Christopher T. Cole
University of Minnesota - Morris

CONTENTS

Syllabus/Schedule
Outline
Topic Schedule
Text
Work Schedule
Grading
Term Paper
Workload Expectations
How Do You Succeed?

"One-Minute Essay" Questions and Answers: Archives from the Past

NEW (9 April 2003): Links for MicroArray analysis and Bio Chips:

eneral Background (from Science)
http://www.sciencemag.org/feature/e-market/benchtop/ddbd_0314.shl

Bio Chip microarrays and cancer:
http://www.future-drugs.com/admin/articlefile/erm030207.pdf

BioChipNet website (links):
http://www.biochipnet.de/scripts/BioChipNetServer.dll/EntranceFrameset

BIO 3121 MOLECULAR BIOLOGY SYLLABUS

Instructor: Christopher T. Cole
Office: 2080 Science Bldg. Lab: 2060 Science Bldg.
Phone: 589-6319 e-mail: colect@morris.umn.edu

Prerequisites for this course include Cell Biology and Genetics (though some students have taken Molecular Biology before Genetics and done well) and Organic Chemistry. Biochemistry is recommended but not required. Consequently I assume that you are familiar with some introductory-level material; if any of this is foggy, you should review your notes and text from the cell bio book, at least.

As indicated in the Table of Contents and in the Schedule of topics, the format of this course is to examine first the "central dogma" (DNA makes RNA makes protein) in some detail, then look at how that process is regulated in prokaryotes, and then look at how that process is modified in eukaryotes. In lecture and lab, this includes an introduction to the fundamental techniques for producing recombinant DNA, and how these techniques contribute to our understanding of molecular evolution and, by extension, to the analysis of other areas of biology as well.

Throughout the course I emphasize the empirical basis for our understanding of how things work. Consequently, the analysis (and design) of experiments is not limited to labs but forms a core of lectures, group activities, problem sets, and exams. For this reason also, we begin the course with a survey of many of the techniques that are now basic skills not only for molecular biologists but for biologists in general-- even those whose primary interests are in evolution, ecology and behavior!

Outline

The overall organization of the course is:

1. MATERIALS & METHODS
2. THE CENTRAL DOGMA
             Prokaryotic Replication & Repair, Transcription, and Translation
3. REGULATION OF GENE EXPRESSION
4. EUKARYOTES & "THE C-VALUE PARADOX"
             Regulation
             mRNA processing
             Duplication and "Hyperdrive": beyond the central dogma
             Immune system rearrangements
             Transposons, Viruses, and Cancer

Topic Schedule

The Schedule of Topics below is approximate. Weaver's text (2002, 2nd edition) is abbreviated as W2, followed by chapter, section, or page numbers.

Text

Weaver, R.F. 2002. Molecular Biology, 2nd ed.. WCB McGraw-Hill.

This up-to-date text emphasizes the empirical basis for our understanding of molecular biology, making it a good partner for our course. However, the sequence of topics is somewhat different than our course, so we will adjust the reading accordingly (see Topic Schedule). Some students are bothered by "jumping around" in the text while others are not. To help with this, I have provided detailed reading assignments. I hope that you find the strenghts of the text outweigh any drawbacks. You may also find chapters of a biochemistry text, such as those by Lehninger or Stryer, to have useful summaries of the main points, though they usually ignore the experimental evidence behind the stories.

For example, we begin our course with a survey of the Materials & Methods used in molecular biology, and Weaver's text presents a good summary of many of these, but that summary is split into chapters 2-5, so we will draw on the appropriate portions of those chapters, augmented by reading material on reserve in the library.

If you have the first edition of Weaver's text, that will work fine; see me for a list of reading assignments. You may also find chapters of a biochemistry text, such as those by Lehninger or Stryer, to have useful summaries of the main points, though they usually ignore th eexperimental evidence behind the stories.

Work Schedule

Tentative: One aim, incompletely accomplished, is to prevent piling up work at the end of the quarter. Another is to accomodate lectures I give in the Freshman Seminar in Biological Principles course, which meets at the same time, so any change in that course's schedule may affect this one.

Problem sets and exams will cover lecture, text and lab material.Ungraded problem sets get used as group problems in class, as well as for your own review. These will be distributed periodically, serving as preparation for exams. One problem set, due during week 3, will be graded.

Grading

                                      "Chance favors the prepared mind."
                                                                        - Louis Pasteur

Bio 3121 is a 5-credit course. In other words, the general expectation is that it will require roughly 25% more work than other biology lab courses!

The grading scheme comes from suggestions from students in the past, and I welcome your recommendations for changes (this year or in the future).

Spreadsheet of scores - click here

Term Paper

As noted on the Grading & Schedule portion of the syllabus (above), the term paper that you will write constitutes a major portion of your effort for this course, and of the grade you receive (20%). You will hand in the three components listed below. Those of you who have taken Bio 3701 (Biological Communications) have a general idea of the scope of work that is involved: the term paper will be roughly that amount of work. I cannot over-emphasize the importance of starting NOW!

One student's evaluation noted that I had never explained why a term paper is required for this course, so here are five related reasons for this assignment:
1) First, the assignment provides (requires) the opportunity to explore an area of molecular biology that is not covered in the lecture part of the course. Molecular biology is the fastest growing field of science, and we can only introduce a few fundamental topics during the semester.
2) Second, and similarly, we will only briefly explore the topics we take up in class, while the term paper will give you the chance to explore a single topic in much greater depth than we can cover in class.
3) Third: Although Weaver's textbook is exceptionally strong at both summarizing the highlights of molecular biology and at presenting the empirical bases for that knowledge, your own exploration of primary and secondary literature is an excellent way to exercise and develop your understanding of molecular biology.
4) Fourth: Writing well is a valuable skill that comes easily to few people; most of us need practice to develop these skills. Just as with physical exercise: "no pain, no gain".
5) Finally: Similarly, the ability to organize and complete a substantial task, while busy with the rest of your work, is important. "Plan the work, work the plan". Some people find this easier than others; what you learn for this project will apply to other tasks later.

You will develop this report in three stages:

Prospectus: Your prospectus will propose your topic. It should identify some of the main issues involved and a few of the principle resources you will use.

Outline & Resources: The more detailed, the better. This will be prepared after you have collected all or most of the resources that you will need. Attach your Prospectus when you hand this in.

Final Draft Must Include the Prospectus and Outline & Resources turned in earlier, and include the electronic copy.. Should be 12 pt. font, 1 inch margins. Also include the electronic copy.

As described below, you can earn Early Bird Award points for up to two of these assignments.

Topic

Your topic should fall within one of the broad areas, listed below.

1. Molecular Evolution: There are two general areas within this.
(a) How does evolution work at the molecular level? What kinds of changes occur? Why? Why are some kinds of changes more common than others? Why do some genes evolve in different ways than others?

(b) What does analysis of molecular information tell us about the evolutionary history of the organisms carrying those molecules? How is molecular information analyzed to draw these conclusions?

2. Molecular Ecology: Interactions among organisms
Relationships among individuals within a populaation, or from different species, can be revealed when molecular markers identify individuals.

2. Development: From molecules to meaning
Development of multicellular animals or plants entails differential gene expression. How is this regulated? What patterns occur, when we compare different genes in one species or in different species?

If you do not have a topic in mind, I recommend that you browse the library (in person and electronically). Some journals to scan include Evolution, Annual Review of Genetics, Annual Review of Ecology and Systematics, Trends in Genetics, Trends in Ecology and Evolution, Journal of Molecular Evolution, Molecular Evolution and Ecology, American Journal of Botany, Systematic Botany, Systematic Zoology, Conservation Biology, Development, Developmental Biology, Differentiation, EMBO Journal, Current Opinion in Genetics & Development, Current Biology, and Cell.

Term Paper Grading Criteria

The total for the project is 100 points, with the schedule and value of different components indicated in the table below. You should consult Pechenik's Short Guide to Writing in Biology. Here are the characteristics I am looking for in the term paper.

Basics:
- Organized
- Subject introduced clearly
- Mechanics correct (grammar, punctuation, citations: text, figures, tables)
- Draws on primary and secondary literature
- Discusses how results are obtained
- Prospectus & Outline are included (lose points if not)
- Topic is in one of the assigned areas (Development, Ecology, or Evolution) (should not be a problem, since this should have been clarified at the Prospectus or Outline stage)

Most Important:
- General statements supported by specific examples
- Includes comparison, contrast, and synthesis, rather than just a summary: not just summary but an analysis. A good summary gets a B. Adding good analysis necessary for A.
- Length: Very hard to do well in a half dozen text pages. I have not seen it done yet, though people have tried. People who turn in short reports are invariably disappointed with the grades they earn. I am too.
- Figures & tables used when appropriate to clarify information

Requirements

Deadlines: The deadlines listed in the Work Schedule for the three parts of the Term Paper assignment (Prospectus, Outline & Resources, Final Draft) are carved in stone. If the Prospectus or Outline & Resources are late, their grade will suffer a penalty of 10% per day. The Final Draft can only be handed in late if you have a Chancellor's excuse or have made prior arrangements to take an Incomplete in the course.

This has happened. Though rarely a problem in the past, students have been dismayed to find that this rule is real.

DO NOT scan images into your papers: the quality degrades so much that they are often illegible. Instead, photocopy any figures you want.

In addition to the printed paper copy, you MUST include an electronic version of your paper, submitted as a disk or as a text file sent to me by e-mail.

If you would like your paper returned to you, include a suitably sized self-addressed envelope when you hand it in.

Note that you can receive bonus points for turning in these assignments early, BUT you can receive at most TWO of the Early Bird awards. Also note that the point values listed in the tables are maximums (for instance, an outline that was early but very skimpy might note even earn a one point bonus).

Term Paper Components, Grading, & Due Dates

Due Dates: by 5p.m.

Note this includes the REVISED (postponed by 1 week) due dates for the Final Draft (& early bird)

Checklist for Term Paper

____ Topic clearly belongs to one of the approved categories

____ Original Prospectus and Outline and Resources attached

____ Stapled, no plastic cover

____ Double spaced, 1 inch margins, 12 point font

____ Electronic version included
____ PC-formatted disk
____ One file (not separate files for title page, text, resources, etc.)
____ Filename is your surname and initials (e.g. "smithtb"
____ Your name is on the disk (unless submitted electronically)

____Grammar (including punctuation) checked and corrected

____ Figures and tables have labels and their sources are indicated

____ Figures and tables NOT scanned

____ All information and opinions derived from others are clearly attributed to original sources

____ Pechenik's Short Guide to Writing in Biology checked for at least major flaws

Workload Expectations

Sometimes students take courses with the idea that they are interested in the big picture, the general principles, and are not going to bother with the details. If you have similar intentions you are welcome to audit the course but my intentions and expectations for enrolled students are different and you are likely to be frustrated.

I expect at least two hours of study for each hour of class. This is in accordance with university credit hour policy. Not all courses have this expectation, but this one does. Moreover it will be important that you do not fall behind. Over the years, the most important factor determining how well students do in this course is how well they keep up with the course-- work on a daily basis is best.

Integrity

Lab reports are team projects, and your score will be based on my evaluation of your report and the scores you receive from your teammates evaluating your contributions. Exams are designed to evaluate your knowledge and abilities as an individual; you may use (and I encourage) any collaboration with others in preparation for tests, but absolutely no assistance from others during the test. The UMM Biology program has a strong tradition of academic integrity (I have never had a problem with this in biology courses at UMM), and any infringement on this would be grounds for immediate dismissal from and failure in the course. Likewise, your Term Paper must be your own creation, though it must be informed by primary and secondary sources (properly cited, of course) and may be improved by discussing the information with others.

How do you succeed as a scientist?

"You've got to try and be with people who are brighter than yourself."

"You've got to be prepared sometimes to do some things that people say you're not qualified to do."

"Since you know you're going to get into trouble, you ought to have someone to save you after you're in deep shit. So you better always have someone who believes in you."

- James D. Watson March, 1993

How do you succeed as a student?

A question that came in on a "One Minute Essay" once was "How and why does all this happen? What is the easiest way to keep everything straight?". Here are my answers.

1. Organize. Review the structure of the course. Note the outline. This is the key to what the main points are at different times during the course.

2. Recall this strategy: material is presented as general principles and specific examples. Make sure you can summarize the general principles and provide a specific example for each. Conversely, know what principle is exemplified by each example. (Examples: What are the general patterns we see, or "strategy", of gene regulation in prokaryotes? What general features of replication and repair are illustrated in the "anomalous" results of Okazaki's experiments?)

3. Know the vocabulary. This is key to clear thinking, and hence to understanding the material-- as well as to being able to communicate that understanding.

4. Make your study active-- don't just read the material. Study should include drawing and writing. Especially, you should make up your own questions.

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