Introduction to Organic & Biological Chemistry CHE 2100 Fall 2013

Introduction to Organic & Biological Chemistry CHE 2100 Fall 2013 Lecture: Mon & Weds 10am-11:50am Science Building (SI) 3079 Laboratory: Mon OR Weds 1pm-3:50pm Science Building (SI) 3093 Course website: http://bonhamchemistry.com

Instructor: Dr. Andrew J. Bonham Office Hours: Wed 12:00-3:00, Thu 10:00-12:00 Contact: [email protected] Office: Science Building 3048

Why Study Organic Chemistry & Biological Chemistry? Organic & biological chemistry encompass the chemical foundations of almost every process that we encounter in our daily lives. A solid understanding of these essential topics will provide a better understanding of how modern industry works, how life functions, and give insight into the endless, fascinating examples of the beauty and complexity of the living world.

What do I expect from you? How can you succeed at this course? Chemistry is a complex topic, and while I believe that every student can succeed at this course, like any challenge, certain expectations must be met for you to succeed.  Regular Attendance and Daily Practice: Science and math are their own language, with specialized vocabulary and ways of approaching problems. Just like the study of a foreign language, I expect regular attendance and daily practice. If you cannot commit to thinking about, and solving problems in, chemistry every day, you will not acquire enough skill to confidently pass the exams and master this topic to the level that you will need for future careers.  Plan for the Future: I expect you to be aware of the lecture schedule and exam dates, and plan accordingly. I expect at least two weeks notification for any quiz you may miss (see Homework & Quizzes, below), and there will not be any flexibility on the date and time of the Final Exam. Review the schedule now, and plan for the future.  Pay Attention and Work Through Problems: It is exceedingly easy to fall into the trap of half-listening to lectures, nodding along with the material, only to find that you cannot answer the test questions. You cannot succeed by listening alone. I expect you to take notes, engage with the class and your classmates, do the homework exercises, and commit to the often difficult process of learning unfamiliar topics. Note well that simply looking at a problem set, then at the answer key, and saying to yourself, “That makes sense,” is not the same as actually solving the problem!  Take the lab work seriously. Labs are designed to reflect, as much as possible, real-world laboratory experiences. This is a great opportunity to learn useful skills, but requires careful attention to safety hazards, details of experiments, and awareness of the lab environment.

What can you expect from the instructor? I will give clear, relevant, on-time lectures that encourage class participation. I will provide clear assignments, clear and fair grading policies as outlined in this syllabus, and relevant practice problems. I will offer reasonable availability outside of class (e.g., office hours). Through my actions, I will encourage your understanding and enjoyment of the science of biochemistry.

Required Materials:  Bettelheim, et al., Introduction to Organic and Biochemistry, 7e.  Laboratory Manual: Available in the Auraria Bookstore.  i>clicker. Available in the Auraria Bookstore.  Molecular models are highly recommended but not required. Four model sets are on reserve in the library.  Safety glasses in the laboratory will be required at all times. A lab coat or an apron is highly recommended.  Scientific Calculator for Quizzes (no cell phones, graphing calculators, laptops, tablet computers, or other web devices).

Reading: The course will be primarily based on lecture notes, which will be available online. However, the Bettelheim textbook is a good, informative read, and reading the suggested chapters will improve your understanding of the material immensely—there is only so much lecture time, and a world of interesting things to learn. Additionally, the practice problems are from the book, and quizzes will partly be based on that content. If you attend lecture, read the textbook, and do the homework problems, you will be well prepared to succeed.

Class Participation / iClickers: Regular attendance and involvement in the classroom learning process is important. This class will use the iClicker evaluation system for in-class responses. These responses, regardless of whether they are “correct” answers, will constitute a 5% (“half a letter grade”) participation portion of your grade.

Homework: We will be using the Sapling Learning online homework system ( http://www.saplinglearning.com ). Additionally, you may want to do practice problems from the textbook, and review sheets that I will provide before tests. There is no way around the need to actually solve chemistry problems; doing homework is your best way to ensure a good grade in this class and a good understanding of the material. The Sapling homework will constitute a 10% portion of your grade.

Laboratory Reports: Lab reports are due for completed labs on the day of the associated quiz (see schedule). All lab reports should be typed and data should be analyzed using an appropriate spreadsheet/graphing program when necessary. There will be 14 lab reports; 13 will used to compute your report portion of the grade. Laboratory reports must be concise, well- organized and be presented well. Do not round your data; record the exact precision in your lab report that you were able to record in the laboratory depending on the measuring instrument used. Calculated values should follow rules of significant figures. Please note that for questions and data manipulations involving calculations, you MUST show your work (one example per calculation type) to obtain full credit. If only the final answer is shown without the work, only partial credit for the computed values will be given. To receive full credit for your work, you MUST show ALL of the work required to solve the problem and you MUST include units in your calculations/answers. Check your work carefully and be sure to include all units and the appropriate number of significant figures; consult a general chemistry text to review rules for addition/subtraction, multiplication/division, and logarithms. Please see the instructor for assistance if you have difficulty with this task.

Typical point values (to total 100 pts. per lab): name (2 pts.), date (2 pts.), partner (2 pts.), objective (5 pts.), data (25 pts.), values (2 pts.), calculations (sample of each type, 5 pts. each), questions (2-5 pts. per part/question), graphs (10-15 points), conclusion (5 pts.). Points will be deducted if these parts are missing or incorrect as well as incorrect number of significant figures (0.5 pts. per number) or missing units (0.5 pts. per number).

Your lab reports should be typed and should be entirely your own work. Graphs and tables may be done in Excel. Use the best fit line for points to calculate the slope. For all graphs, if you work with a partner, do not hand in photocopy or word-processing replicas of their report materials and call them your own. This is plagiarism. When in doubt, cite your source. Late laboratory reports will be penalized 5 points per day and will not be accepted after 7 days (1 week).

Quizzes: Quizzes will be given approximately bi-weekly (see schedule for dates). The six quizzes will consist of 30 short answer / calculation / structure and/or multiple choice questions. Quizzes are worth 50% of the course grade and will cover the material stated on the lecture schedule (2-3 chapters per quiz). Study questions and old quiz questions will be provided on MetroConnect. The quizzes will be given during the first 45 minutes of the class. Lecture will follow. At the end of the course, your lowest quiz grade will be dropped (we all have bad days).

Final Exam: The final exam will be the American Chemical Society General-Organic-Biochemistry exam. The final is required for all students. It is worth 20% of your course grade and will be given during finals week in December (TBA).

Grade Calculation & Policies: Class Participation / iClicker points 5 % Sapling Homework 10% 4 Quizzes (lowest dropped, remaining three are 15% each, 25 questions) 45 % Lab Experiments & Writeups 25 % Final Exam 15 % Total 100 % Points are tentative and subject to change by the instructor. The grading scale is as follows: A (90 -100%), B (80 - 89%), C (70 - 79%), D (60 - 69%), F (< 60%)

Grades will be available at the next regularly-scheduled course meeting. For Finals, final grades will be available from me in person on Friday of finals week (Dec 14th). Grades will be available by web and kiosk on Dec 21st at noon at connectu.msudenver.edu. FERPA policies prohibit me from releasing your grades via phone or email unless you register with the Registrar’s office and obtain a non-identifying security code.

Drop Dates: Students will be expected to know and observe the MSU Denver regulations regarding class drop dates. It is the student’s responsibility to withdraw from a course. See www.msudenver.edu/MetroCal/tools/acal.jsp Effective fall 2013 the NC grade notation will no longer be applied to academic records. For information on this and other academic policy changes, please see http://www.msudenver.edu/advising/student/academicpolicies/. Academic Dishonesty: Academic dishonesty is a serious offense. Any occurrence diminishes the quality of scholarship and the learning experience for everyone on campus. An act of Academic Dishonesty will lead to sanctions including a reduction in grade (up to and including a permanent F for the course), probation, suspension, or expulsion. Academic dishonesty includes cheating, fabrication, plagiarism, submitting the same paper or work for more than one class, and facilitating academic dishonesty. For definitions and more information, see the Student Handbook which is available online through Metro-Connect.

Disability Accommodation, Discrimination Policy, and Class Attendance on Religious Holidays: The Metropolitan State University of Denver is committed to making reasonable accommodations to assist individuals with disabilities in reaching their academic potential. If you have a disability, which may impact your performance, attendance, or grades in this class and are requesting accommodations, then you must first register with the Access Center, located in the Auraria Library, Suite 116, 303-556-8387. I cannot provide accommodations prior to my receipt of a faculty notification letter from the Access Center. Please note that accommodations are never provided retroactively (i.e., prior to the receipt of your faculty notification letter.) Once I receive your official Access Center faculty notification letter, I would be happy to meet with you to discuss your accommodations. All discussions will remain confidential. More information is available by visiting the Access center website www.MSU Denver.edu/~access/ ------The Metropolitan State University of Denver does not discriminate on the basis of race, color, creed, national origin, sex, age, sexual orientation or disability in admission or access to, or treatment in, its educational programs or activities. Inquiries concerning Title VI, Title IX and Section 504 may be referred to Dr. Percy Morehouse, Director, Equal Opportunity, Metropolitan State University of Denver, 303.556.2939; or to the Office for Civil Rights, U.S. Department of Education, 1244 Speer Boulevard, Suite 300, Denver, CO 80204. Discrimination based on disability in admission to, access to or operation of programs, services or activities of the University is prohibited by the Americans with Disabilities Act. ------Students at Metropolitan State University of Denver (MSU Denver) who, because of their sincerely held religious beliefs, are unable to attend classes, take examinations, participate in graded activities or submit graded assignments on particular days shall without penalty be excused from such classes and be given a meaningful opportunity to make up such examinations and graded activities or assignments provided that advance written notice that the student will be absent for religious reasons is given to the faculty members during the first two weeks of the semester. Nothing in paragraph one of this policy shall require MSU Denver faculty members to reschedule classes, repeat lectures or other ungraded activities or provide ungraded individualized instruction solely for the benefit of students who, for religious reasons, are unable to attend regularly scheduled classes or activities. However, presentations, critiques, conferences and similar activities involving individual students shall be scheduled to avoid conflicts with such students’ religious observances or holidays provided that reasonable advance notice of scheduling conflicts is given to faculty members. Because classroom attendance and participation is an important aspect of learning, MSU Denver students should not register for courses if regularly scheduled classes or activities routinely conflict with their religious observances or holidays (e.g., conflicts resulting in weekly absences for an entire semester). Any MSU Denver student who believes that an MSU Denver faculty member has violated this policy is entitled to seek relief under Section V of the MSU Denver Equal Opportunity Grievance Procedure.

Syllabus Changes and Policy: Any changes in this syllabus I may deem necessary during the semester will be announced in class and made available in writing. I reserve the right to revise the syllabus and grading policies at any time. CHE 2100 Lecture Schedule (subject to change) Fall 2013 Week Dates Topics Reading Suggested Problems 1 Aug 19th  Introduction Chap 1,2 1, 2, 4, 7, 9, 11, 13, 15, and Aug  Alkanes 17, 19, 21, 23, 27, 29, 33, 21st 41 2 Aug 26th  Alkanes Chap 2 1, 2, 4-9, 11-15, 17 ,19, and Aug Last “drop day” Aug 26th) 21, 24, 25, 27, 30, 31, 28th 33, 35, 37, 41, 43 Sept 2nd Labor Day break -- 3 Sept 4th  Alkenes and Alkynes Chap 3 1-6, 8, 10, 11, 13, 17, 19, 21, 23, 25, 29, 31, 33, 37, 39, 41, 43, 45, 53, 55, 57 4 Sept 9th  Aromatics Chap 4 1, 3, 7, 9, 11, 13, 15, 17, and Sept  Quiz Sept 11th Ch 1,2,3 21, 23, 29, 31, 41, 43, 47 11th

5 Sept 16th  Alcohols, Ethers and Chap 5 1-7, 9, 11, 13, 15, 19, 21, and Sept Thiols 23, 25, 27, 31, 33, 35, 18th 41, 43, 53, 57, 59 6 Sept 23rd  Aldehydes, Ketones Chap 9,10 Chap 9: 1, 3-9, 15, 17, 19, and Sept  Carboxylic Acids 21, 23, 25, 27, 29, 31, 25th 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 57, 59 Chap 10: 1-3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 27, 29, 33, 35, 37 7 Sept 30th  Carboxylic Anhydrides, Chap 11 1-3, 5, 7, 9, 11, 13, 15, nd and Oct 2 Esters, and Amides 17, 21, 25, 27, 35, 37, 41, 43  Quiz Oct 2nd Ch 4,5,9,10 8 Oct 7th and  Amines Chap 8 2, 7, 9, 11, 15, 17, 19, Oct 9th 25, 29, 31, 37, 39, 41, 43, 45 9 Oct 14th and  Chirality Chap 6 4-6, 9, 11, 13, 15, 17, 21, Oct 16th 23, 29, 31, 33, 37 10 Oct 21st  Carbohydrates Chap 12,13 Chap 12: 1-5, 7, 9, 11, 13, and Oct  Lipids 15, 17, 19, 21, 23, 25, 27, 23rd 29, 31, 33, 37, 39, 41,  Quiz Oct 23rd Ch 6,8,11 43, 45, 47, 49, 51, 53 Chap 13: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 25, 27, 29, 33, 39, 43,45, 47, 49, 51, 55, 59, 65, 71 11 Oct 28th  Proteins Chap 14 1, 2, 5, 7, 11, 13, 15, 17, and Oct (Last day to withdraw 19, 21, 25, 27, 29, 31, 33, 30st 35, 37, 39, Oct 28th) 41, 45, 47, 51, 55, 57, 69, 73, 75 12 Nov 4th and  Enzymes Chap 15,17 Chap 15: 1, 5, 7, 9, 11, Nov 6th  Nucleotides 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 Chap 17: 5, 7, 9, 13, 15, 17, 19, 21, 23, 25, 27, 31, 33, 35, 37, 39, 45, 49, 53, 55, 59, 63,65, 95 13 Nov 11th  Gene Expression Chap 18,19 Chap 18: 2, 3, 5, 7, 9, 11, and Nov  Bioenergetics 15, 17, 19, 21, 23, 25, 27, 13th 29, 41, 43, 61 Chap 19: 1, 3, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33 14 Nov 18th  Metabolic Pathways Chap 20 3, 5, 7, 9, 13, 15, 17, 21, and Nov  Quiz Nov 20th Ch 23, 25, 27, 29, 33, 35, 20th 37, 39, 41, 43, 12,13,14,15,17 45, 51, 53, 55, 57, 59, 61, 63, 65 Fall Nov 25th to -- -- th Break Nov 29 15 Dec 2nd  Review and Dec 4th FINAL TBA Final Exam TBA