Hot Links

• If you haven't chosen a paper and had it approved, you should e-mail Christiaan or Raphael with a link to the paper you indend to write about. Also note that we'll be happy to look at an outline or rough draft.
• November 26 Lecture Notes (big)
• More information about due dates for your project is on the project page.
• November 21 Lecture Notes (big)
• Homework 13 Problem Set
• November 19 Lecture Notes (big)

Course description and philosophy

The sequencing of the human genome, and the drive to understand its meaning, have created an overwhelming need for quantitatively trained scientists and engineers familiar with the details of molecular biology. The intense demand for trained bioinformaticians comes from industries as diverse as agribusiness and the pharmaceutical industry, and is driving the recruitment of faculty in university departments ranging from engineering to zoology. Unlike physics or chemistry, many quantitatively trained scientists and engineers have had little or no exposure to biology. The typical “introductory” molecular biology textbook weighs in at 1000+ pages, and assumes some background in biology generally. Quantitative scientists wishing to explore molecular biology encounter their first significant obstacle when they first visit the bookstore.

The purpose of this course is to provide a serious introduction to the core elements of molecular biology using a unique, engaging approach that assumes a quantitative background, not a biological one.

The motivating metaphor that we will use is Learning about biology is like learning a new language. An important aspect of learning a new language is vocabulary. Biological language is rich and complex because the phenomena being described are rich and complex. We will have vocabulary words to learn every week, and course work will include tests of students' ability to use those terms correctly. Students will also learn how to put these terms together to express (and understand) more complex biological ideas.

As when learning a new language, it is important that the students in this class come to appreciate the cultural differences that distinguish biology from other sciences. For example, physicists have often been heard to dismiss biology as mere “stamp collecting”. The emphasis of biology on developing detailed descriptions of living phenomena, and the deemphasis of grand, overarching theories is correct, but perhaps a better analogy would be to collecting biographies, rather than stamps. Yes, the similarities among living things (and among great peoples' lives) are remarkable; however, a detailed study of each individual case can be more illuminating than necessarily simplified universal theories. As you will see, despite the radical differences between biology and, say, physics, there is a great deal of scientific rigor and creativity in the history and practice of molecular biology.

Course Materials

There is no required textbook for this course. There are many excellent textbooks on molecular biology, but none that covers the breadth of topics we will attempt, nor one that is both rigorous and comprehensible to the non-specialist. For those of you who would like a more visual complement to my lectures and lecture notes, I highly recommend The Way Life Works, by Mahlon Hoagland and Bert Dodson, ISBN 0812928881. It's available at Amazon, and from many local bookstores. Another excellent book is Molecular Biology Made Simple and Fun by David Clark and Lonnie Russell, ISBN 0962742295 (order from Amazon). Both are on reserve at the library, and the Clark and Russell book is available in the CU Denver bookstore.

Everything you need for this course can be obtained in class and from the course web site http://compbio.ucdenver.edu/Hunter/bio5099/ . You should check the web site often. I will try to make my lecture notes available for each class before it meets, so you can take your own notes on them.

You can explore the syllabus. There is also a glossary of vocabulary terms, organized alphabetically or by the lecture where the terms were introduced. The complete set of lecture notes is also available, as are videotapes of past classes, as well as problem sets and solutions.

Grading

There will be short weekly problem sets which should take you about 90 minutes to complete. These problem sets will test your comprehension of the terms and concepts discussed in class that week. Problem sets will be handed out Thursdays in class and due at the beginning of class the following Tuesday. TA office hours are just before class on Tuesday if you have questions about the problem sets (or other issues). The course graders are Christiaan van Woudenberg and Raphael Bar-Or. Please contact them with questions about the problem sets or your grades.

No late assignments will be accepted. You can email problem sets to Christiaan van Woudenberg at christiaan@xiaan.com or fax them to 303-556-2889 (clearly marked as BIO 5099 problem sets) so long as they arrive by 4pm Tuesday. Problem set answers will be given at the beginning of class Tuesdays. The lowest scoring problem set will be dropped from your homework grade.

The Center for Computational Biology and its Certificate Program

I would encourage you to become a member of the Center for Computational Biology. The CCB puts on seminars, workshops and is a great place to get to know the computational biology community within CU and around Colorado. The CCB was instrumental in the creation of this course.

The course is one of the requirements for the CU Computational Biology Certificate. You can apply this course to the Certificate requirements, but only if you are enrolled in the program before November 1. Enrolling in the Certificate program does not conflict with any other degree program in which you may also be enrolled. If you want to enroll in the Certificate, please fill out and submit this form (Word format, PDF format).

Useful links

Here is a list of web sites that are useful to people learning about biology. This list will grow during the semester as we cover new topics. These sites should help you answer the research questions on the problem sets.

• Human Genome Project (DoE) education pages
• National Human Genome Research Institute (NIH) education pages
• The National Library of Medicine (NIH) provides excellent molecular biology textbooks free online, including Lodish, et al's Molecular Cell Biology 4th edition (1999).
• AcademicInfo.net biology pages, and their biology education pages.
• A followup on the Peppered Moth story
• The All Species Foundation is attempting to catalog all the species on earth.
• Information about dating and the age of the earth
• Mass extinction exhibit at the Hooper Virtual Paleontological Musuem
• An excellent web site collecting information about the possible anthropogenic mass extinction event.
• Taxonomy web site The Tree of Life Web Project
• Awesome images of Archea
• Online study guide to Brock's classic text, The Biology of Microorganims
• Essay by Ford Doolittle about lateral gene transfer in the evolution of Prokaryotes
• Pointers to online images of early life.
• Jere Lipps on the origin of multicellular organisms (great pictures, too).
• University of California Museum of Paleontology History of Life online exhibits
• The journal Palaeontologia Electronica
• 3D computer animations of Burgess Shale fossils
• Are birds really dinosaurs?
• Lambert & Ostrom's The Ultimate Dinosaur Book from Amazon.com, including the first chapter free online.
• You'll need a Periodic Table of the Elements.
• ChemTutor is a great place to start your research for homework 4. You might also visit A Tutorial for High School Chemistry.
• Homework 5 requires you use a codon table and have access to view amino acid structures.
• Homework 5 also discusses hemoglobin, a good introduction is located here.
• The Protein DataBank's molecule of the month entry on the ribosome
• RNAbase, a database of RNA structures, and their excellent primer on RNA structure
• The International Enzyme Commission nomenclature, with introductions to Oxidoreductases, Transferases , Hydrolases, Lyases, Isomerases, and Ligases.
• Some of you have asked to see articles that would "test" your understanding of concepts in the course. Your first article is about Alzheimer's from Science Magazine. Download it from sciencemag.org. You may need to be on a CU campus for the link to work.
• The KEGG metabolic pathway database. Also check out the BioCyc database of E. coli pathways
• Harold Morowitz's A Theory of Biochemical Organization, Metabolic Pathways, and Evolution Complexity 4(6):39-53, 1999. Also his computational experiment, The Origin of Intermediary Metabolism. Proceedings of the National Academy of Science U S A 2000 Jul 5;97(14):7704-8 with a supporting commentary and an opposing viewpoint.
• John Huberman's slides and notes on DNA damage and repair, covering both prokaryotic and eukaryotic systems.
• Michael Manson, et al, Bacterial locomotion and signal transduction, Journal of Bacteriology 1998 Mar;180(5):1009-22
• Protsville, a web site dedicated to protists.
• Human Genome Project Ethical, Legal and Social Implications (ELSI) materials: Societal Concerns Arising from the New Genetics, and NIH's ELSI Publications and Research Products
• Precautionary Principle information, including the European Commission's 2002 statement,, a New York Times story and a report from a Harvard conference in 2000,