Syllabus, Chemistry 421, Fall2011
Instructor: Dr. Jenq-Kuen Huang, Currens 548B,Tel:298-1207, Fax: 298-2180, e-mail:
Lecture meeting time and place: MWF 8:00-8:50 a.m. Currens 202
Lab meeting time and place: T 8:00-10:50 a.m. or 2:00-4:50 pm, Currens 535
Office hours: MWF 1:00-2:20 p.m., other times by appointment
Course prerequisite: Chem.330 or Chem.332, or equivalent
Course objective: The course is intended to teach the chemistry of major cellular constituents and their metabolism.
Text: "Biochemistry" 6th edition by Berg, Tymoczko, and Stryer; W. H. Freeman and Company. Stryer Home Page URL:
Grading: This course consists of three credits of lecture work and one credit of laboratory. Therefore the semester grade will consist of 75% (750 points) from the lecture and 25% (250 points) from the lab. 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. Your letter grade will be based on your total accumulated points.
3 exams / 330 pointsBest 8 of 10 quizzes / 120 points
Research Term paper / 80 points
4 Homework assignments / 120 points
Comprehensive final (Standardized exam issued by American Chemical Society) / 100 points
Laboratory / 250 points
Grading Scale (including plus/minus grading)for undergraduate or bridge credits
90.00% and above / A86.70 - 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 / A80.00 - 89.99% / B
70.00 - 79.99% / C
60.00 - 69.99% / D
59.99% and below / F
Exams and Quizzes: Three 50-min exams and a 100-min final exam will be given during the semester. Short quizzes will be given on Fridays unless otherwise stated. To accommodate absences due to illness and other excused absences, the lowest two quiz grades will be dropped. No makeup quiz is allowed. No makeup exam is allowedunless you have acceptable reasons such as personal illness or family emergencies or university sponsored functions (i.e. WIU band trips, field trips in other WIU classes, professional meeting [notsorority/fraternity, or other clubs], WIU athletics). In all cases, documentation is required, and must be submitted to the instructor ASAP. Makeup exam must be completed in the following week. It is the student’s responsibility to make arrangements with the instructor.
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 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.
Attendance: You are expected to attend class regularly and punctually. If you are a graduate student attending class is required and will be checked for each class, five points for each missing class will be deducted from your total score. All students are responsible for all information and materials given in class whether you are present or not.Excessive absences will be reported to the financial aid office and your academic advisor. Any student who arrives late for an exam loses that amount of time to work on the exam.Attendance at the laboratory is required and will be checked for each lab. Please turn off cell phones and beepers 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.
Outside work requirements: Students are expected to read ahead and be prepared for class.You will probably find that this is a very fast-paced course. Therefore, it is highly advisable to keep up with the materials. Past experience suggests that reading the designated chapter before the class and going over the notes after each class is essential. A daily minimum of two hours of out of class work is needed to do well in this class. Write down any questions related to this course, you may submit the questions by email or ask them in class.
Research term paper: Research term paper must on a topic of biochemical relevance and must be chosen in consultation with the instructor. A topic of your term paper along with the abstract of six journal articles (the contents of these six articles must be relevant to the topic of your term paper) must be submitted to your instructor by email for approval by Oct. 21.There are three useful websites for articles searching. (1) ACS homepage (access to ACS homepage through WIU library to avoid “pay-per-view" charge. Once in the WIU library homepage, look for ACS database). (2) PubMed/PMC (a service of the National Library of Medicine located in the campus of National Institutes of Health). Once in the PubMed homepage, move the cursor to PMC (PubMedCentral, NIH digital repository for biomedical research). There are about 130 medical related journals in the PubMed/PMC website, and all articles in this website are free for downloading. (3).Science Direct. ScienceDirect offers more than a quarter of the world's scientific, medical and technical information online. Although some articles are free for downloading, most articles are pay-per-view. If articles are not available online or they are pay-per-view, you may request them through WIU interlibrary loan. You can also search articles through SciFinder (through WIU library).
The term paper is to be approximately 8 typed, double-spaced, pages and must include no less than six references (citations) published after 2001(please see “term paper format and literature search guideline” for details) . The term paper must be your own work and in your own words. Sources of ideas or information must be referenced. The paper will be graded on the basis of content, construction and conciseness, and must be submitted by Dec. 2. Please keep in mind, term paper and the associated hard copy of the six full scientific articles must be submitted to get credit (Your paper will not be graded if the articles are not submitted).
Graduate and bridge students have additional course requirements compared to undergraduates. Graduate and bridge students will be required to complete an extended 12 pages research report involving an in-depth discussion of the approved topic. In addition, graduate and bridge 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.
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. The following action is prohibited under the Student Conduct Code: Disorderly Conduct: Any behavior which disrupts the regular or normal functions of the University community, including behavior which breaches the peace or violates the rights of others. Plagiarism, cheating, and other forms of academic dishonesty constitute a serious violation of University conduct regulations. Any student convicted of academic dishonesty, can receive a failing grade and may be subject to further academic penalties. Web address for Academic Integrity Policy ( Please remember that you are expected to do your own work at all times. You can’t directly copy the homework, lab report, or term paper from your classmates or other sources. However, discussing homework questions or lab reports with your classmates and others is fine.
Students with Disabilities. In accordance with University policy and the Americans with Disabilities Act (ADA), academic accommodations may be made for any student who notifies the instructor of the need for an accommodation. For the instructor to provide the proper accommodation(s) you must obtain documentation of the need for an accommodation through Disability Resource Center (DRC) and provide it to the instructor. It is imperative that you take the initiative to bring such needs to the instructor's attention, as he/she is not legally permitted to inquire about such particular needs of students. Students who may require special assistance in emergency evacuations (i.e. fire, tornado, etc.) should contact the instructor as to the most appropriate procedures to follow in such an emergency. Contact Disability Resource Center (DRC) at 298-2512 for additional services.
Emergency Preparedness. The WIU Office of Risk Management and Emergency Preparedness provide resources on how to respond to emergency situations. Please view the video resources at (Click “Resources” on the right side of the page). If the fire alarms sound and/or students are asked to evacuate the building all students should proceed immediately to the nearest exit and gather at the southwest corner of the Higgins parking lot (near the fence) until the “all clear” is given.
STATE ACCREDITATION POLICY INFORMATION:
“In accordance with Illinois State Board of Education certification rules, all candidates seeking teacher certification are required by Western Illinois University to obtain a grade of “C” or better in all directed general education course, all core courses, and all courses in the option. Note: A “C- ” is below a “C”.” Please note: any secondary science teacher certification student wanting to see how this course is aligned with the State and National Standards should see their advisor and/or examine the Secondary Science Teacher Certification WesternOnline Advising site.
Tentative Lecture/Exam Schedule:
Ch1. Biochemistry: An Evolving science
Ch2. Protein Compositions and Structure
Ch3. Exploring Proteins and Proteomes
Friday, Sep. 16 ------first 50-min examination
Ch4. DNA, RNA, and the flow of genetic information
Ch5. Exploring Genes and Genomes
Ch11. Carbohydrate
Friday, Oct. 14------second 50-min examination
Ch7 & Ch10. Hemoglobin and Regulatory Strategies
8. Enzymes: Basic Concepts and Kinetics
Ch12. Lipids and Cell membrane
Friday, Nov. 11------third 50-min examination
Ch16. Glycolysis and Glucogenesis
Ch17. The Citric acid cycle
Ch18. Oxidative Phosphorylation
Monday, Dec. 12, 8:00 am- 9:50 am----- final exam
Holidays and Other Important Dates:
Date / EventAugust 22, 2011 / First Day of Classes
September 5, 2011 / Labor Day Holiday
November 21-25, 2011 / Fall Break and Thanksgiving
December 12-16, 2011 / Final exam week
December 17, 2011 / Commencement
SYLLABUS IS SUBJECTED TO CHANGE WITH NOTICE
Last Updated on August6, 2011 by Dr. Jenq-Kuen Huang, Department of Chemistry, Western Illinois University
Syllabus, Chem 421 Laboratory, Fall 2011
Lab Instructors: Dr. Jenq-Kuen (Jack) Huang, Currens 548B, Tel: 298-1207, e-mail: ; Dr. Lisa Wen, Currens 548A, Tel: 298-1667, e-mail:
Teaching Assistant: Mr. Vamshi Takkalapalli
Laboratory meeting time and place: T 8:00 am - 10:50 a.m.or 2:00-4:50 pm., Currens 535
Office Hours (Huang): MW F1:00 –2:20 pm., other times by appointment
Office hours (Wen): Tu 8:00-9:50 am, Th 9:00-10:50 am, F. 2:00-2:50 pm; other times by appointment.
General: Safety is the first concern in a chemistry lab. Material Safety Data Sheets (MSDS) information about all chemicals utilized in the laboratory can be found at the following web site. Proper handling of chemicals, especially correct pipetting technique is expected. Safety glasses are to be worn at all times. A notebook is required for data recording. A carbon copy of the raw data for each experiment is to be turned in at the end of each lab period.
Attendance: Attendance in the lab is required. If it should be necessary to miss a lab, please notify your instructor by e-mail before the fact if possible. No makeup lab or lab exam will be allowed unless you have acceptable excuses such as personal illness or family emergencies 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 within a week. Makeup lab or exam must be completed in the following week.
Lab Reports: Lab reports will consist of two parts: pre-lab and post-lab. The reports are to be typewritten (Font-12 and Times New Roman is preferred).
Pre-lab: Pre-lab part of the write-up will consist of cover page, objective, theory/background, materials, and procedures (in your own words). The pre-lab section of the report is to be completed before coming to the lab. Your instructor will check your pre-lab report during each laboratory period. Failure to complete the pre-labsection of the lab report before the start of the lab will result in losing5.75 points for that report.
Post-lab: Post-lab of the write-up will consist of results (include experimental data and calculations), discussions, conclusion, and answers to the post-lab questions. All questions should be answered unless otherwise indicated by your instructor.
Both pre-lab and post-lab sections of the report must be submitted together at the beginning of the next lab period. Late lab reports will be docked by 3% each day, and 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 format and the distribution of points for each lab report are listed below:
1. Cover page- must include the title of the experiment, course number, your name, your lab partner’s name, your instructor’s name, and date. (0.25 points)
2. Objective - state two to three sentences about the objectives of the experiment. (0.5 points)
3. Theory/Background information. Write about half to one page to summarize the basics of how the objectives will be realized. This may include important reactions, techniques or instrumental methods. It should not include procedures. (2 points)
4. Materials: List chemicals, reagents and their concentration, instruments being used. (0.5 points)
5. Procedures: The details should be sufficient so that your fellow students can read your report without any guessing. Any last minute change in procedures or concentration during lab session must be recorded. Use your own words to write up a lab procedure, do not directly copy the procedure from online lab handout. You must use past tense and passive voice to write up your lab report, which is the standard format for a scientific report. (2.5 points)
- [Sample examples] These two sentences are not appropriate: (a). I weigh out 0.6 g glycine and put it into a 100-mL volumetric flask (not a right style), and (b). I weighed out 0.6 g glycine and put it into a 100-mL volumetric flask. Notice, the present tense or past tense is used (not a right style). The following two sentences are rightbecause the past tense and passive voice are used: (c). Glycine (0.6 g) was weighed out and put into a 100-mL volumetric flask, and (d). An amount of 0.6 g glycine was weighed out and put into a 100-mL volumetric flask.
- [Pitfall]Avoid placing a numeric number at the beginning of a sentence. For instance, the sentence “0.6 g glycine was weighed out and put into a 100-mL volumetric flask” must be edited to “Point six gm of glycinewas weighed out and put into a 100-mL volumetric flask” or “An amount of 0.6 g glycintwas weighed out and put into a 100-mL volumetric flask.”
6. Results- the accuracy/quality of your data will be graded. (6.5 points)
- These should include tables, graphs and calculations, if any
- Tables and graphs should have self-explanatory titles
- Numbers should have appropriate units
- X and Y axes should be labeled
- All calculation should be included with appropriate units
7. Discussionsand conclusions - What you have learned from this experiment? You are aware of the objectives of the experiment and the expected outcomesbefore doing the experiment; you record any observations and data during the experiment; and you analyze the data and give a conclusion (or conclusions)after completion of the experiment. The conclusion(s) may or may not agree with the expected outcomes, either way you need to interpret your results. For instance, if your data agree with the expected outcome which means your lab skills were good and no mistake was made; if an unexpected result was obtained which might resulted from using dirty tubes or wrong reagent was used, or other reasons. (2 points)
8. References-List cited references. (0.25 points)
9. Answer all questions at the end of each experiment, unless otherwise directed (2 points)
Tentative lab exercises and grading scale
Date / Lab # / Activities / Points(raw data/report)
8/23 / Class lecture, Currens 202. (8:00-8:50 am & 9:00-950 am)
8/30 / Class lecture, Currens 202. (8:00-8:50 am & 9:00-950 am)
9/6 / 1 / a). Online literatures search(meeting place: Chemistry Computer Lab, Currens 529)
b). See animation for the several techniques that will be used in the lab this semester. Source of the animations comes from the “Lab Techniques Manual,” Massachusetts Institute of Technology (MIT). / 16
9/13 / 2 / Titration of glycine
Animations:
/ 1/15
9/20 / 3 / Methyl red colorimetry / 1/15
9/27 / 4 / Protein color reactions / 1/15
10/4 / 5 / a). Isolation of β-amylase (part I). The protein extract will be stored at 4 oC in the presence of toluene until April 19.
b). SDS-polyacrylamide gel and determination of molecular weight of proteins. / 1/15
10/11 / 6 / a). How to use a pipetman (see video: and )
b). Set up Polymerase Chain Reaction (PCR), get ready for next week (see PCR animation)
c). Isolation of plasmid DNA from bacteria / 1/15
10/18 / 7 / a). Agarose gel electrophoresis (theory)
b). Analysis of PCR product by agarose gel / 1/15
10/25 / Lab midterm / 30
11/1 / 8 / Carbohydrates / 1/15
11/8 / 9 / Carbohydrates continued / 1/15
11/15 / 10 / Kinetics of beta-fructofuranosidase / 1/15
11/29 / 11 / Beta-amylase (Part II), continued from Lab 5 / 1/15
12/6 / - / Comprehensive lab final / 45
Grading (250 points total): Eleven lab exercises and two lab exams are scheduled. The laboratory portion of the course will be graded based on two lab exams (midterm and final exams/75 points), lab reports (165 points), and raw data (10 points). You must turn in the raw data right after finishing each lab to earn points (1 point/each lab).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.
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. The following action is prohibited under the Student Conduct Code: Disorderly Conduct: Any behavior which disrupts the regular or normal functions of the University community, including behavior which breaches the peace or violates the rights of others. Plagiarism, cheating, and other forms of academic dishonesty constitute a serious violation of University conduct regulations. Any student convicted of academic dishonesty, can receive a failing grade and may be subject to further academic penalties. Web address for Academic Integrity Policy ( Please remember that you are expected to do your own work at all times. You can’t directly copy the homework, lab report, or term paper from your classmates or other sources. However, discussing homework questions or lab reports with your classmates and others is fine.