BIOL 263 Molecular Biology and Genomics

Joan Slonczewski Office: HIG 302		Fall 2008 MWF 10:10-11:00, TOM 101
BIOL 263 Molecular Biology and Genomics Syllabus 2008 Note: Some resources can only be accessed on Kenyon campus. Biomolecules at Kenyon Find Molecules: PDB and NIH *Jmol Script Index (to make your own)* Stereo molecules

Date	#	Subject	Required Reading	Work Due
AUG	29	DNA intro. B-DNA. A-RNA	Amino Acids & bases	Review
SEP	1 3 5	Weak bonds. CAP. FAB.; B-DNA. Adv DNA; Z-DNA ; Triplex; Quad. RNA. Ha 05; Au. Amino Acids (Jmol) in proteins. Leptin; Identify; Practice	Ch 3; Ch 5 p 71-73 Ch 6; Gillen p 1-15 Ch 5 p 73-93	-
SEP	8 10 12	X-ray diffraction ;FT; Applet; Bragg; MAD maps. MIR. Erythropoietin. Space groups. DNA-protein binding; Human ADAR1; Retraction. Transcription initiation	X-ray; Advanced Schwartz 99; Au; Vocab Ch 12, p 377-390	-
SEP	15 17 19	Elongation; Complex; RnaPol-Bact; RnaPol-Euk Bacterial Gene Regulation. CAP-CTD; CAP Transcription Factors. UP; NikR; DNA; Ribbon-H-H; Schreiter paper	Ch 12 p 390-396 Ch 16 --	-
SEP	22 24 26	Eukaryotic General TFs. TBP; TAF Splicing; Lupus; Test review Thursday: 11:10 and 4:10 Review for Test (optional) TEST 1	Ch 12, p 396-413 Ch 13 Test 1 Practice
SEP OCT	29 1 3	Splicing, continued: Splicing2; Spliceosome; Lupus; Spliceosome--Practice Experiments Herpesviruses. Viral mol bio: Baltimore. Animation. Joanne Trgovcich, Herpes 4:00 Thurs. Hig Aud Genome structure: Human genome.**	[Ch 13] Herpes Ch. 7, p 135-144
OCT	6 8 10	Microarrays. Expression ratios. Exercise. Bacterial transcriptomic analysis. Nobel. Virochip. OCTOBER BREAK	Stekel; Gillen p 16-42 Maurer 04; Au --
OCT	13 15 17	Nucleosomes. Histone code; Hist-PDB; Bromo-PDB; Regulation; Spec. TFs; Identify; Disease; PHD-PDB A histone demethylase regulates gene function	Histone Code; Ch 7, p 156-191 Ch 17 Lan 07; Au PRACTICE (Test 2)
OCT	20 22 24	Translation initiation. Initiation. 30S-PDB; tRNA; Ser Eukaryotic Initiation. Ribosome 30S structure. Model. Periodic Table 70S; Elongation; Ribosome	Ch 14, p 457-479 Wimberley 00; Au Ch 14, p 479-518	PDB Proposal
OCT	27 29 30 31	Ribosome function Translation; DMD cure Translation in the Nucleus? Notes; NMD Review; Code Review 3:00-5:00 RBH 215 TEST 2	Carter 00 Iborra 01; Au Test TF	-
NOV	3 5 7	BIOL 114; DNA Replication. Walk-through. Helicase; Beta-clamp; Loader; Telomeres: 12-mer; 22-mer Mutation. Diseases. OxoG.	Ch 8 -- Ch 9, 257-268	-
NOV	10 11 12 14	Repair. MutS article; MutS; MutS-DNA Molecule Workshop 11:10-1:00 RBH 215 -- Pizza! Recombination; Experiments; RuvA; PNAS; Tn Genome Maps. MGI; CMR NCBI; Result. Exercises	Ch 9, 269-282 Ch 10 Ch. 20, 703-715
NOV	17 19 21	Exaptation. npe2; ENSEMBL; CORE-SINE Diencephalon; Alu1; Batzer, 02; Exercises; Enhancers Systems biology: genetic circuits. Clone a mammoth? Somites	RNA; Santangelo 07; Au -- Ch. 20, 715-731	Individual Web project consultations
		NOVEMBER BREAK
DEC	1 3 4 5	Regulatory RNA. Riboswitch; RNAi Argonaute Review 3:00-5:00 RBH 215 TEST 3	Ch. 18 Liu 2007; Au Test 3 Practice Sunday 7-9pm Jmol
DEC	8 10 12	Transgenic mice: Tilghman video. Insulators. H19-Igf2 H19; Igf2; Beckwith-W. Transgenic primate. Student projects & course evaluation Student projects	--- --- ---	--- Web Due
DEC	16	Web Tutorial Finished 4:30PM. No broken links.

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, 6E (Pearson), 2008
Gillen, C. M.. Reading Primary Literature (Pearson)
Articles are linked to syllabus or provided in class.

Pokescope for stereo viewing may be 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; no more than two partners are permitted. 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. Beyond that, each absence subtracts one full letter grade.
You are responsible for the content of every class, whether present or absent.

10% Quizzes. Quizzes will be unannounced.
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 16 at 4:30pm. Both partners share full responsibility for the completed project.

Laptop Computers. Each student brings a laptop PC to use in class, either their own or one loaned by the Biology Department. Rules for PC use during class:

No email or other messaging. Email during class will result in loss of PC.
Access material presented by the professor, such as Jmol models and Genbank.
You may Google a class topic, at your discretion. You are responsible for 100% of what the professor is presenting.
Departmental PCs: If any problem occurs, obtain replacement immediately from the professor.

Standards for Projects and Tests. The standard College guidelines on individual authorship and plagiarism apply to all work, as stated in the Student Handbook 08-09. 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.