Introduction to Organic Chemistry
and Biochemistry (X402)


Instructor: Bob Bruner
Model of ATP
Quick links to selected Organic/Biochem (X402) materials...    (More information about all these items and more links are below.)
Visitors (students from other courses, those studying on their own, and those who are just curious): The items most likely to be of interest are those in the section of this same color, just below. But then, look around. Questions and comments/suggestions (about the web materials or about course content) welcome. It is fine to ask about questions that have come up in the course you are taking. Contact information
 
Pages likely to be of particular interest to prospective students (and to those just getting started)...
Syllabus  (includes textbook information) Supplemental information Background information
Study Guide Molecular models High school students? Tips for success
            For more information about items in this section, see below.
Pages most likely to be of interest to students during the course, and to students of similar courses looking for ideas or help -- in addition to those shown above for prospective students...
Handouts Practice quizzes Tests Internet resources
Glossary Metabolism Name these chemicals
Omitting numbers Terms: Primary (etc.) Aromaticity Phenyl group
Amides E-Z system Rings: Showing cis/trans and axial/equatorial relationships
Balancing organic redox reactions
Writing, drawing and viewing chemical formulas (general)
   Direct links to pages for:    ChemFormula    ChemSketch    ISIS/Draw    RasMol
            For more information about items in this section, and more, see below.
General information about this site and general resources...
Contact information FAQ - Frequently asked questions
about this web site
Metric prefixes
Chemistry practice problems Using your scientific calculator Downloads
Library matters Evening chem courses (San Francisco Bay area) Unusual microbes
Further reading (FR):    Medical topics    Old articles    Classic papers.
      FR in Chapter handouts for    Chemistry (Intro, General)    Chemistry (Organic, biochemistry) (this course)    Molecular biology.
      Materials posted under Biotechnology in the News. BITN.
Musings (newsletter) Books: Suggestions for general science reading
            For more information about items in this section, see below.

To contact the instructor, see contact information at bottom of this page.

? FAQ - Frequently asked questions about this web site.


The following part of this page lists the same links as in the colored section above, but gives more information.


Pages likely to be of particular interest to prospective students (and to those just getting started)...

Syllabus (partial), showing    overview and prerequisites,    textbook information,    list of topics.

Supplemental information. Miscellaneous additional information about the course, especially for prospective students with questions. This might be thought of an a supplement to the syllabus.

Background information. Information about the introductory chapters of the textbook, and how they may help you with the background material we would like for you to know when you start Organic/Biochem (X402). This may be useful for prospective students, in judging whether they have the expected background. Students taking the course may use this either for preparing some in advance, or for reviewing during the course.

Study Guide. Information about the optional Study Guide for the Ouellette textbook.

Molecular models. Information about obtaining or improvising molecular models. Although we do not require that students have models for this level of course, most students would benefit from using them at least some. The Ouellette textbook has a section of exercises using models for each chapter.

High school students? X402 may be suitable for high school students. See this section for more information.

Tips for success. This was written in a different context, but the idea is the same. Those who are new to college-level classes, or who have not taken one in a long time, might find this page useful. Read it for the general tone.


Pages most likely to be of interest to students during the course, and to students of similar courses looking for ideas or help -- in addition to those shown above for prospective students...

Handouts. Most class handouts (as PDFs).

Practice quizzes (some with answer keys).

Tests. Sample tests, with answer keys, and other test-related information, including use of a note page on tests.

Internet resources. Includes all links mentioned in class handouts, plus others that may be of interest.

Glossary. This is intended to highlight terms that come up, allowing us to build our own supplemental glossary. It is not intended to be complete. Suggested additions (and comments) encouraged. (This glossary was started for the Organic/Biochem course, but terms from other fields are being added, too.)

Metabolism. My own chapter on metabolism. This is now a core chapter for my Organic/Biochem (X402) course.

Name these chemicals. A worksheet, showing some fairly complex chemical structures. Your goal is to try to name them -- or at least to match names and structures. Challenging.

Omitting numbers. A discussion of when you can -- and cannot -- omit the usual numbers in the name of an organic chemical.

Terms: Primary, Secondary, Tertiary, Quaternary -- as used in various contexts in organic and biochemistry. (Ouellette 2/e Ch 3, 4, 8, 14, 15. Bettelheim 6/e Ch 10, 11, 12, 13, 16, 21. The main purpose is comparison of the various usages encountered in these chapters. With the Bettelheim book, not all were clearly presented; in any case, a page having all the meanings together may be helpful.)

What does "aromatic" really mean? A discussion of the nature of aromaticity, beyond the simple example, benzene, that is presented in Bettelheim 6/e Ch 14. The Ouellette book presents this reasonably well (Sect 5.2), but my page does show more examples.

The phenyl group and related terms. A brief comparison, with structures, to show what the terms benzene, phenol, phenyl, and benzyl mean. Ouellette 2/e Ch 5 or Bettelheim 6/e Ch 14. The coverage in Ouellette is fine for our purposes, though you may find this page a useful supplement.

Amides. A brief discussion of some properties of amides that you might not have expected. Ouellette 2/e Ch 14, 15 or Bettelheim 6/e Ch 18 & 21. The coverage in Ouellette is fine for our purposes, though you may find this page a useful supplement.

The E-Z system for naming alkenes; examples of using the CIP rules. An introduction to an "absolute" system for naming alkene isomers based on the structure. The Ouellette book presents this fine, in Sect 4.3. The page now includes more examples, including how to apply the CIP priority rules. (This was originally written as a supplement for use with the Bettelheim book, Ch 12, 15. Alkenes are in Ch 12, but the E-Z system builds on the R-S system that is introduced in Ch 15.)

Rings: Showing cis/trans and axial/equatorial relationships. Beginning students quickly encounter problems of drawing substituted cyclohexane rings, and showing cis/trans and axial/equatorial relationships. A particular problem often is distinguishing these two quite distinct designations. This page leads you through some of the issues of drawing rings and their conformations.

Balancing organic redox reactions. There are various ways to balance redox equations, and the ones you learn in general chem are sometimes not convenient with redox equations involving organic chemicals, or other complex chemicals. This page focuses on an approach that is especially suitable with organic chemicals: emphasizing H and O atoms. Also see my practice quiz on "Oxidation and reduction".

Writing, drawing and viewing chemical formulas. An overview of programs that help you write, draw or view chemicals. It refers to the following:

ChemFormula. ChemFormula is a Word macro to assist you in formatting chemical expressions.

The programs listed below are for drawing molecular structures. The drawings can be converted to 3D, and viewed either within a module of this program or within RasMol (below). The drawings are also easily imported into Word. The links are to guides that I have written.
* ChemSketch - An Introductory Guide.
* ISIS/Draw - An Introductory Guide.

RasMol - An Introductory Guide. Help getting started with the RasMol computer program for viewing molecular structures on your computer. Especially useful with Ch 3-4 (basic organic structures), 6 (chirality) and 15 (proteins), but also generally useful. Also see items above, for drawing structures that can be viewed with RasMol.

Updates. This page is maintained during the semester, to announce what was covered in recent classes, what is likely to be covered soon, and other announcements. The page will give you an idea of how the course flows.


General information about this site and general resources...

Metric prefixes, from yotta to yocto. Examples are shown, to help you relate to the size of the units that include these prefixes.

Chemistry practice problems. This page links to a variety of problems at various places on the web site. They include the "quizzes" and "tests", shown above. They also include a range of self-help worksheets for selected introductory chemistry topics. For many, the general approach is that basic knowledge of the topic is assumed (that is, these are intended for review and practice), the main issues are presented briefly, and there are lots of practice problems.

Using your scientific calculator. A form to help you discover key features of your calculator, and to submit that information for inclusion here. Information for a small sampling of calculators is now available.

Files available for download. Current files include a periodic table handout; ChemFormula, a macro that helps you when using Microsoft Word for writing chemical expressions; and a kit for making your own buckyballs. It also links to the page of Chemistry practice problems. (Files for current handouts are not on this page; they are on the Handouts page.)

Library matters. Information on using the library system, including electronic resources, and information on searching for articles, using databases such as PubMed (Medline). Includes sources of online journals, some of which are free. Parts of the page focus on UC Berkeley, but much of the information here will be generally useful to people not at UC. For example, PubMed is freely available to the public. Further, some may adapt the given information to their library system, and to other databases. Major topic areas here include: UC Berkeley library; electronic journals; journal articles; PubMed searches; citation searches. This page is also listed on the Site Home Page (under General resources), on course pages, and on the list of pages of Internet resources.

Evening chem courses. Information about chemistry courses, especially Organic Chemistry, available in the evening in the San Francisco Bay area.

Unusual microbes. A brief discussion of some of the oddities of the microbial world, organisms that capture our imagination by being different.

Further reading:

Chapter handouts for    Chemistry (Intro, General)    Chemistry (Organic, biochemistry) (this course)    Molecular biology

Materials posted under Biotechnology in the News. BITN

Further reading: medical topics. Chapter handouts contain a section of "Further reading", for those who want to explore more. For some chapters (especially Lipids & Metabolism), there is quite a range of related medical topics, many dealing with nutrition. Because those reference lists have become rather long, I have decided to split off this page, focusing on medical topics here. The distinction is not clear-cut; some medical articles will continue to be in Chapter handouts, when they are very closely related to class material. However, this page will be for a range of general medical (nutritional) topics, loosely related to class material.

A page of older articles, which used to be in chapter handouts -- still of some interest, but older than I prefer for current handouts. Old articles

A page describing how to find classic papers. Classic papers. This page lists sources of "classic papers", in both chemistry and molecular biology. Some are sources on the Internet, some are notes about printed collections. Reading some of the classic papers in a field can be a fun way to explore history -- and to discover the different style of scientific papers long ago.

Musings is an informal newsletter mainly highlighting recent science. It is intended as both fun and instructive. Items are posted a few times each week. See the Introduction on the Musings page for more information.

Books: Suggestions for general science reading. Includes chemistry, but also a wide range of science.


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Last update: June 29, 2016