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Introduction to Organic Chemistry
and Biochemistry (X402)

Updates/Handouts

Introduction

Handout files. A few files are provided at this web site normally, as web pages or DOC/RTF files. These include the syllabus, first chapter handout, and some practice tests and quizzes. These are all available from the Organic/Biochem home page. In addition, I will try to make most handouts available here, but only as DOC files. That is, the handouts will not be displayed here, but you can download them and open them at home. In general, I will make the handouts available after the class period in which they are distributed; in some cases, they may actually be available here earlier. If a handout is listed with a link to the DOC file, it is the official version. Posted handouts will lack (occasional) paste-in attachments. If there are any problems with this arrangement, please let me know.

You can also access all of the handouts from the Organic/Biochem Handouts page. This is the page that "visitors" will probably find most useful.

Most files listed here are less than 70 kilobytes. One exception is noted.

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X402 Updates/Handouts

For information on how to download or read files, see page File problems. That page also discusses file formats.

Please let me know if you have trouble accessing any files; sometimes, your comment is the way I find out that there is a problem.

Spring 2006:

Entries in this section are in reverse chronological order (i.e., most recent first).

Last update in this section: May 30, 2006.

Fur fun... Link listed at end of answer key (final exam): http://archives.starbulletin.com/1996/09/17/features/story1.html.

Class 14. May 15. Plan: We can spend a little class time reviewing, tying up loose ends. No fundamentally new material. Bring questions! Final exam. (Sample tests) (Those who want to start the test early are welcome to do so. Those who know they take longer than average to do a test are encouraged to start early.)
Actual: We did it.
Handout: Final exam (not posted here).

Final exam will cover Ch 13-end. Now that we have finished, "end" = Metabolism Section I. I will not introduce major new material in the last class that you are responsible for; the discussion of metabolism the last night will be to help tie things together, perhaps some additional examples, but nothing fundamentally new.
(The exam will include copies of relevant Figures, such as a chart of the fatty acids, amino acids, citric acid cycle.)

Sample tests.

Please bring a SASE to the exam, for exam return (along with answer sheet and course grade).

See the "end-of-course notes" handout, class 10, for more about the final exam, including exam returns.

You must sign the grade option form and turn in course evaluations before getting a final exam. Last minute changes to the grade option form ok, if necessary. See the "End-of-course notes" handout, class 10, for information about course evaluations. Also see the Supplemental information page for more information about evaluations, including suggested questions that you might address.

How about keeping the class e-mail list active with questions and comments during this final period.

If you are not taking the final exam (i.e., you signed for "no credit")... bring a SASE to the last class you come to, and I will mail you the exam and answer key. Or you can get the exam and key from me by e-mail; send me an e-mail request. I will mail/email these about two weeks after the course is over. (And remember to sign the grade form, and choose NC.)

Link to my page on bird flu: Biotechnology in the News (BITN): Influenza. Mentioned in class. I encourage you to look around other parts of the BITN pages. Comments/questions welcomed. This link is also listed above, under Special files; you can always reach the BITN pages from my home page.

Class 13. May 8. Plan: Metabolism, "finish". We will briefly review and finish the Enzyme section, and then continue, as far as time permits. We will emphasize Section G, on the citric acid cycle.
Course evaluations. See the "End-of-course notes" handout, class 10, for information about course evaluations. Also see the Supplemental information page for more information about evaluations, including suggested questions that you might address.
Sign grade option form.
Actual: We discussed the Metabolism Ch through Section I. A simple view is that Sections C, E & G are the core material for this Chapter, and Sections F, H & I are more briefly noted to give perspective. This leads to test coverage: Ch 13-15 plus Metabolism, through Section I.
2 Handouts: Test 3 answer key (not posted here). Course evaluation form (not posted here).

Grade option forms, class 12 or 13. If for some reason you are unable to complete the course, I encourage you to sign for "No credit", rather than just disappear. Happy to discuss individual situations.

Class 12, May 1. Test 3 due.
Plan: Ch 14, finish. Ch 15, all. The big issue is discussing protein structure. Metabolism, start. It is likely that we will get through about Sect E. I suggest that you read at least that far in the handout, and read the assigned web site on enzymes.
Actual: We reviewed and finished Ch 14. We discussed why amides are not basic. For fun, we surveyed a range of amines -- natural and synthetic -- with pharmacological activities. We discussed all of Ch 15. We introduced the amino acids -- especially the set of 20 "standard" amino acids for proteins -- and showed how they are joined into protein polymers, which are polyamides. The main new issue is protein structure -- an important idea. Note that we are unable to predict protein structure, but we can see many factors that influence it. We started the Metabolism chapter. We discussed big picture vs detail, an important issue of perspective as you study biochem. We began to talk about enzymes, the biological catalysts which not only speed up reactions, but which -- perhaps more importantly -- by their specificity determine which reactions occur.
1 Handout: "Name these chemicals" worksheet. The worksheet is now available as a web page, at Name these chemicals. (This is "advanced", and is "for fun".)

If there are any problems with picking up or turning in the test, please contact me, by e-mail or phone. Please don't just wait for the next class.

Class 11, Apr 24. Test 3 handed out, due next time. Ch 10-12 (official coverage). Sample tests. I think you will benefit by working on the "Distinguishing isomers" quiz posted here. Practice quizzes.
Plan: Ch 13, finish. We will mainly discuss cell membranes, with both chemical and biological perspectives. Ch 14, all. Ch 15, might start. (Note that Ch 14-15 are related.)
Actual: We finished Ch 13. We looked at how lipids can spontaneously assemble into various structures, including the micelle and bilayer. The latter leads us to a "cell". That is, it is a useful idea that a biological membrane is built on the notion of a self-assembling lipid bilayer. This basic lipid structure is then enhanced, largely by the addition of proteins (Ch 15) that provide specific functions. We covered most of Ch 14. Most of Ch 14 relates to other material. Amines are based on ammonia; amides are analogous to esters; and a key reason for discussing these is that we need them to discuss proteins.
4 handouts: Test 3 (not posted here); ( Sample tests). Three Metabolism handouts: Metabolism chapter (Caution. Large file: ~180 kB); Glycolysis worksheet; Pathways Quiz.

For more about the Metabolism handouts, see the Metabolism page. That page will give you links to all the Metabolism files, including extra copies of the citric acid cycle figure. It will also offer guidance if you have trouble printing them out.

Apr 17. No class. Feel free to contact me over the break.

Class 10, Apr 10. Plan: Ch 12, finish. We will discuss acids and esters. We will then discuss the role of the high energy carboxyl derivatives. Ch 13, much of it.
Actual: We reviewed and finished Ch 12. We discussed the high BP of carboxylic acids, due to their greater H-bonding. We discussed polymers of esters, an example of condensation polymers. (The polysaccharides are polyacetals -- also condensation polymers.) Recall Ch 4 for an introduction to polymers, with the type discussed there being addition polymers. Am important idea is how the high-energy derivatives (acyl chloride, anhydride, thioester) allow us to drive reactions that would otherwise not be favorable. Fig 12.3 is important as a concept; note that the carboxylic acid and ester should be at about the same level there. We discussed much of Ch 13. We developed the general nature of lipids. We then looked at the triacylglycerides, which are typical of storage fat. An interesting issue here is the role of saturated vs unsaturated fatty acids.
2 handouts: Ch 15 -- the last Ouellette chapter handout. End-of-course notes, on course evaluations and final exam (not posted here).

Class 9, Apr 3. Plan: Ch 11, finish. Ch 12, start/most. Might start Ch 13.
Actual: We finished Ch 11, with miscellany about sugars, their polymers and derivatives. Note the role of acetal formation in connecting sugars. We started Ch 12. There are many functional groups in this Ch, but the acid and ester are the top priorities for now. Amides are also important, but we will leave substantive coverage of them until Ch 14. The acid anhydride, acid chloride, and thioester play a special role, of high energy intermediates.
3 handouts: Ch 14; Test 2 key (not posted here); Puzzles (for fun; not posted here).

Class 8, Mar 27. Test #2 due.
Plan: Ch 10, finish (brief). We will review the reactions for acetal formation, and then finish. Ch 11 all or most.
Actual: Finished Ch 10. We then made a good start on Ch 11. We focused on glucose, as a "typical" and also the "most common" sugar. We emphasized that simple sugars exist largely in the cyclic hemiacetal form, following on Ch 10. Note that you cannot predict which hemiacetal is most likely; some sugars form as many as four distinct hemiacetals. Typically, hemiacetal formation with sugars creates a new stereocenter, at the "anomeric" C. This leads to two hemiacetals, called α (alpha) and β (beta).
1 handout: Ch 13.

If there are any problems with picking up or turning in the test, please contact me, by e-mail or phone.

Class 7, Mar 20. Test #2 handed out, due next class. It will cover Ch 5-9. Coverage will be as noted in the handouts, except that it will not cover sulfur compounds (except possibly on the bonus part). Sample tests.
Plan: We will review and finish Ch 8-9. We will spend some more time on the reactions. The only really new material will be a brief note about the sulfur compounds, but they will not be on Test 2 (except possibly on the bonus part). Your questions on any test material. We should then cover all/most of Ch 10; Ch 10 is not on Test 2.
Actual: Finished Ch 8-9, with an elaboration on all the reactions. We briefly noted thiols and their redox reaction, which is quite different than for alcohols -- and is important in biology. We discussed most of Ch 10, which is not on this test. In doing this, we noted some issues that reinforce earlier Ch. For example, the redox reactions of Ch 10 are (mainly) the reverse of those from Ch 8. We spent considerable time on hemiacetal formation. In part, this is an ordinary reaction involving addition across a double bond, but there is a new major issue here: how the polarity of the chemicals determines the direction of addition.
2 handouts: Ch 12; Test #2 (not posted here) (Sample tests).

Class 6, Mar 13. Plan: Ch 6, finish. The main remaining topic is naming of chiral compounds. We will then start Ch 8-9, but probably won't finish. Note that we will cover these two chapters together, not one after the other. At the end of class, we will decide officially how far Test 2 will cover. I will post that information here, and it will also appear on the Test cover page. It is "likely" that Test 2 will cover Ch 5 through 9. Remember that Sample tests are posted.
Actual: We finished Ch 6, discussing the three ways of describing chiral compounds (+/-, D/L, R/S). Remember, these systems are independent of each other. The R/S system uses the same priority rules introduced earlier for E/Z naming of alkenes; you should know these priority rules. We discussed most of Ch 8-9. We introduced the major functional groups of these chapters, alcohols and ethers, plus the minor ones of phenols and sulfur compounds. We discussed the importance of the highly electronegative O for physical properties, and noted the special importance of the -OH group as an H-bond donor. This is also emphasized in the handout. We began to discuss the reactions of alcohols, in particular oxidation and elimination. We briefly noted the acidity of phenols (but the non-acidity of ordinary alcohols). We will spend some more time on these reactions next time. Note the three little handouts, attached to Ch 8 handout, which summarize some of this material. The only part of Ch 8-9 we really missed was sulfur compounds. Test 2 will cover Ch 5-9; no sulfur compounds (except possibly on the bonus part). Sample tests.
1 handout: Ch 11.

Class 5, Mar 7. Plan: Ch 5; 1 hr or so should be enough. Ch 6, good serious start.
Actual: As planned. For Ch 5, emphasize the key reaction type for aromatics, substitutions. For practice on the reactions, do the page of problems I attached to the handout, before doing the more advanced reaction questions in the book. For Ch 6, we talked about the nature of chirality and its implications. A key point is that you should be able to recognize stereocenters, using the rule of thumb... a C atom with four different groups attached. The main remaining topic for this chapter is how to name chiral compounds.
2 handouts: Ch 10; test answer key (not posted here).
Article related to test question about the plane crash: J Shepherd, Learning from a tragedy: Explosions and flight 800. Engineering & Science Vol 61 #2, p 19. 1998. A very readable article about the National Transportation Safety Board's investigation. Free online at: http://pr.caltech.edu/periodicals/EandS/archives/LXI_2.html. Scroll down to the article.

If you missed the test, please contact me as soon as practical, phone or e-mail. If possible, please do not wait until next class.

Class 4, Feb 27. Test #1, in class, 2nd hour. See test coverage info, below. See Sample Test handout, Class 2.
Plan: Before the test... your questions; finish Ch 4. Note that all new material from Ch 4 discussed in this class will not be on this test. Ch 5, which is fairly short; realistically, we won't finish it. Our final topic for Ch 4, orbital model for bonding, is a good transition from Ch 4 to Ch 5.
Actual: We finished Ch 4. We talked about the three remaining Ch 4 issues. First, we discussed the mechanism behind Markovnikov's rule, which depends on the greater stability of more highly substituted carbocations. Note that you can often use the M rule without this understanding, but if you are going on in organic, learning about mechanisms becomes more important. Second, we introduced the E,Z system for naming alkenes. The priority rules used here will be used again in Ch 6. The last part of our discussion was the generally advanced topic of orbitals, introducing π bonds. Most importantly, π bonds are due to sideways overlap of p orbitals. This leads us directly to Ch 5: The key issue in Ch 5 is the surprising non-reactivity of a type of highly unsaturated hydrocarbons; this can be explained in terms of an overlapping ring of p orbitals.
2 handouts: Ch 8-9; Test #1 (not posted here). Attached to the Ch 8-9 handout are three pages on oxygen functional groups, available here as separate files: Oxygen functional groups, Reactions, Comparison of physical properties, vs functional group. These pages summarize issues from Ch 8-12.

Test coverage (Test 1). Ch 3, and Ch 4 except...
* You are responsible for the addition reactions, and you are responsible for knowing how to use Markovnikov's rule empirically. You are not responsible for explaining the reaction mechanism, or why Markovnikov's rule works.
* No E,Z nomenclature on this test -- but note that it is important to learn it, and an important Ch 6 topic builds on it.
* We also did not discuss the orbital model for alkenes or π bonds; this is introduced in Sect 1.8, and is an "advanced" topic. No orbitals or π bonds on this test. We will discuss this next time, as a bridge from Ch 4 to Ch 5.
* See handouts for basic info on "skipped" and "advanced" sections.
* The spirit of these comments is that test coverage is intended to go as far as we got in class, class 3. Remember that advanced or skipped material may show up in the bonus section of the test, but that should never be a major concern for you in preparing for the test.

The test will be after the break. You can leave when done. We are flexible on time. Those who work slowly or otherwise need more time are welcome to work as needed (within reason).

More homework? Any homework I get in the mail, even on Saturday, I will mark and bring to class. With luck, even things you mail to me on Friday may get to me on Saturday, though that is stretching your luck. As an alternative, e-mail me key questions where you want some feedback.

Feb 20. No class. Feel free to mail me more homework during this break time, and to contact me via e-mail or phone.

Class 3, Feb 13.
Ch 3 homework due. (If you would like it back sooner than "next class" -- on test night -- include a SASE.)
Plan: Finish Ch 3; we are substantially done, but will spend a few minutes on some review. Also, your questions. Ch 4, more or less all of it, though it is possible we won't quite finish. At the end of class, we will officially decide what Test 1 covers, based on how far we get in class. I will post that information here.
Actual: We reviewed Ch 3. About the only new point raised was the role of shape in determining the extent of intermolecular interactions, hence BP. We covered most of the assigned parts of Ch 4, except for three specific topics: orbital model for alkenes, the E,Z system for naming geometric isomers, and the mechanistic explanation of Markovnikov's rule. We did discuss the empirical aspect of Markovnikov's rule, which itself is useful. See special note above re test coverage.
2 handouts. The Ch 5 handout consists of two files, Ch 5 and Ch 5 supplemental problems. Ch 6. (Why are the Ch handouts coming so fast? I would like to get ahead of you on them.)

Response to comment. A student asked about having the course in Berkeley. Current plan is to teach both of my chem classes in SF. The major reason is enrollment. Enrollment numbers for X402 have been consistently better in SF than in Berkeley. (Reasons presumably include the high population density in SF, especially in the daytime, plus the central location that is readily accessible by public transportation from areas such as East Bay and Peninsula.) One recent Berkeley section was canceled because it did not meet minimum enrollment. Berkeley is more convenient for me personally, and the classroom facilities are generally better on the UC campus, but enrollment is the major consideration. I pass on comments about such matters to the office, so they do hear your view. We re-examine this from time to time.

Class 2, Feb 6. Plan: Ch 3; we will discuss most of it in this class period. If possible, read over the chapter (and the chapter handout) in advance, and maybe begin to try some problems.
Actual: We substantially finished Ch 3. Ch 3 homework is due next time. We discussed the nature of alkanes, and their general physical and chemical properties. We made a useful start on naming them; you need to practice this, and then we can do more next time. We discussed rotation around single bonds, and conformations. For cycloalkanes, this rotation is restricted, thus leading to cis and trans isomers for di-substituted compounds. For cyclohexane, we discussed issues of the common chair conformation, and how large substituents are more stable in the (more spacious) equatorial positions. Be sure to keep the issue of cis-trans distinct from the issue of axial-equatorial.
3 handouts:
* Ch 4.
* Comment sheet (not posted here).
* Sample test + notes; this one handout consists of three files: Sample test info, General test notes, and the sample test itself. The test and its answer key, all other samples tests and keys, and other test-related information, are at Organic/Biochem (X402) Tests: Sample tests, with answer keys.

Class 1, Jan 30.
Plan: Introduction to the course. We will discuss some basic background chemistry, to set a perspective for our discussion of organic and biochemistry. We will start talking about alkanes, and will cover some basics from Ch 3.
Actual: We discussed the nature of organic chemistry. We focused on the special properties of C. We developed the idea that C compounds are thermodynamically unstable, but kinetically stable -- and that it is that combination of properties which makes them so useful. We introduced the organic chemistry periodic table, which is dominated by four elements: CHNO; you should know these.
4 Handouts (as DOC files): Ch 3, Class e-mail list information (not posted here), Syllabus (not posted here), sign-in form (not posted here). The Ch 3 handout also includes a page of supplemental questions, on combustion; that page is a separate doc file: Ch 3 supplementary questions.
The syllabus and Ch 3 handout are also available here as web pages.

Obviously, I will not assume that you have read anything for the first class. If you do get the book in advance, look over Ch 3. I also encourage you to look at my web page on X402 background for the class, which includes some suggestions for how to read Ch 1 and 2 of the textbook for review. Any time you spend on any of this, and studying background that helps you with it, is great.

Textbook. If possible, get a textbook before the first class. The textbook is listed in the Syllabus, with information on how to get it. (It will not be available at the class site.) Please note that only the main textbook is required. You should buy the Study Guide (mentioned in Syllabus) only if you think you will find it useful. I suggest that you look at it first before buying it; also see my Study Guide page.

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Last update: January 24, 2009