Introduction to Organic Chemistry
and Biochemistry (X402)

This partial syllabus will give you a general idea of the course structure.

Course syllabus (General information handout) (partial)

Quick reference
Introduction. Overview, prerequisites
Textbook; supplies
Course outline
Chapter handouts
Homework
Feedback and withdrawals
Supplemental information. Miscellaneous additional information about the course, especially for prospective students with questions. This might be thought of as a supplement to the syllabus.

Organic/Biochem (X402) home page

Bottom of page; return links and contact information


Quick reference

Overview of the course format.

Monday evenings; 14 classes.

Class starts at 6:30 promptly; 10 min break ~7:30; out ~8:35. Office hours: 6:00-6:30, in the classroom. I will also stay after class for questions.

Tests:
1) Class 4, in class (last hour).
2) Class 7, take home test due next class period.
3) Class 11, take home test due next class period.

Final exam: Last class. (I can return the exam by mail, with an answer sheet and your course grade; please give me a SASE on exam night.)

Your course grade is based on the four tests, weighted equally. Special consideration will be given to students who do well on the final. Students can take the course on a pass-fail basis; you must take the tests and earn a C or better to pass. Registered students can also take the course without credit. See "Grades" section of Extension catalog; you can choose your grade option late in the course.

If you have a schedule problem with a test, please see me -- in advance if possible. If you miss something, please call and make arrangements.

All tests: You may use one page (one side) of notes. The notes must be in your own handwriting. (More about the note page later, or see Note page information at the web site.) Except for the note page, tests are closed book.

Instructor e-mail: See contact information at bottom of page. Other contact information is in the printed syllabus handout.

Web site.
http://bbruner.org/ (The page you are now reading is part of this site.)
Syllabus, some practice quizzes and sample tests, some supplementary materials, Internet links (including all mentioned in handouts), and materials for my other classes. Updates/handouts page: each week I will post updates/announcements about current schedule; it also links to most handouts, so you can download them if you miss a class, and class slides.

A quick way to get to my site is to Google on "chem X402" or "chem Bruner" (without the quotes; capitalization should not matter).

Please sign up for the class e-mail list. This is for discussions, but it is also the best way to make announcements during the semester; messages go to everyone who is signed up. To reduce junk mail, details of list info are not posted on this page.

There is one assignment that requires access to the Internet. If you do not have Internet access, even for occasional use, please check with me, and we will try to accommodate. Except for this special case, use of the Internet is optional.

Please let me know of corrections or suggested additions to the course web site. In many cases I can respond promptly to requests, so that your comments during the course benefit the current class. In particular... Please let me know of topics for which the book's problems/exercises are inadequate, and let me know of suggested additions to the Glossary.

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Introduction. Overview, prerequisites.

The course is an introduction to organic chemistry and biochemistry. Most of the course is organized around topics of organic chemistry, but with some biological perspective. The level of the course is what is sometimes called "chemistry for nursing students". Many of our students have a primary interest in some aspect of the biological sciences, but the course is broadly suitable for anyone who wants to learn or review basic organic chemistry. It also may serve as a preview of more advanced courses such as college level Organic Chemistry, Biochemistry or Molecular Biology.

We start by discussing the main classes of organic compounds, with some emphasis on functionalities and properties of particular relevance to biology.

In the biochemistry part of the course we survey the major classes of compounds in biological systems. We present biopolymers and the principles behind their synthesis and design. We introduce the general plans of metabolism, for energy and biosynthesis, showing how pathways are interconnected. The goal is to show the logic of that complex chemical system we call "life", but time does not permit much study of the details. Some of the biochemistry is presented along with the appropriate organic chemical topics.

Prerequisites. Familiarity with basic concepts of chemistry, such as atoms and molecules, elements and compounds, ionic and covalent bonds, moles, and the periodic table. The course is suitable for students without prior background in organic or biochemistry. For more about the background we expect, and some help reviewing it from our textbook, see the X402 Background Information page at my web site.

X402 may be suitable for high school students. See the section of the Supplemental information page High school students? for more.

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Textbook; supplies

This part shows information for the Spring 2006 section.

Textbook: Organic Chemistry - A Brief Introduction, by R J Ouellette. Prentice Hall, 2/e, 1998, paperback. ISBN-13 978-0138-41933-2 (ISBN 0-13-841933-7). See the "box" below for information about buying the book.

For information about an optional Study Guide (SG) for this book, see my Study Guide page. The SG is also mentioned below, under Homework.

"Recommended":

Book prices vary widely. Before you make a purchase, I strongly encourage you to get some basic information about the range of prices for the book. A good easy way to do that is to go to the price check service AddAll, at http://www.addall.com. Choose ISBN search, and put in the ISBN number of the textbook; you can paste it in: 0-13-841933-7.

The following link, if it works, should take you directly to the AddAll output for this book: Direct link to AddAll output for X402 textbook.

The AddAll output typically shows this book being offered widely. Prices vary. Numerous used copies are available at a greatly reduced price (many are around half the list price, some much lower); tax and shipping varies. I do not recommend any particular store. Please do a check yourself, then make a purchase as suits your preferences.

For more information about buying books, see my page Buying Books. That page also lists other price check services you might try.

If you have any questions/comments/concerns/complaints, please e-mail me.

Please bring the textbook (and models, if you have them) to class.

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Course outline

This part shows information for the Spring 2006 section.

General plan is to follow Ch 3-15 of Ouellette's book. For some topics, we will do only selected portions of the chapter, since this book is for a somewhat more advanced course than ours. At the end we will spend some time on the general ideas of biochemical metabolism, which is not explicitly in the book. Ch 1-2 are mainly background material; we will refer to them as needed.

A tentative and approximate course outline, by class, follows.

  1. 1/30. Course introduction. Goals. Background discussion; basic chemistry. What is organic chemistry? (Review: periodic table, non-metals, covalent bonds, Lewis structures, VSEPR.) (Start Ch 3; for the review, Ch 1-2 excerpts)

    Chapter handouts are posted. For more about these handouts, see the Chapter handouts section below.

  2. 2/6. Saturated hydrocarbons: alkanes and cycloalkanes. Isomerism. Organic nomenclature. Combustion reactions. Physical properties; polarity. (Review: bond polarity, intermolecular forces.) (Ch 3)
  3. 2/13. Unsaturated hydrocarbons: alkenes and alkynes. Multiple bonds, (loss of) rotational freedom, cis-trans isomerism, E-Z nomenclature. Addition reactions; addition polymers. (Ch 4)

    2/20. No class.

  4. 2/27. Aromatic compounds. Addition vs substitution reactions. Heterocyclic compounds. (Ch 5) [Test 1; in class, second hour. This test typically covers through Ch 4.]
  5. 3/6. Chirality: mirror image molecules. What is the phenomenon and why is it important? The first oxygen functional groups: alcohols, phenols, and ethers. Sulfur functional groups. Redox and elimination reactions. Hydrogen bonding: donors and acceptors. (Review: oxidation-reduction, intermolecular forces.) (Ch 6; Ch 8; Ch 9 Sect 1-3)
  6. 3/13. More oxygen functional groups: aldehydes and ketones; (hemi)acetals. (Ch 10)
  7. 3/20. Carbohydrates. A type of biochemical that builds on the organic chemistry we have discussed so far. Simple sugars; linear and cyclic forms. Sugar derivatives, polymers. (Ch 11) [Test 2 handed out. This test typically covers through Ch 9.]
  8. 3/27. [Test 2 due.] More oxygen functional groups: acids and esters. "High energy" acyl compounds: acyl chlorides, acid anhydrides, and thioesters. Acid strength. (Review: Ka.) Esters and anhydrides of phosphoric acid. Condensation polymers. (Ch 12)
  9. 4/3. Lipids. Diverse molecular structures with a common property. Roles: structural, hormonal, storage. Membranes: lipids, proteins, fluidity. Hydrophobic and hydrophilic interactions. Cholesterol. (Ch 13)
  10. 4/10. The major nitrogen functional groups: amines and amides. Basicity. (Ch 14)

    4/17. No class.

  11. 4/24. Proteins: what they are and what they do. Amino acids, proteins, protein structure (primary to higher level). Enzymes: role, specificity and regulation. (Review: reaction rates and equilibria; catalysts.) (Ch 15, and Enzymes section of Metabolism handout; see Metabolism page at the web site.) [Test 3 handed out. This test typically covers through Ch 12.]
  12. 5/1. [Test 3 due.] Metabolism. Bioenergetics. Burning food; conserving energy for biological needs, by using coupled reactions. ATP as an energy currency; other "carriers". Citric acid cycle and oxidative phosphorylation. Metabolic pathways, catabolic and anabolic. Glycolysis. Flow of carbon, nitrogen and energy through interconnected pathways. Energy storage. (Review: energy.) (Not in book; continue with Metabolism handout.)
  13. 5/8. Metabolism (continued).
  14. 5/15. Final exam. Last class. The final exam typically covers through Section I of the Metabolism handout.

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Chapter handouts

These handouts give specific reading assignments for upcoming classes. Notes discuss areas of emphasis, and even give a brief overview of omitted material. Students who are new to a topic should emphasize the issues noted as most important. Those who are doing well in a particular area are encouraged to go beyond the required assignment. In general, customize the course in the light of your background, needs and interests.

A few "Essay" sections are noted as "required," but most are not considered core material. However, I think you will find many of these to be interesting supplementary material. One possible approach is to skip the Essay sections the first time you read over a chapter, then read those that interest you later.

The handouts will list some "suggested" homework problems. See Homework, below.

"Further reading" and "Computer resources" are optional material.

Errata. If you find further errors during your reading, please tell me about them; experience shows that students are better at finding errors than I am. (Also, please tell me about errors or other problems in the handouts.) An Errata list file is at the web site: Errata file, Ouellette 2/e; I will update this as I learn of errata. [Errors in the Study Guide (especially answers to evens) are not in the handouts, but are in the Errata list file. Students who have the SG should get this file.]

Chapter handouts are posted.

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Homework

Ouellette's book includes extensive problems and questions. I strongly encourage all students to do the Problems that are within the chapters. Each Example is followed immediately by the worked-out solution. However, I suggest that you cover the solution, and try the Example yourself. The in-chapter Problems are usually quite basic; the answers are at the end of the book.

End-of-chapter exercises. Answers to odd-numbered questions are in the back of the book; evens are in the Study Guide. A set of answer sheets from the Study Guide is at the web site; see Updates page, special files. I will also have answer sheets with me in class. (If you don't agree with the book answer, or don't understand it, see me.)

Doing problems is important in learning chemistry. However, it is largely up to you how you do homework. You should do enough to meet your learning objectives. Be sure to do enough to become comfortable with the material, not just enough to get by; your retention to test time (and beyond) will be better. Try to choose some problems that challenge you, and force you to re-study key material in order to do them. Be sure to do a variety of problems, representative of the entire assignment, rather than just the first few for a chapter.

In general, you should prepare for class by doing the reading shown for the class period, and the problems within the chapter. You can then do the end-of-chapter problems for the following class.

For each chapter I will list some end-of-chapter exercises as "suggested homework." This is not intended as a complete assignment. Rather, it is a guide to the types of problems that I think are more important.

There will be occasional written assignments, but mainly I do not plan to formally mark homework. A good way to get personal attention on homework questions is to see me before or after class. Further, I am happy to look at any homework on which you would like some feedback; an IN envelope for turning in homework will be available each class. I'll return work the next class. (If you would like it back faster, provide a SASE, and I'll try to return it within a day or so. Also, feel free to send me homework, by e-mail or mail.)

Those who are using my web site materials for self-study... You are welcome -- and encouraged -- to ask me questions when difficulties arise. (My contact information is at the bottom of each of my web pages.) It always helps if you include how you would answer the question and why. That lets me respond to what you are thinking, lets me focus my reply on where you are having trouble. Sometimes questions can be interpreted in more than one way, and sometimes book answers are simply wrong. The level of discourse -- and your learning of chemistry -- is enhanced by trying to focus on reasons, not simply answers. If you are asking about a question from another book, be sure to include the question, and some context; some questions can be answered at more than one level, and I don't know what is expected of you unless you say something about the context.

Those who like to turn in regular written work might consider turning in, say, 2 pages of current problems each class period.

I encourage you to keep a homework log. Each day, record the date, chapter, problems done, and then add a comment about what you have accomplished and what needs to be done. Such a log can help you see how many things you conquered after an initial difficulty.

As a rule of thumb, since this is a college level class you should spend an average of ~6-8 hr/week on the course outside of class. A major portion of that should be spent working problems.

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Feedback and withdrawals

Formal course evaluation is done at the end. However, you are encouraged to offer comments and suggestions as the course proceeds. Anonymous comments in the IN envelope are fine. Comments from those who decide not to finish the course are particularly important. See the web page "Supplemental information" for some suggested areas to comment on.

I encourage you to make notes as the course proceeds about what you like and what you would like to see changed. That will allow a more detailed evaluation.

Supplemental information. A page of miscellaneous additional information about the course is posted at the web site: Supplemental information. It includes discussion that may help you decide whether this course is at the right level for you, as well as some comments about how the course works. It might be thought of as a supplement to the syllabus.

The last section of that page includes some comments about the course from previous classes.

Contributions and suggestions welcomed!


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Last update: March 10, 2017