BIOL 363 Molecular Biology and Genomics

Joan Slonczewski

Office: Hig 302

Fall Semester 2001

MWF 10:10-11:00

HIG 009
(Basement PC Lab)

BIOL 363 Molecular Biology and Genomics
Syllabus 2002--Revised 12-02-02.
Note: Some articles can only be accessed on Kenyon campus.
Web resources
Biomolecules at Kenyon
Chime Manual
Class Chime Page

Date		Subject	Required Reading	Work Due
AUG	26 28 29 30	Nucleic acid structure. Molecules. DNA-1. Nucleic acids; OMIM DNA & RNA; Z-DNA ; HIV Triplex; Frataxin; Quadruplex; Quad model Web help Thursday 4:10 Amino Acids; AA2 in proteins. X-Ray; X-local; Estrogen Receptor; Schiff Base Riff	O'Brien; MB 21-32 Sinden 99 MB 39-44; 234-237	# Sequence DNA-1
SEP	2 4 5 6	Protein structure. Ras/G-protein; Memory Mouse DNA-protein binding. CAP; Human ADAR1; RNA editing 4:15 David Williams, Seminar; Rac DNA; Transcription initiation	Scheffzek 97 MB 232; 236-249; Schwartz 99 MB 133-143	Amino Acid web page
SEP	9 11 13	Elongation; RnaPol-Bact; RnaPol-Euk Eukaryotic RNA Polymerase Bacterial Attenuation. TRAP-RNA Euk. General TFs. DAB PolII; Zn-finger	MB 154-171; 266-269 Gnatt 01 MB 197-202; MB 297-301
SEP	16 18 20	Eukaryotic TFs; TBP Histone acetylation. TAF TEST 1	MB 301-321; Kim 00 Jacobson Antson 99 (Test 1) TRAP-RNA	TEST 1 (class)
SEP	23 25 27	Activators. Identify TFs Transcription factor; Tubby; Mice Hydra. Wnt; 2-snake; twins	MB 342-369 Boggon 99 Hobmayer 00
SEP OCT	30 2 4	Genomics: An Overview. Genomics; Microarray Expression profiling. cDNA_Micro; Proteome; Chime The Human Genome: Nature Guide	Brent Schenck; White HGP Intro
OCT	8 10 11 12	OCTOBER BREAK Human Genome; Proteomics 11:10 or 4:10 (HIG 009) Chime Microarray analysis of breast tumors: M. Radmacher, guest	-- Simon	DUE: Molecule proposal--PDB
OCT	14 16 17 18	Retransposon fossils. Transposase Histone code. Figures. 4:15 Seminar--David Schultz Translation initiation. Initiation. PDB	Smit 96 Schultz MB 534-545	TEST 2 handout FOXO
OCT	21 23 25	Ribosome 30S structure. Model. Periodic Table Ribosome function 70S; Elongation; Ribosome "Protein Jive Sutra:" Translation Dance	MB 607-612; Wimb 00 MB 617-621; Carter MB 576-590	# TEST 2 DUE 4:00 10/24
OCT NOV	28 30 1	No class [replaced by seminars] No class [replaced by seminars] Translation in the Nucleus? Notes	--- --- Iborra 01
NOV	4 6 7 8	DNA Replication Conferences (cont.) Replisome 4:15 Seminar--Danielle Hamill Repair enzyme. MutS; MutS-DNA; Figs.	DNA; MB 665-692 MB 694-700 Obmolova 00	Individual Web project consultations
NOV	11 13 15	RNA Splicing; Lupus; Pre-fab Spliceosome Ubiquitin: regulation by protease Di-Ubi; Tetra-Ubi; Research Parkinson's disease	MB 418-439 Proteasome; Ubiquitin Shimura 01
NOV	18 20 22	Dopamine and Parkinson's. Biochemistry; Cocaine; Medical Dict. Programmed Cell Death. C. elegans. Ced genes. Movies: Cell div, Cell death Human Cloning--Epigenetics. Nuclear pores	Conway 01; Supp. Hersh 01 Rideout 01
#	#	NOVEMBER BREAK	#	#
Dec.	2 4 6	Human Cloning--ES Cell Library. Male preg; Mouse/Human Parkinson's; Amniotic TEST 3 In Class Student projects	Adjaye Yang 00	TEST 3 Yang 00 Web tutorial, working draft
Dec. Dec.	9 16	Student projects & course evaluation Web Tutorial Finished 4:30PM No broken links--on web server		Web Due

INTRODUCTION. The molecular and genomic basis of life is at the heart of biology today. How do molecular machines build organisms, based on the blueprint of the genome? How are genomes shaped by the function of genomes? We will learn the techniques and explore research questions at the forefront of molecular research.

A basic understanding of chemistry and molecular genetics is assumed. You are advised to review on your own the BIOL 114 web site, particularly Weeks 1-9.

Web resources will be used in class, and for your assignments.

COMPUTER ETIQUETTE. This class is held in HIG 009, where we make extensive use of the computers. When you arrive, please open a computer to this page. All e-mail must close by 10:10, and do not open e-mail during class. Be sure to close your account before you leave. Neglect of computer etiquette will detract from your grade.

Required reading.
MB Robert F. Weaver, Molecular Biology, 2e, McGraw-Hill, 1999.
Articles linked to syllabus, or provided in class.

Tests. There are three tests, one of them take-home.
The Molecular Tutorial Project substitutes for the final exam.

Final Projects. A Molecular Tutorial is required. It is recommended that two partners share a project, especially if you have not previously used Chime. Examples of past projects may be viewed on the Molecular Tutorials page.

GRADES. Your grade is based on the following:

10% Attendance and Participation. 100% attendance is expected, including the listed Thursday seminars. All articles need to be read and annotated for discussion in class. Article copies will be collected after each class.
10% Quizzes and amino acid web. Quizzes will be unannounced.
60% Three tests (each 20%).
20% Molecular Tutorial Project. A working model must be complete by Dec. 6. The final version, with zero broken links, is due December 16 at 4:30pm. Both partners share full responsibility for the completed project.

Standards for Projects and Exams. The standard College guidelines on individual authorship and plagiarism apply to all work, as stated in the Student Handbook 01-02. All projects, including html, must include footnotes and references cited in detail comparable to that of a term paper. Each exam must represent the work of one individual student.

Disabilities. If you have a physical, psychological, medical or learning disability that may affect your ability to carry out assigned course work, please contact the Office of Disability Services at 5453. The Coordinator of Disability Services, Erin Salva, will review your concerns and determine, with you, what accommodations are appropriate. All information and documentation of disability is confidential.

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