BIOL 263 Molecular Biology and Genomics

Joan Slonczewski

Office: HIG 302

Fall 2007 MWF

10:10-11:00, TOM 101

BIOL 263 Molecular Biology and Genomics
Syllabus 2007
Note: Some resources can only be accessed on Kenyon campus.
Web resources
Biomolecules at Kenyon
Find Molecules: PDB and NIH
***The Jmol Index***
Stereo molecules

Date	#	Subject	Required Reading	Work Due
AUG	27 29 31	DNA intro; B-DNA; A-RNA; DNA & RNA Weak bonds. CAP; FAB Adv DNA; Z-DNA ; Triplex; Quad; Topo; Kos; RNA Z-B-DNA; B-DNA	Amino acids & bases Wat Ch 3; Ch 5 p 69-73 Wat Ch 6; Ha 05
SEP	3 5 7	Amino Acids; in proteins. Leptin. Ident; Practice Erythropoietin. FT; X-local; Bragg; Maps. Anomalous. DNA-protein binding; Human ADAR1. Retraction.	Ch 5 p 73-92; X-ray Advanced X-ray Schwartz 99; Vocab
SEP	10 12 14	Transcription initiation; UP Elongation; Complex; RnaPol-Bact; RnaPol-Euk Bacterial Gene Regulation. CAP-CTD; CAP;	Wat Ch 12 p 347-363 TBA Wat Ch 16
SEP	17 19 21	Transcription Factors. CopG; NikR; DNA; Riboswitch Euk. Gen. TFs. TBP; TAF Splicing; Lupus; Splicing2; Spliceosome; Test; Benoff	Schreiter 07 Wat Ch. 12 363-377 Wat Ch 13
SEP	24 26 28	TEST 1 Genome Maps. MGI; CMR Exercises Comparing Genes. Human genome.	--- Gibson Ch. 1 Dehal 01
OCT	1 3 5	Microarrays. Transcriptomics. Exercise. Dave Markwardt, Yeast Arrays 4:00 Thurs. Hig Aud Analysis. Maurer.**	Gibson Ch. 4 Mendell 04 Maurer 04
OCT	8 10 12	OCTOBER BREAK Nucleosomes. Figures; Histone-PDB; Bromo-PDB; Lan Regulation; Spec. TFs; Identify; Disease; PHD-PDB	-- Wat Ch 7 pp 151-180; Lan 07 Wat Ch 17
OCT	15 17 19	Transcription factors Translation initiation. Initiation. 30S-PDB; tRNA; Ser Ribosome 30S structure. Model. Periodic Table Jmol: Sunday 8:00PM	TBA Wat Ch 14 Wimberley 00	PDB Proposal
OCT	22 24 26	Ribosome function Translation 70S; Elongation; Ribosome "Protein Jive Sutra" Translation in the Nucleus? Notes; NMD Review	Carter 00 Iborra 01
OCT NOV	29 31 2	TEST 2 Key BIOL 114; Replication Helicase; Beta-clamp; Loader Telomeres: 12-mer; 22-mer	Test 2 Practice Wat Ch 8 --
NOV	5 7 8 9	Mutation and repair. MutS article; MutS; MutS-DNA Molecule Workshop 11:10-1:00 TOM 206 -- Pizza! Recombination; Experiments; RuvA; PNAS; Tn	Wat Ch 9 -- Wat Ch 10
NOV	12 14 16	Genome Sequencing and Annotation NCBI; Result Exaptation: Sant. 07; npe2; ENSEMBL; CORE-SINE Diencephalon; Alu1; Alu2 Exercises	Gibson Ch. 2 Santangelo 07 --	Individual Web project consultations
		NOVEMBER BREAK
NOV	26 28 30	RNAi Argonaute Transgenic mice: Tilghman video. Insulators. H19-Igf2 H19; Igf2; Beckwith-W. Transgenic primate. Sunday 3:00 Test Review, TOM 101	Hannon 2002 Liu 2007 ---
DEC	3 5 7	Human Cloning. "No primate clone." Stem cells without cloning Cloned animals Teratoma TEST 3 Test Sequence Student projects & course evaluation	Byrne 2007 Test 3 Practice ---
DEC	10 17	Student projects Web Tutorial Finished 4:30PM. No broken links.		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.

Required reading:
Watson et al, Molecular Biology of the Gene, 5E, 2004.
Greg Gibson and Spencer V. Muse, A Primer of Genome Science, 2E, 2005

Articles are linked to syllabus or provided in class.
Pokescope for stereo viewing is purchased through the Biology department

Tests. There are three tests in class. The Molecular Tutorial project substitutes for the final exam.

Final Projects. A Molecular Tutorial using Jmol is required. It is recommended that two partners share a project. Examples of past projects may be viewed at Biomolecules at Kenyon.

GRADES. Your grade is based on the following:

10% Attendance and Participation. All articles need to be read and annotated for discussion in class. E-mail discussion also receives credit.

100% attendance is expected, including the Oct. 4 Thursday seminar.
Three class absences may be excused without penalty for any reason, including illness and athletic events.
Nevertheless, you are responsible for the content of every class missed.

10% Quizzes. Quizzes will be unannounced. One quizz may be missed without penalty. No make-ups.
60% Three tests (each 20%).
20% Molecular Tutorial Project. A working model must be complete by Dec. 10. The final version, with zero broken links, is due December 17 at 4:30pm. Both partners share full responsibility for the completed project.

Laptop Computers. Each student receives a laptop PC to use in class, and at home throughout the semester. Rules for PC use:

Use in class to access material presented by the instructor.
No email or other messaging. Email during class will result in loss of PC.
Internet browsing on class topic is permitted, at your discretion. You are responsible for paying attention in class.
Outside class, take appropriate care of the PC. If a malfunction occurs despite proper care, replacement is available immediately from the professor.
Two brief surveys on your PC use will be requested during the term, for course assessment purposes.
At the end of the term, students may request to keep the PC for the spring term, based on need for other science courses. Requests will be granted depending on availability.

Standards for Projects and Exams. The standard College guidelines on individual authorship and plagiarism apply to all work, as stated in the Student Handbook 07-08. 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.