maintain financial aid and full time student status. If you are unsure of your options please speak to the financial aid office BEFORE withdrawing. 

Lab partners:  Generally you will work with one other person while performing experiments.  Th is is your baby, I do not assign partners.  If you find your self unhappy with your initail partner you may pursue other arrangements. It is your job to have a partner or to do the labs on your own if you wish.  If you are performing experiments on your own you will be required to share equipment agreeably with other persons.