Syllabus - Western Illinois University



Chemistry 422 Advanced Biochemistry

Spring 2012[pic]

Instructor: Dr. Lisa Wen, Currens 548A

Lecture meeting time and place: MWF 8:00-8:50 a.m. Currens 315

Lab meeting time and place: Th 2:00-4:50 p.m. Currens 535

Office hours: MWF 9:00-10:20 a.m., other times by appointment

Tel.: 298-1667, Fax.: 298-2180, e-mail: L-Wen@wiu.edu

Course description: A continuation of Chem. 421 emphasizing the regulation of biosynthetic pathways and gene expression

Course prerequisite: Chem. 421 or equivalent

Recommended Text: "Biochemistry," 6/e, 2002, by Berg, Tymoczko, and Stryer; W. H. Freeman and Company

Textbook homepage URL:

Other supplemental materials:

Web links

Any other recent biochemistry textbook

Attendance: Regular and punctual class attendance is vitally important to a student's academic achievement. Students are expected to attend every class possible. Attendance will be checked. Students will be allowed to miss 3 lecture classes during the semester; each additional absence will lower your class grade by 1 percentage point (or 8 points). For example: If you have a 90% average and miss 8 classes, then your loss 5 % and your final grade is an 85%, a B+. Any student who misses more than 10 minutes of class by either arriving late or leaving early, then the student will be counted as absent. Missing fewer than 10 minutes of class is a tardy. Three tardies count as one absence. If you miss more than 15 classes, you will automatically fail the class. The only exception would be a serious documented medical illness. It is your responsibility to keep me informed of your situation during extended absences. Students who are called away from the campus to participate in University sponsored trips such as athletics or professional meeting (not sorority/frat, or other clubs) may be allowed to make up missed work, if, and only if, the student provides a signed memo from the faculty sponsor.

All students are responsible for all information and materials given in class whether you are present or not. Any student who arrives late for an exam loses that amount of time to work on the exam.

Students are not to go in and out of the class during lecture or an exam unless there is an emergency. Students leaving the classroom will be counted tardy for missing any time or absent for missing more than 10 minutes of class time. Students should make arrangements to go to the restroom between classes, not during class.

Cell phones and beepers must be turned off while in class out of consideration for your classmates. It can be very distracting – especially during an exam! Also, class time is not a social hour. Please refrain from casual conversation during class time.

Writing Component: “This course has been designated to meet the Writing Instruction in the Disciplines (WID) graduation requirement. WID courses provide instruction in the processes and formats for the writing content and style needed to be an effective professional in a student’s chosen field.”

This course requires a significant writing component, involving 10 lab reports throughout the semester and a research term paper. All reports and papers are to be submitted electronically as Word Files. An oral presentation of the research paper is required at the end of the semester. Lab reports will be in scientific paper format and will be 3 to 6 pages in length. The instructor may assign peer review of the lab report drafts before submitting. The instructor will read and make written comments on selected reports and the student will have opportunities to revise the report and re-submit. See the description of lab component below for detail.

Research term paper: Term paper must be on a topic of biochemical relevance and must be chosen in consultation with the instructor. It is strongly encouraged that you start working on your term paper early in the semester. The topic and journal articles should be approved by the instructor by March 19. The first draft of the paper is due by April 9. The paper is to be approximately 10 typed, double-spaced, pages and must include no less than five journal references with publication dates of 2000 or later. Use an Arial, Times New Roman, or Georgia typeface, a black font color, and a font size of 12 points. Use an inch margins (top, bottom, left, and right) for all pages. The term paper must be your own work. Sources of ideas or information must be referenced. The paper will be graded on the basis of content, construction, and conciseness (70%) and the presentation (30%). The final version of the term paper is due April 23 and the presentation dates will be April 27 - May 4. The penalty for late term paper is 5% each week; the first penalty is applied 3 days after the deadline. Term paper will not be accepted after the end of classes.

Graduate students (including undergrads taking bridge credit) have additional course requirements compared to undergraduates. Graduate students will be required to complete an extended 16-20 page research report involving an in-depth discussion of the approved topic. In addition, graduate students will be expected to demonstrate a higher level of understanding of concept presented; a greater amount of detail and understanding of complex processes when answering exam questions; a greater independence in performing laboratory exercises and assisting others as needed.

Grading: This course consists of three credits of lecture work and one credit of laboratory. Therefore the semester grade will consist of 75% (600 points) from the lecture and 25% (200 points) from the lab. In order to receive credit for the course as a whole, one must complete the lab with at least 60%. Failure to complete the lab will result in failure of the course. There are 800 points possible during the Semester. Your letter grade will be based on your total accumulated points.

|Three 50 min exams |300 points |

|Class discussion |100 points |

|Research term paper |100 points |

|Comprehensive final |100 points |

|Laboratory |200 points |

Grading Scale (including plus/minus grading) for undergraduate or bridge credits

|90.00% and above |A |

|86.70 - 89.99% |A- |

|83.40 - 86.69% |B+ |

|80.00 - 83.39% |B |

|76.70 - 79.99% |B- |

|73.40 - 76.69% |C+ |

|70.00 - 73.39% |C |

|66.70 - 69.99% |C- |

|63.40 - 66.69% |D+ |

|60.00 - 63.39% |D |

|56.70 - 59.99% |D- |

|56.66% and below |F |

Grading Scale for graduate credits

|90.00 % and above |A |

|80.00 - 89.99% |B |

|70.00 - 79.99% |C |

|60.00 - 69.99% |D |

|59.99% and below |F |

Make up exams: The only acceptable excuses for missing an exam will be for personal illness, family emergency, or University sponsored functions (i.e. WIU band trips, field trips in other WIU classes, WIU athletics, etc.). In all cases, documentation is required, and must be submitted to the instructor in advance or as soon as possible in case of emergency. Make-up exams are always designed to be at least as difficult as the regular exam.

An incomplete grade will NOT be given to a student with a failing grade. No incomplete will be given to a student without documented evidence of an emergency that requires that the student be away from the university or requires that the student miss the final examination. The student shall notify the instructor of the emergency as soon as possible and prior to the final examination.

Statement on Ethics: Western Illinois University, like all communities, functions best when its members treat one another with honesty, fairness, respect, and trust. Students have rights and responsibilities (). Plagiarism, cheating, and other forms of academic dishonesty constitute a serious violation of University conduct regulations. Students who engage in dishonesty in any form shall be charged with academic dishonesty. Please remember that you are expected to do your own work at all times.

Emergency evacuation procedures for the building: If a fire alarm should happen to ring, or if students are ordered to evacuate a lab or classroom by the instructor, the students should walk to the nearest stairwell (Do not use the elevators) and proceed to the ground floor and out the building.  Any student on an upper floor who cannot physically proceed down the stairs should go to the southernmost stairwell and await assistance. If the building should be evacuated all students and personnel should gather at the southwest corner of the Higgins Parking lot near the fence (parking lot just outside the building) to wait further instructions.

Emergency Preparedness: WIU Office of Risk Management and Emergency Preparedness provides resources on how to respond to emergency situations. Please view the video resources at wiu.edu/rmep/ (Click “Resources” on the left side of the page).

Students with Disabilities: It is the policy of Western Illinois University to accommodate individuals with disabilities pursuant to federal law and the University's commitment to equal educational opportunities. It is the responsibility of the student to inform the instructor of any necessary accommodations at the beginning of the course. Any student requiring accommodations should contact the Disability Resource Center (DRC).

TENTATIVE LECTURE/EXAM SCHEDULE:

DNA, RNA, and the flow of genetic information (Chap 4)

Exploring genes and genome (Chap 5)

Friday, February 10 ------------first 50-min examination

Exploring genes and genome, continued

DNA replication, repair, and recombination (Chap 28)

RNA synthesis and processing (Chap 29)

Friday, March 9----------- second 50-min examination

Protein synthesis (Chap 30)

Control of gene expression (Chap 31)

Friday, April 13 ----------- third 50-min examination

Signal-transduction pathways (Chap 14)

Oncogenes

April 27-May 4 -------- Student research term paper presentation

Monday, May 7 at 8:00 a.m. ----------- final examination

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Holidays and Other Important Dates:

| Date |Event |

|January 17, 2012 |First Day of Classes |

|February 13, 2012 |Lincoln’ birthday, no classes |

|March 12-16, 2012 |Spring Break |

|May 7-11, 2012 |Final exam week |

|May 12, 2012 |Undergraduate Commencement in Macomb |

SYLLABUS IS SUBJECTED TO CHANGE WITH NOTICE

Last Updated on January 13, 2012 by Dr. Lisa Wen, Department of Chemistry, Western Illinois University

Chem. 422 Laboratory

Lab Instructor: Dr. Lisa Wen, Currens 548A, Tel: 298-1667, email: L-Wen@wiu.edu

Laboratory meeting time and place: Th. 2:00 – 4:50 p.m. Currens 535

Office Hours: MWF. 9:00-10:20 a.m.; other times by appointment

Safety: Safety is the first concern in a chemistry lab. Safety glasses are to be worn at all times. Proper handling of chemicals, especially correct pipetting technique is expected. Material Safety Data Sheets (MSDS) information about all chemicals utilized in the laboratory can be found at the following web site.



Suggested reading:

1. Molecular Cloning: a laboratory manual (Vol. 1, 2, and 3), 2/e, by Sambrook et al. Cold Spring Harbor Laboratory Press, 1989 or 2001.

2. Current Protocols in Molecular Biology (Vol. 1 and 2) by Ausubel et al. Greene Publishing Associates and Wiley-Interscience, 1989.

These books are available in room 548. They should only be used in the lab. These two items are also available in the Physical Sciences library in Currens Hall.

Computer software:

1. Gene cloning and sequencing a strategic approach, Smith and Hames, IRL press, 1989.

2. Protein purification

Grading (200 points total): The laboratory portion of the course will be graded based on two lab exams (midterm, 35 points; final 40 points) and lab reports (125 points).

Lab reports: Lab reports are to be typed. The reports are due electronically before the beginning of the following lab period, unless otherwise directed. Late lab reports will be docked by 10% each week. Lab reports turned in two weeks after the due date will not be graded. The lab reports should represent the individual student's work.

The lab report is to be in Journal format. The journal selected is Protein Expression and Purification which is relevant to the lab experiments. The author guide for the journal can be found at Please focus on the article structure and essential title page information.

Attendance: You are expected to attend ALL of the lab meetings punctually. If it should be necessary to miss a lab, please notify me in writing (by e-mail), before the fact if possible. The only acceptable excuses for missing a lab are personal illness or family emergencies. If you miss a lab it is your responsibility to complete the make up lab within the week or ASAP to receive credit. Only one make up lab is allowed.

This laboratory is designed to introduce the principles of cloning and expression of a gene by E. coli expression system. You will amplify, subclone, express, purify, and characterize an enzyme.

Tentative lab schedules:

|Date |Activity |Points: |

|1/26 |Lab check in; go over safety rules; learn to use micropipettor; |5 |

|2/2 |Plasmid DNA isolation & agarose gel electrophoresis |12 |

|2/9 |Review PCR and design primers. PCR to amplify the desired gene |-- |

|2/16 |Agarose gel electrophoresis and DNA extraction |12 |

|2/23 |Restriction enzyme digestion of plasmid DNA and insert |12 |

|3/1 |Alkaline phosphatase treatment of the plasmids; agarose gel electrophoresis of plasmids |12 |

|3/8 |Gel purification of DNA |12 |

|3/15 |Spring Break | |

|3/22 |Midterm; |35 |

|3/29 |Ligation; Gene cloning (computer work) |12 |

|4/5 |Preparation of competent cells and transformation |12 |

|4/12 |Selection of transformants |12 |

|4/19 |Protein expression; SDS polyacrylamide gel electrophoresis |12 |

|4/26 |Enzyme activity assay |12 |

|5/3 |Comprehensive lab final |40 |

 Syllabus may subjected to change with notice

Last updated on January 13, 2012 by Dr. Lisa Wen

 

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