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Bob Bruner's

Chemistry and Molecular Biology Resources

This site was originally designed to provide supplemental materials for my classes. 
It also served as a preview and information source for prospective students. 
Many of these materials should be useful to others taking similar classes or just interested in the subject matter.

Welcome 
      to my new site


This page lists most of the site contents. It is organized largely by course. In the section below that, many pages of general resources are listed.

If you are referred here from the old site... This new site is set up the same way as the previous site. If you have a URL for the old site, the part past /b_bruner or /5118 there should work here; just put it past the bbruner.org. For example, if you have a link to my page 
"www.geocities.com/b_bruner/obc/arom.htm" 
or "www.geocities.com/Athens/Thebes/5118/obc/arom.htm", 
it is now "bbruner.org/obc/arom.htm".

Please let me know of any problems or questions. See the link below for contact information.

For more information... My email. A link to "contact" is at the top and bottom of almost every page.


Course listings. Much of the content at this site is organized by course. 
      Introductory Chemistry (X11) 
      Introduction to Organic and Biochemistry (X402) 
      Molecular Biology (X107) 
      Biotechnology in the News (BITN) 
         (More detail on all of these below.) 

General resources
Recent changes to the web site, most recent first.
Model of amino acid cysteine
 Bottom of page; contact information.
?FAQ - Frequently asked questions

Course listings

Introductory Chemistry (X11) (formerly called Refresher Chemistry). 
      Quick links to selected X11 materials...    Practice quizzes    Tests    Internet resources    Chemistry practice problems    Significant figures   Using your scientific calculator    Metric prefixes, from yotta to yocto    Handouts    Syllabus  (includes textbook information) 
     More information and more links are on the Intro Chem (X11) main page.

Introduction to Organic Chemistry and Biochemistry (X402)
     Quick links to selected X402 materials...    Practice quizzes    Tests    Metabolism    Internet resources    Aromaticity    E-Z system    Glossary    Phenyl group   Terms: Primary (etc.)    Rings: Showing cis/trans and axial/equatorial relationships    Balancing organic redox reactions New November 2008    Amides    E-Z system   Handouts    Syllabus  (includes textbook information)    
Writing, drawing and viewing chemical formulas (general) 
   Direct links to pages for:    ChemFormula    ChemSketch Updated for v 12, 5/18/09    Symyx Draw New, 4/16/09    ISIS/Draw    RasMol 
     More information and more links are on the Organic/Biochem (X402) main page.

Principles of Molecular Biology (X107)
      Quick links to selected Molecular Biology materials...    Syllabus    Chapter handouts    Tests    RasMol    Amides    Internet resources    Unusual microbes 
      More information and more links are on the Molecular Biology main page.

Biotechnology in the News (BITN). Topics focus on news stories relating to biotechnology. 
      Quick links to selected BITN materials...    DNA and the genome    Cloning and stem cells    Agricultural biotechnology (GM foods) and Gene therapy    Prions (BSE, CJD, etc)    Influenza (Bird flu)    Other topics    
     More information, including "General Resources", and more links are on the BITN main page.

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General resources

      Quick links to selected General resources...
FAQ - Frequently asked questionsUnusual microbes
Writing, drawing and viewing chemical formulas    (Includes:    ChemFormula    and introductory guides for    ChemSketch Updated for v 12, 5/18/09    Symyx Draw New, 4/16/09    ISIS/Draw    RasMol    and more.)
Chemistry practice problemsSignificant figures - a beginner's guide.
Files available for downloadGlossary
Books: Suggestions for general reading
Further reading    (Includes:    Medical topics    Old articles    Classic papers    and more.)
Library mattersInformation about buying books (including textbooks)
List of pages of Internet resources    (Includes:    Introductory Chemistry    Introduction to Organic and Biochemistry    Molecular Biology   Science on the Internet: an introduction    Biotechnology in the News (BITN)    Biology - Miscellaneous    Chemistry - Miscellaneous    Miscellaneous    and more.)
Using your scientific calculatorMetric prefixes, from yotta to yocto
Evening chem courses (San Francisco Bay area)Tips for success
JournalProject
     More information about these and other "general resources" is immediately below.
 
?FAQ - Frequently asked questions

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

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

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

The programs listed in this group 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 GuideUpdated for v 12, 5/18/09 
Symyx Draw - An Introductory Guide New, 4/16/09 
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.

Chemistry practice problems. This page links to a variety of problems at various places on the web site. They include "quizzes" and "tests". 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.

Significant figures - a beginner's guide. A major purpose of the page is to help the beginning student sort out the most important -- higher priority -- parts of the sig fig story.

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.

Glossary. This glossary was started for the Organic/Biochem course, to supplement the textbook. However, over time, it seems useful to add terms for other courses or other web site topics that come up. Suggested additions (and comments) encouraged.

Books: Suggestions for general reading. (science-related)

Further reading. 
* Chapter handouts for    Chemistry (Intro, General)    Chemistry (Organic, biochemistry)    Molecular biology 
* Materials posted under Biotechnology in the News. BITN 
* A page focusing on articles with a medical emphasis; this page relates most directly to the Lipids and Metabolism sections of the Organic/Biochem course, but is becoming more general. Medical topics 
* 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.

Information about buying books (including textbooks). Includes links to sites that search Internet bookstores for a specified book.

Library matters. Information on using the library system, including electronic resources, and information on searching for articles, using databases such as 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, Medline 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; Medline searches; citation searches.

List of pages of Internet resources. Many are listed by course, but many are general. 
     Quick links to selected pages of Internet Resources...    Introductory Chemistry    Introduction to Organic and Biochemistry    Molecular Biology    Library matters   Science on the Internet: an introduction    Biotechnology in the News (BITN)    Biology - Miscellaneous    Chemistry - Miscellaneous    Miscellaneous 
     More information and more links are on the List of pages of Internet resources.

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.

Metric prefixes, from yotta to yocto.

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

Some miscellaneous ideas for students... Each of these was written for a specific situation, and the details are dependent on context. Nevertheless, others may adapt them or get some ideas from them. 
Tips for success. Some general ideas to help students succeed in chemistry. 
Journal. Encourages a student to be aware of chemistry in the news. 
Project. Guides a student to study a particular chemical of interest in some detail.

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Recent changes    (most recent first)

May 18, 2009. My page ChemSketch - An Introductory Guide has been updated to reflect the new version, 12, which was made available in March.

April 16, 2009. There is a new page to help users with the new molecular drawing program Symyx Draw: Symyx Draw - An Introductory Guide. This guide is also listed on the page Writing, drawing and viewing chemical formulas.

April 15, 2009. There is now a navigation bar at the top of each page. It tries to show the current page in the context of the main topic-oriented hierarchy of the site; it also includes a contact link. The information that has been at the bottom of each page linking to other pages at the site will be maintained. The new navigation bar has been phased in over recent months.

November 10, 2008. New page: Balancing organic redox reactions. This page focuses on an approach to balancing redox equations that is especially suitable with organic chemicals: emphasizing H and O atoms. (Preliminary versions of this page have been here for a while. This is the "official" release of it.)

October 27, 2008. Another new section has been added to the page Biotechnology in the News (BITN): Cloning and stem cells. It is on Trans-differentiation. Further updating and revision of this page are in progress.

September 23, 2008. Two new sections have recently been added to the page Biotechnology in the News (BITN): Cloning and stem cells. They are on Terminology and Induced pluripotent stem cells (iPSC). Further updating and revision of this page are in progress.

September 7, 2008. New section on the page Library matters: UC Berkeley library; electronic journals; journal articles; Medline searches; citation searches. It introduces the use of DOI (digital object identifier) for finding articles.

August 16, 2008. New section on the page Library matters: UC Berkeley library; electronic journals; journal articles; Medline searches; citation searches. It introduces citation searching. It describes the purpose of citation searching, and gives some resources for doing it, including free ones.

May 8, 2008. New page: Significant figures - a beginner's guide. An overview of a topic that is important in beginning chemistry. (Actually, this page has been here for a while, almost but not quite finished. This is the "official" release of it.)

Mar 24, 2008. My page ChemSketch - An Introductory Guide has been updated to reflect the new version, 11, which was made available in February. One new feature that is now included in my page is antialiasing, for smoother appearance of lines on the screen.

February 3, 2008. Page on Library matters: UC Berkeley library; electronic journals; journal articles; Medline searches has been revised and updated. Among other things, the sections on using Medline have been substantially expanded.

December 3, 2007. New topic added for Biotechnology in the News (BITN), on Brain (autism, schizophrenia).

October 11, 2007. New page: Internet resources: Biology - Miscellaneous. At the start, this consists of sections split off from Internet resources: Miscellaneous. However, splitting these off to a fresh page will allow me to organize it better.

September 9, 2007. New topic added for Biotechnology in the News (BITN), on Bio-inspiration (biomimetics).

July 11, 2007. New topic added for Biotechnology in the News (BITN), on Synthetic biology. Other recent additions to this page include: HPV (Human papillomavirus) and Measles.

July 6, 2007 . New section on page Books: Suggestions for general reading. A boxed section near the top lists the most recent additions to the page.

June 10, 2007. New page: Unusual microbes. A brief discussion of some of the oddities of the microbial world, organisms that capture our imagination by being different. For "fun", for the general audience.

For an archive of selected older changes that may still be of interest, see the Old changes page.


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?FAQ - Frequently asked questions about this web site.

For more information... My email, or see the Contact page.

Site home pageThis page.

Last update: September 20, 2009

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