Principles of Molecular Biology

Materials here are from my course, Principles of Molecular Biology, Fall 2001. I have only slightly updated these materials since that semester; I have tried to keep Internet links and references to basic books in the field current. Much of the information on core molecular biology remains sound, and many of these materials should still be useful to students taking basic molecular biology courses. DNA

Quick links to selected Molecular Biology materials...    Syllabus    Chapter handouts    Tests    RasMol    Amides    Unusual microbes    Library matters    Internet resources    Downloads    Metric prefixes    Further reading: Old articles    Classic papers    Books: Suggestions for general science reading
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This is part of a larger site, with materials over a range of science. Home page. Among featured pages that may be of general interest...

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.

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

Books: Suggestions for general science reading is an annotated book list. Many are for the general audience. The list includes some books of historic interest.

Some pages of specific course-related content that may be of wider interest are:
* Metric prefixes, from yotta to yocto
* Significant figures - a beginner's guide
* ChemSketch - An Introductory Guide.
* Chemistry practice problems. Links to practice quizzes, self-help worksheets, and more -- for a range of topics in general and organic chemistry.

More about the molecular biology materials...

Syllabus (partial). Sections include:    Overview and prerequisites    Textbook    Supplementary books    Course outline (topics).

Chapter handouts. All chapter handouts, as Word DOCs. The first handout is also available as a web page -- a quick way to see what one handout is like. Ch 1 handout web page.

Sample tests (with answer keys). Information about using a note page on tests.

RasMol - An Introductory Guide. Help getting started with the RasMol computer program for viewing molecular structures on your computer. (Introduced in Weaver Ch 3 handout, in context of protein structures.)

For more about programs in this general area, see my page Writing, drawing and viewing chemical formulas.

Amides. A brief discussion of some properties of amides that you might not have expected. Peptide bonds are amide bonds, and this page is introduced in the Weaver Ch 3 handout, with proteins.

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

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.

Molecular Biology Internet resources. Includes all links mentioned in class handouts. Also includes sections of molecular biology links beyond those in handouts.

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; a kit for making your own buckyballs; and some supplemental self-help materials for introductory/general chemistry. (Files for Molecular Biology class handouts are not on this page; they are on the Handouts page.)

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

Further reading: Old articles. A list of some older articles that used to be referred to in various class handouts. Although these are no longer current, they may still be of interest.

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.

Books: Suggestions for general science reading. Includes molecular biology, but also a wide range of science. (Also see the list of supplementary books in the Syllabus - Supplementary books section.)

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Molecular Biology Tests
   Sample tests, with answer keys

The sample tests are actual tests from previous classes. A complete set is posted below, with answer keys. (For an actual class, I also hand out the sample for Test #1, to make sure everyone gets to see at least the first one before going into the test. The purpose of doing this is so you can see not only the contents of the test, but also what a real test looks like.)

Caution: Exactly what is covered, or even the order of topics, does not always agree from one semester to another. Therefore, you should not rely on sample tests as precise guides to test content. Approximate coverage of each test is shown below.

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. Further, it gives me a feel for the level at which you are addressing the question -- which may vary depending on your background and course level. The level of discourse -- and your learning of the subject matter -- is enhanced by trying to focus on reasons, not simply answers.

Information about the note page, which you may use on all tests.

Fall 2000

Test or answer key PDF File Test coverage (chapter titles, keyed to Weaver 2/e book); other notes.
Complete set Complete PDFs Zip archive; contains all the files listed below.
Test #1 Test #1, PDF file * Ch 1-3. (A brief history; Molecular nature of genes; Introduction to gene function.)
* Includes general review of cells and genetics.
Answer key for Test #1 Key 1, PDF file
Test #2 Test 2, PDF file * Ch 6-10. (Transcription apparatus of prokaryotes; Operons: Fine control of prokaryotic transcription; Major shifts in prokaryotic transcription; DNA-protein interactions in prokaryotes; Eukaryotic RNA polymerases and their promoters.)
* Test includes the "Cover sheet", which explains the procedure for a take home test.
Answer key for Test #2 Key 2, PDF file
Test #3 (final exam) Test 3, PDF file * Ch 11-13, 17-21. (General transcription factors in eukaryotes; Transcription activators in eukaryotes; Chromatin structure and its effects on transcription; The mechanism of translation I: Initiation and II: Elongation and termination; Ribosomes and transfer RNA; DNA replication I: Basic mechanism and enzymology and II: Detailed mechanism.)
* You need a copy of the standard genetic code. If you don't have one handy, here is one on the web: (From S M Carr, Memorial University of Newfoundland.)
Answer key for Test #3 Key 3, PDF file

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Last update: January 6, 2016