Fall Semester 2013

Nov. 13, 2013
(Latest update overrides all previous versions, electronic and print.)

Reading Materials and Resources:

• Required text: Watson et al., (2014) Molecular Biology of the Gene, 7th edition.
• Journal Articles are linked to syllabus and/or provided in class.
• Web resources will be used in class and for your assignments.
• Laptop Computers. Each student will semi-frequently need a laptop computer in class, either his/her own or one loaned by the Biology Department. Tablet devices and phones may be adequate if they support Java (i.e. not ipads or iphones). Please pay attention to the syallabus and my announcements about this.

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

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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, religious holidays, etc. In accordance with College policy (see Provost's web site), all students with scheduled conflicts must meet with me to initiate resolution by Friday, Sept. 6.
• Participation and preparation: To participate fully in class, you must thoughtfully read the assigned material before each meeting. Expect to be called on; better yet, sing out or raise your hand! Please feel free to ask questions, add insights, correct the instructor's innacuracies, etc. at any time during class.
• Electronic device policy: Full participation in class activities is crucial for success. Electronic devices can enhance particiatipation, but they can also become a distraction. Texting, phone calls, social media, and unrelated web surfing are not appropriate. Note taking, calculations, and accessing relevant databases are encouraged on your laptop, tablet, or phone.
• Scheduling and Deadlines. Meeting deadlines is an important aspect of professionalism in science and all other careers. 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 situations are granted only in rare situations.
• Academic Honesty. Do not lie, cheat, or plagiarize. Do your own work on exams. In writing projects, properly acknowledge your sources of information, and acknowledge the help you receive from others. Kenyon's policy on academic honesty (Kenyon College Catalog) 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.

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

• 10% Course Participation. 100% attendance is expected. To participate fully in class, you must thoughtfully read and annotate the assigned material before each meeting. Active, vocal contribution is expected from all members of the class and will be the primary determinant of class participation grade.
• 10% Quizzes. Approximately ten quizzes over the semester. Quizzes can be given in class (announced or unannounced) or as take-home assignments. 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 one quiz without penalty or prior permission. The quiz average is determined based on the percentage of total available points. For students who take all quizzes, the lowest score will be dropped.
• 60% Three Exams (each 20%). There are three regular exams in class.
• 20% Molecular Tutorial Project. A JMol Molecular Tutorial Project substitutes for the final exam. Ordinarily, two partners share a project. Examples of past projects and instructions for creating new ones can be viewed at Biomolecules at Kenyon. A working model must be ready for presentation to the class on Dec. 11. The final version, with zero broken links, is due December 18 at 4:30 pm. Both partners share full responsibility for the completed project.

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

• Web resources
• Biomolecules at Kenyon
• Find Molecules: PDB and NIH
• Companion web site for Watson text (requires access code from textbook; see front matter).

Day	Date	Topic; interesting links	Primary Reading Assignment	Notes	Supporting Reading
Part I: Molecular Interactions
F	Aug 30	Course Introduction. DNA intro; B-DNA; A-RNA
M	Sept 2	Weak bonds. Amino Acids; CAP; Ident	Watson Ch 3, pp. 51-69; Ch 4, pp. 78-79 + Fig. 4-3; Ch. 6, pp. 121-122 + Fig. 6-2.
W	Sept 4	Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topoisomerase	Watson Ch 4
F	Sept 6	AA2 in proteins.	Ch 6, pp. 121-128.		Ch. 6, pp. 128-144.
M	Sept 9	Introduction to crystallography methods; basic X-Ray; crystallography tutorial; crystallography terminology; Fourier transform; FT applet.	Protein Purification: Ch. 7, pp. 148-149. Ch 4, p. 88. basic X-ray; "Molecules of Life;" crystallography terminology; Fourier transform; FT applet; crystallography tutorial another explanation (pdf).		How do you tell if a reported structure is correct? Biochemistry vs. structural biology
W	Sept 11	DNA-protein binding; Vocab; Human ADAR1; ADAR activity and consequence	Schwartz 99; The famous Gillen guide to reading journal articles.
Part II: Gene Expression
F	Sept 13	Transcription initiation, termination Structures: RNAP open complex; RnaPol-Euk; movies!	Watson Ch 13, pp. 429-442 and pp. 445-447.
M	Sept 16	Transcription Elongation; transcriptional road blocks	Epshtein & Nudler 2003 [Background: Conaway et al. 2003 (2nd and 3rd paragraphs); Watson Ch. 13, pp. 442-445		Electrophoresis: Watson Ch 7, pp. 148-149. DNA footprinting: Watson Ch. 7, pp. 184-185.
W	Sept 18	Bacterial Gene Regulation at level of transcription initiation. CAP-CTD; Lac repressor; Benoff Cooperative binding	Watson Ch 18, pp. 615-636
F	Sept 20	Regulation of intiation, cont'd; Regulation of events after initiation: Attenuation in E. coli.	Watson Ch 20, pp.707-708;
M	Sept 23	Attenuation in Bacillus. TRAP-RNA;	Antson 99;
W	Sept 25	Regulation without regulatory proteins: Riboswitches. Breaker Lab Riboswitch site (Yale) &movie	Watson Ch. 20, pp. 701-706; Soukup 2004 review riboswitch methods/data
F	Sept 27	Exam I (in class) Points to ponder for the exam.
M	Sept 30	Eukaryotic Basal Transcription Factors. DAB Pol II; TBP; TAF; solving the structure of RNA pol II.	Watson Ch. 13 pp.448-464		gel shifts: Watson Ch. 7, pp. 183-184 chromatography: Ch. 7, pp. 173-177.
W	Oct 2	Eukaryotic Transcriptional Regulation; Spec. TFs. Identify	Watson Ch, 19, pp. 657-665 + 669-686
F	Oct 4	Eukaryotic Transcription, cont'd.
M	Oct 7	Eukaryotic Transcription Research: Promoter Clearance	Pal et al. 2005
W	Oct 9	Nucleosomes & Transcriptional regulation; Histone Code. Nucleosome Nucleosome tutorial	Watson Ch. 8 pp. 219-255; Ch. 19 pp. 665-669; Ch. 7, pp. 185-187. Histone binding sites: Nature N&V 2006
F	Oct 11	October Reading Days; No Class
M	Oct 14
W	Oct 16	Research in Eukaryotic Transcriptional Regulation: Histone acetyltransferase recruitment	Sharma 2002		ChIP:Watson Ch. 21, pp. 751-752; 778-780. Chromatin IP; cross-link chemistry PCR: Watson Ch. 21, pp. 751-752 Remember PCR?Due date: JMol PDB Proposal
F	Oct 18	Transcript Splicing; Splicing2; Spliceosome	Watson Ch. 14: pp. 467-477, 480-487, 491-496.
M	Oct 21	Translation basics; initiation. Initiation. PDB; ribosome structural primer	Watson Ch. 15, pp. 509-535.		Family Weekend; Summer Science Poster Presentation
W	Oct 23	Translation elongation, termination.	Watson Ch. 15. pp. 535-549.
F	Oct 25	Translation Research: ribosome hybrid state	Dorner et al. 2006		Watson Ch. 15: pp. 552-553
M	Oct 28	Translation elongation, termination., cont'd	Watson Ch. 15. pp. 549-557.
W	Oct 30	RNA Interference Animation from Nature Reviews Genetics .	Meister 04 (RNAi review paper) Watson Ch. 20, pp. 710-727.
Part III: DNA Replication, Repair, Recombination
F	Nov 1	Exam II (points to ponder)
M	Nov 4	DNA Replication; Beta ring; DNA Rep; Replisome	Watson Ch. 9, pp. 257-287
T	Nov 5	Web Project Workshop, HIG 120, 7-10 PM
W	Nov 6	DNA Rep., cont'd.; Web Project Workshop, HIG 120, 7-10 PM	Watson Ch. 9, pp. 288-296
R	Nov 7	Web Project Workshop, HIG 120, 7-10 PM
F	Nov 8	class cancelled
M	Nov 11	Mutation and repair. Web Project Workshop, HIG 120, 7-10 PM	Watson Ch. 10
W	Nov 13	MutS; MutS-DNA; Figs.	Obmolova 00
F	Nov 15	Recombination; Experiments; RuvA; PNAS; Tn;	Watson Ch. 11: pp. 341-368 and 371-375
M	Nov 18	Knockout mice in molecular biology Knockout mice, cont'd	H19 Gene; Generation of Transgenic animals; MIT core facility
W	Nov 20	Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1	Watson Ch. 9 p. 302-310. Blackburn 2000 review
F	Nov 22	Telomerase research: telomeres and cancer cell proliferation.	Li et al. 2004
Nov. 23 - Dec. 1: Thanksgiving Break
Part IV: Genomic-scale molecular biology
M	Dec 2	Sequencing: cycle; pyrosequencing (454); illumina video; another illumina video; cheap genomes	Watson Ch. 2, p. 40-41; Ch. 8, p. 199-208; Ch. 7, p. 158-171.
W	Dec 4	Measuring Expression: RNAseq; Intro to Microarrays; Gene Chip Manufacturing; Spotting arrays;	Watson Ch. 7, p. 151-154
F	Dec 6	Genomic scale gene expression research	Andreasen et al. 2006		points to ponder
M	Dec 9	Exam III (points to ponder)
W	Dec 11	Student Project Presentations	.		Completed JMol Tutorial
F	Dec 13	Student Project Presentations	.
W	Dec 18	Revised JMol Tutorials Due	No Broken Links		4:30 PM

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