Mary Spratt - William Woods University

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William Woods University

Course Syllabus: Biology 405/406
Cell and Molecular Biology-Lecture/Discussion
Spring, 2008
S&L # 200, 201, 202


Mission

An independent voice in higher education, William Woods University distinguishes itself as a student-centered and professions- oriented university, committed to the values of ethics, self-liberation, and lifelong education of students in the world community.

Instructor: Mary L. Spratt, Ph.D. Phone: (573) 592-1143
Office: S&L # 205 email: mspratt@williamwoods.edu
Office Hours: Please check in the labs if you don't see me in my office.
Monday 4:00-5:45 PM
Tuesday 5:00-5:50 PM
Wednesday 10:00-11:50 AM
Thursday 2:00-2:50 PM
Friday 10:00- 11:50 AM --and by appointment


Textbook, etc

Cooper & Hausman, The Cell: A Molecular Approach, 4th ed. 2007: ASM Press and Sinauer Associates, Inc., with on-line access to animations, and other ancillary materials. A lecture notebook is packaged with the text. You will also find it useful to have access to your old Campbell & Reece Biology text, or access to that of a current student's. Laboratory directions will be provided as handouts, or students will access them on-line. A majority of class/lab time will be spent in accessing computer genomics programs and data banks used by molecular researchers, in order to do original research on genomics of Drosophila spp. Students are strongly advised to bring a Flash Drive to enable easy and repeated saving of genomics work.


Some Web Sites to be Used


Course Description

This course with its companion lab (Bio 406) expands molecular analysis to include cellular structure, organelles, genomes, bioenergetics, regulation, and proteomics. Current scientific literature will be read and analyzed, and model organisms studied. In addition to standard text topics, students will work on projects involving detailed analysis of portions of yet-unpublished genomes. This year the lecture and lab component will be integrated within two 3-hour time blocks with mini-lectures & discussions, "wet-lab" cell experiments, and an emphasis on computer-based genomics finishing and annotation.


Prerequisites to Learning

Satisfactory completion of Bio 114, 115, 124, 125, 301, 302, Chm 114, 115, 314, 315 and math through Calculus (Mat 124). It is presupposed that students are able to construct graphs by hand or with Excel, analyze data, access on-line data banks and manipulate these and other computer resources, follow scientific protocols, read scientific articles with basic comprehension, keep careful records, write accurate reports, and observe safety precautions in a working scientific laboratory.


Degree/Major Objectives

This course covers the following Biology Program objectives:

  1. Demonstrate knowledge of cell ultra structure and basic cellular processes and develop an understanding of the requisites of life. 1m
  2. Converse with basic tenets of transmission, molecular, developmental and population genetics. c
  3. Give an overview of the major organ systems of the human body and the normal and pathological functioning of those organ systems. c
  4. Demonstrate knowledge of the diversity and taxonomy of organisms, and the significance of variation in morphology, behavior, and life history. c
  5. Explain the role that natural selection, genetic drift, and other phenomena have had on the production of biological diversity and the role evolution has in integrating explanations of both the unity and diversity of life. m
  6. Demonstrate knowledge of scientific methodologies and usage of current scientific equipment and technologies. m

c = contributes to this objecive; m = major component of this course


Class Objectives

Students will be able to:

  1. Demonstrate knowledge of cell ultrastructure and the interrelationship of form and function in cell/molecular biology, particularly in regard to cellular structure, organization, and regulation. (Bio Obj #1)
  2. Discuss major human cellular and genetic diseases, mechanisms, pathways, and genes involved, and progress that has been made in redressing some of these problems (Bio Obj #3).
  3. Summarize the salient characteristics of and reasons for use of the particular model organisms used in cell and molecular research. (Bio Obj 4, 5)
  4. Demonstrate ability to read and interpret basic points in timely scientific journal articles dealing with current cell and molecular topics of interest. (Bio Obj 1, 2, 5, 6)
  5. Explain major ethical issues raised by advances in biotechnology, stem cell research, and cloning, giving cogent arguments on both sides of the issue and rationally defending one's position.(Bio Obj 6)
  6. Display knowledge of theory and practice in genomic and protein analysis, cell culture, hybridization, cloning, PCR, gel electrophoresis, DNA sequencing. (Bio Obj 6)
  7. Demonstrate through one's individual genomics project the purpose, methodology, and outcomes of genomic analysis.
  8. Exemplify the ability to work productively both independently and cooperatively as a member of study and lab teams.


Degree/Major Requirements

Cell & Molecular Biology is a required course for majors in Biology B.A. and B.S. degrees. It fulfills the 4-hour upper division elective for Biology Education majors.

Assessment Procedures:

  • Comprehensive final exam
  • Weekly quizzes on readings/discussion; unit tests
  • Classroom presentations of assigned topical reports using computer, lab, or other technologies
  • Oral/Poster presentation of genomics research results computer, lab, or other technologies
  • Completion and Submission on-line of final genomics research project
  • Use of both state-of-the art laboratory equipment, as well as such computer technology as sophisticated bioinformatics and GenBank programs
  • Keeping current with assignments, topics, internet resources, on-line discussions, etc. through Owlnet,
  • Timely and scholarly contributions to all assignments and discussions
  • Active and timely participation with benchmates in group assignments and study.
  • Analysis and rewriting of scholarly journal articles; other topical writings
    • All major writing assignments specified above for this class are expected to reflect college level communication skills and will be reviewed for clarity, grammar, spelling, and other formatting components. Any writing assignments requiring research or information from other sources should cite those sources using scientific style. Other research information can be found at http://www.williamwoods.edu/ULIS/tipsheeets/webvsdb.htm.
  • Late assignments will be assessed as following: -10% from earned grade any time the same day after papers are collected; -20% the second day; after the second day-work not accepted. If you intend to be absent, assigned work must be made up/turned in ahead of time unless the professor agrees to other arrangements; if you find you are sick, send papers with a classmate or e-mail it by class time.


Attendance Policy

It is expected that students will be in class/lab for every session, and will come on time. Missing class for any reason puts you at a disadvantage due to the sequential nature of the materials, and the full agenda. Students who miss class frequently are seldom able to achieve good grades in the sciences. Unexcused absence and/or tardiness will result in the dropping of one's grade by one or more letters. (guideline: >2 absences generally ) You will be held accountable for information missed and will not be allowed to make up quizzes or other work missed. Athletes and others on official school absences are to: 1) give me a schedule early in the term of expected absences, 2) remind me a few days before the particular absence, 3) make arrangements to take any scheduled exam before the absence.


Drop / Add Deadlines Holidays
Add: January 21, 2008
March 7, 2008-Midterm end February 15, 2008 Winter Holiday
Drop: March 26, 2008 March 17-21, 2008 Spring Break


ADA Guidelines

Students who choose to disclose a disability are responsible for notifying the University of their disability on a timely basis. Questions about disability services should be directed to Margie White, the University's coordinator for disability services. Her office is AB 99 and she may be reached at 592-1194 or margie.white@williamwoods.edu .

Integrity Policy and Community Codes

It is the expectation of the University that all of its members will uphold the Academic Integrity Policy and the Community Code in adherence to high ethical standards. Details of the Honor Code and the Community Code can be found at the following web address: http://www.wmwoods.edu/2007catalog/poldetail.asp?sectionid=273 Details of the Community Code can be found in the Student Life Handbook.


Academic Policy - Plagiarism

In all academic work, it is important that the ideas and contributions of others be appropriately acknowledged, and that work that is presented as original is, in fact, original. Insuring the honesty and fairness of the intellectual environment at William Woods University is a responsibility that is shared by the entire campus community. Cheating and plagiarism will not be tolerated. Major student writings will be submitted to Turnitin.com for verification of originality.


Computer technology

Dr. Spratt is responsible for the content of this course. She is not responsible for technical problems with OWLNet, Internet, e-mail, printers, computers or equipment in the electronic classroom or satellite biology (or other) computer labs. For these issues please contact call 592-4244 or write to helpdesk@williamwoods.edu . We will be heavily dependent upon our computer lab and technicians this semester; if you find problems with computers, please let them know immediately.

OWLNet can be accessed on-line: https://owlnet.williamwoods.edu. Students are responsible for referring frequently to Owlnet for assignments, schedule changes, etc.

  • For the schedule on the following page, the first chapter listed in the blocks is the designated quiz for that week; the 2nd ch. Listed in each block is the discussion topic.


Tentative Lecture / Discussion and Lab Schedule

9:25-12:25 T & R

WEEK DATES LECTURE COMPONENT WET LAB AND / OR COMPUTER
1 Jan 15, 17 Overview, Pretest, Cells & Cell Research, Model Organisms ; review of basic cell molecules, protein structure (ch. 1&2) Review basic organismal classification; Phase Contrast Microscopy & use of ocular & stage micrometers; View prokaryotic & protistan cells under light and phase contrast microscopy;

Counting cells with a hemocytometer

2 Jan 22, 24 Qz ch. 1, 2; Intro to Genomics, Proteomics, Bioinformatics; the Genomics Education Partnership; cell metabolism, generation of ATP; enzymatic function (ch. 3) Presentations by Dr. Spratt & Ashley Miller on the Genomics Education Project

On-line pre-genomics survey; introduction to various websites and data banks: NCBI scavenger hunt, & a Genomics Primer, BLAST, GenBank, Ensembl

3 Jan 29, 31 Qz ch. 3 (ch. 4)methods of detecting nucleic acids & proteins; review DNA RNA protein; HIV/AIDS Repeat Masker, Repetitious DNA; register for & try out Biology Workbench.;start Blast Ex. I: detecting & interpreting Genetic Homologies
4 Feb 5, 7 Qz ch. 4; Bioinformatics & Systems biology; DNA repair, rearrangements, molecular medicine (ch. 5), 6) Genes, pseudogenes & homologies; BLAST ex 2: Using mRNA & EST evidence in Annotation
5 Feb 12, 14 Qz ch(5), 6; transcription & translation in prokaryotes & eukaryotes (ch. 7) NCBI A Science Primer, ESTs, Finding repeats; Annotation exercise using mRNAs & ESTs; UCSC Genome Browser
6 Feb 19, 21 Qz: ch 7.; protein Synthesis, Processing & Regulation (ch. 8) Introduction to Finishing and the Consed program. Work thru a simple Drosophila fosmid for Finishing; consultation on claiming projects; Using Consed graphically
7 Feb 26, 28 Qz ch. 8: Bioenergetics & Metabolism; Mitochondria, chloroplasts & photosynthesis (ch 11) Claim Annotation & Finishing Projects (about 1/2 of class will work on each project; students may work in pairs.) Begin work on Annotation/Finishing
8 Mar 4, 6 Quiz ch. 11 Cytoskeleton & cell Movement:Types of filaments (ch.12) Work on Annnotation & Finishing: call for sequencing reads
9 Mar 11, 13 Qz ch. 12; Plasma Membrane: Types of Movement into/out of cell (ch. 13) Finishing: call for sequencing; continue projects; 1st journal on projects due
Mar 18, 20 Spring Break Holiday-Spring Break
10 Mar 25, 27 Qz: ch. 13; Cell Wall, ECM & cellular interactions (ch. 14) Extraction & preparation of fish muscle proteins for SDS-PAGE; analysis of product & discussion; work on genomics projects
11 Apr 1, 3 Qz ch. 14; Apoptosis, stem cell issues: processes, medical applications, the controversy (ch. 17) Discuss form of final presentations; oral-posters & written reports of project; [cycle sequencing in lab] , continue with projects; 2nd journal on projects due
12 Apr 8, 10 Qz; ch.17; Cancer: types, causes, relationship to viruses, oncogenes, etc. molecular tx (ch. 18) Annotation & Finishing

"Tree Thinking" Challenge: problem sets

13 Apr 15, 17 Qz ch. 18; Cell Signaling: cell receptors, signal transduction (ch. 15) Annotation & Finishing; assign articles from Nature reprint
14 Apr 22, 24 Qz ch. 15; Slighted topics--- Wrap up work on projects; put together reports
15 Apr 29-Ma 1 Loose ends; final presentations oral presentations, and discussions
Final Comprehensive Exam Project submission if not done previously


Comments on 1st year of including Genomics as part of a required upper-divison class for biology majors

  • Glad we did it!
  • The problems we encountered in modifying PC computers to accommodate Consed were more complex and took longer than we had anticipated. Although we started in early fall, the problems were not resolved until the last week in February. We did not claim projects on either Finishing or Annotation until these were resolved (most students wanted preferentially to work on Finishing) and I was unclear whether we could work on Finishing at all. The invaluable help of first Chris in conceptualizing what we were to do, and then Wilson's infinite patience in working with our mostly new computer staff & our class to resolve the problems that came up at each step of the process, were invaluable; we could not have done it without this great support! (Wilson has a huge folder of e-mails regarding these problems; I'm sorry we used so much of his time!) Hopefully, next time these obstacles will already have been overcome (although our computer staff still has not committed to supporting us another time).
  • Ideally, each student would participate for real in both annotation and finishing projects after practicing with exercises to each; we did not have time to do this, largely to the problems in getting the computer adaptations up and running.
  • Since Cell & Molecular Biology, a normal, required course for biology majors at or school, was the course into which the genomics material was presented, I believed that students still needed a minimally decent typical cell/molecular component. This was probably too much to do well, especially the first time through. "Lecture/discussion" time was primarily on more typical Cell material, while the "lab" component was devoted almost entirely to Genomics.
  • I am anxious to see more annotation curricular materials developed to fill the gap between the practice materials and actually beginning the Annotation research. Despite spending nearly 3 weeks on the "practice" materials, most students starting annotation felt lost, and I felt somewhat lost at how best to help them make the connection.
  • The articles from the reprint of Nature that Sally sent us were helpful in helping students see the broader aspects of the project. I wish I had used them earlier in the semester.
  • We used a few other curricular materials to supplement the provided genomics curricula:
    1. an overall broad introduction to the NCBI website by NCBI, in the form of a scavenger hunt is available at: http://www.angelfire.com/ga2/nestsite2/bioinform.html.. Some of the data pulled up here is somewhat out of date, as is everything on NCBI very quickly, but it gives a basic introduction to Pub-Med, Entrez, BLAST, OMIM, Taxonomy Browser, etc.
    2. a "wet lab" protein preparation, electrophoresis, and analysis using SDS-PAGE with a number of fish muscle samples, to heighten awareness of protein differences and predicting evolutionary relationships from protein visualization
    3. problem sets using Bioquest materials on the Tree Thinking Challenge by Baum, Smith, & Donovan: can be accessed at http://www.sciencemag.org/cgi/content/full/310/5750/979/DC1 & the supplement quizzes downloaded from this site, which is from Science Magazine, 11 Nov, 2005 Vol 310, #5750, pp 979-980.
    4. Biology Workbench: http://www.ngbw.org/ This integrated tool allows students to compare DNA, RNA, or protein data from different species, generate rooted and unrooted trees, model proteins, and keep various aspects of their project in a personal folder that can be saved from one session to another.
    5. My dilemma for next year is that I will not teach Cell/Molecular again until Spring, 2010; instead I will be teaching Microbiology, an elective course for Jrs/Srs (which most students do take). However, if I put genomics into this course, it should be focused on Prokaryotes rather than the current Eukaryotic projects. Will comparable projects be available with Prokaryotes thru the GEP? An alternative would be to offer an Independent Studies class in Genomics, which very few (if any) students would take, because it currently has not been placed in our catalogue as an approved alternate elective course for this coming year.

Some Teaching Websites

PowerPoint Presentation for August Alumni Workshop.