BIOL 263 Molecular Biology and Genomics

BIOL 263: Molecular Biology and Genomics

Fall Semester 2005
Last modified Nov. 30, 2005
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MWF 10:10 AM-11:00 AM (Period 3)
Tomsich Hall Room 101
(Owen York Lecture Hall)

Dr. Wade Powell
FSH 202, PBX 5396
powellw[a]kenyon.edu
Office hours: M 11 AM - noon and 3 - 4 PM; W, 11AM - 1 PM; F, 11AM - noon
(and by appointment)

Introduction:
The molecular and genomic basis of life is at the heart of modern biology. In BIOL 263, we will learn techniques and explore research questions at the forefront of molecular research, focusing on the mechanisms by which the information of the genome is expressed to form the functional molecules of living cells and organisms. The processes of DNA replication, recombination and repair, transcription of RNA from DNA templates, and translation of RNA into protein are discussed in the context of current research, frequently using primary literature. The function of genes and regulation and measurement of gene expression are treated in depth. Students analyze and publish interactive tutorials on the structure and function of key macromolecules. This intermediate-level course presumes a strong background in the basics of protein structure/function, central dogma processes, fundamental molecular techniques for manipulating nucleic acids and proteins, and general chemistry.
Required prerequisites: BIOL 113, 114; one year of chemistry; or permission of the instructor.
Recommended prerequisite or co-requisite: CHEM 231 and 232 (Organic Chemistry).

Reading Materials and Resources:

Required text: Watson et al., (2004) Molecular Biology of the Gene, 5th edition.
Optional text: Primrose and Twyman (2004) Genomics: Applications in Human Biology.
Journal Articles are linked to syllabus and/or provided in class. Journal articles are also available on e-res course reserves. Please see instructor for password.
Web resources will be used in class and for your assignments.
Pokescope for stereo viewing is purchased through the Biology department.

All reading assignments must be completed before class on the date indicated on syllabus.

Policies and Expectations:

Class attendance: 100% attendance is expected, and absences will detract from one's grade. Please see me immediately about conflicts due to sports events, performances, etc.
Class participation: To participate fully in class, you must thoughtfully read the assigned material before each meeting. Please feel free to ask questions, add insights, correct the instructor's innacuracies, etc . at any time during class.
Scheduling and Deadlines. Please plan carefully. Exam schedules and deadlines for submitting assigned work are firm, and extensions will not be granted for conflcits with the workload for other courses. Accomodations due to illness or other personal situation must be requested and negotiated through the Dean of Students or the Health and Counseling Center.
Academic Honesty. Do not lie, cheat, or plagiarize. Do your own work on exams. In writing projects, properly cite your sources of information, and acknowledge the help you receive from others. Kenyon's policy on academic honesty (pp. 26-29 of the Course of Study) will be strictly observed. Explicit guidelines relating to final projects or other collaborative assignments will be discussed in class.
Special Needs. For assistance related to a physical, psychological or learning disability that may impact your ability to participate fully in the course, please speak with me and with Erin Salva, Coordinator of Disability Services (PBX5453; salvae@kenyon.edu). All information and documentation of disability is confidential. Please see the Disability Services web site for more information.

Assignments and Grades: Your grade is based on performance in the following areas:

10% Attendance and Participation. 100% attendance is expected, including one Thursday seminar. To participate fully in class, you must thoughtfully read and annotate the assigned material before each meeting. Active, vocal participation is expected from all members of the class and will be the primary determinant of class participation grade.
10% Quizzes. Eight to ten quizzes over the semester. Quizzes will be unannounced. NOTE: Make-up quizzes will not be possible. Please don't ask. To compensate for conflicts due to athletics, performances, illnesses, busy schedules, etc., you may skip up to two quizzes without penalty or prior permission.
60% Three Exams (each 20%). There are three regular exams in class.
20% Molecular Tutorial Project. A Chime Molecular Tutorial Project substitutes for the final exam. It is recommended that two partners share a project. Examples of past projects may be viewed at Biomolecules at Kenyon. A working model must be ready for presentation to the class on Dec. 9. The final version, with zero broken links, is due December 17 at 8:30pm (time corresponds to the scheduled time for the final exam). Both partners share full responsibility for the completed project.

Important Links:
(Note: Some resources can only be accessed on Kenyon campus.)

Course Schedule

Day

Date

Topic

Reading

Notes

Work Due

Part I: Molecular Interactions

Aug 29

Course Introduction. DNA intro; 3D; B-DNA; A-RNA; DNA & RNA

Aug 31

Weak bonds. Amino Acids; CAP; FAB; Ident

Watson Ch 3; Ch 5, pp. 69-73

Sept 2

Adv DNA. FT; Z-DNA ; HIV; Triplex; Quad; base tautomers; supercoiling; Topo

Watson Ch 6