Syllabus

Fall Semester 2017

August 15, 2017
(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: Provided on moodle and/or in class. We will read one almost every week.
• Web resources will be used in class and for your assignments. Look for the growing collection of these in moodle. Some links may also be found on this page.
• 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, but they are rarely as effective as a computer. 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. 1.
  • Please let me know in advance if you must miss class due to illness.
    
   
• Participation. 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 inaccuracies, etc. at any time during class. Pull your weight in small group activities. Note that good attendance is necessary but not sufficient for a good Participation grade. Showing up regularly is necessary to earn a B. A's are awarded for excellent attendance and active engagement. Participation can take many forms, including class discucssion, strong contribution to small group work, attending course-relevant relevant seminars, visiting office hours, etc.  Periodically, students may be asked to document and/or reflect on their participation in short assignments.
  

• Electronic devices. Full participation in class activities is crucial for success. Electronic devices can enhance participation, but they can also become a distraction. Messaging, phone calls, social media, and on-line shopping are are distracting and disrespectful to your classmates and to me. Note taking, calculations, 2-factor authentication, and accessing relevant databases are encouraged on your phone, laptop, or tablet.

• 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 conflicts with the workload for other courses. Accommodations due to illness or other personal situations are granted only in rare situations.

• Academic Honesty. Conduct your work with integrity. 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 Course 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, Director of Student Accessibility and Support Services (1-740-427-5453; salvae@kenyon.edu). All information and documentation of disability is confidential. Please see the Student Accessibility and Support Services web site for more information. Accommodation requests should be made immediately, well in advance of the first assigments and exams.

• Title IX/VAWA. Kenyon College seeks to provide an environment that is free of gender bias, discrimination, and harassment. If you have been the victim of sexual harassment/misconduct/assault, interpersonal violence, or stalking, we encourage you to report this. If you report this to me, I must notify Kenyon's Title IX coordinator of any information about the incident that you provide. Kenyon College's Title IX ane VAWA policy is available at: http://www.kenyon.edu/titleix

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Assignments and Grades: Your letter grade is assigned at the end of the course 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 to class discussion and small group activities is expected from all members of the class and will be an important determinant of class participation grade.
• 10% Quizzes and assignments. Approximately 8-10 quizzes over the semester. Quizzes can be given in class (announced or unannounced) or as take-home assignments. Every student gets one quiz "free pass." No notification or permission is required. This compensates for conflicts due to illness, busy schedule, athletics, performances, or any other reason. I encourage you to use your "free pass." Make-up quizzes will not be possible. For students who take every quiz, the lowest score will count as the "free pass" in the calculation of the quiz average.
• 60% Three Exams (each 20%). There are three regular exams in class. Scores will be returned with the class score distribution to enable estimation of letter grades for individual exams.
• 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. 6. The final version, with zero broken links, is due Thursday, December 14 at 9:30 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	Supporting Reading
Part I: Molecular Interactions
F	Aug 26 5	Course Introduction. Nucleic acid and nucleotide structure.		DNA intro; B-DNA; A-DNA
M	Aug 28	Amino acid structure.  Weak bonds in macromolecules.	Watson Ch 3, pp. 55-63; Ch. 6, pp. 121-122 + Fig. 6-2.	Weak bonds. Amino Acids; CAP; Ident
W	Aug 30	Advanced DNA structure:  Base Tautomers, Supercoiling	Watson Ch 4.	Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topoisomerase
F	Sept 1	Protein Structure: Helices, strands, sheets, interactions between aa residues	Ch 6, pp. 121-129.	AA2 in proteins. Ch. 6, pp. 130-144.
M	Sept 4	Methods for Solving Macromolecular Structures. Intro to pdb and JMOL RSCB Protein Data Bank	Protein Purification: Ch. 7, pp. 148-149. Ch 4, p. 88. NIH Structure Primer basic X-ray; another explanation (pdf). Cryoelectronmicroscopy ("Cryo-EM"); Cryo-EM Primer. Solution NMR	Protein purification by liquid chromatography Critical Thinking: How do you tell if a reported structure is correct? Biochemistry vs. structural biology
W	Sept 6	Structure of a DNA binding protein, ADAR1	Schwartz 99; pdb; ADAR1 structures in rcsbPDB ADAR activity and consequence	The famous Gillen guide to reading journal articles. Vocab;
Part II: Gene Expression
F	Sept 8	Transcription initiation, elongation, termination	Watson Ch 13, pp. 429-447.	Structures: RNAP open complex; RnaPol-Euk; movies!
M	Sept 11	Transcription Research:  RNA polymerase "scrunching"	Kapanidis et al. 2006 Supporting Info Watson Ch. 13, pp. 441-442	Background: Single-molecule techniques explained. DNA footprinting: Watson Ch. 7, pp. 184-185.
W	Sept 13	Bacterial Gene Regulation at level of transcription initiation.	Watson Ch 18, pp. 615-636	CAP-CTD; Lac repressor; Benoff Cooperative binding
R	Sept 14	Chemistry/BMB Seminar: Susan Schroeder, Dept. of Chemistry and Biochemistry, University of Oklahoma	Exploring RNA structure, function, and energetics
F	Sept 15	Bacterial gene regulation, cont'd; Regulation of events after initiation: Riboswitches, attenuation	Watson Ch. 20, pp. 703-708;	-Soukup 2004 review -Breaker Lab Riboswitch site (Yale) &movie -riboswitch methods/data
M	Sept 18	Unique mechanism of attenuation in Bacillus.	Paper:  Antson 99
W	Sept 20	Catch-up
R	Sept 21	Biology/BMB Seminar: Arianna Smith Dept. of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University and Biology Department, Kenyon College	Exploring the Role of Prenatal Maternal Stress on Allergic Asthma Development in Offspring
F	Sept 22	Exam I (in class).		score distribution
M	Sept 25	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	Sept 27	Eukaryotic Transcription, cont'd.
F	Sept 29	Eukaryotic Transcription Research:  GTFs and promoter clearance	Pal et al. 2005
M	Oct 2	Eukaryotic Transcriptional Regulation	Watson Ch, 19, pp. 657-665 + 669-686
W	Oct 4	Nucleosomes & Transcriptional regulation; Histone Code. 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 6	October Reading Days; No Class
M	Oct 9	Research in Eukaryotic Transcriptional Regulation: Chromatin Immunoprecipitation; Histone acetyltransferase recruitment	Sharma 2002 See moodle for guided meditation assignment.	ChIP:Watson Ch. 21, pp. 751-752; 778-780. cross-link chemistry PCR: Watson Ch. 21, pp. 751-752 Remember PCR?
W	Oct 11	Due date: Molecular Tutorial Proposal		(instructions and electronic submission page on moodle)
R	Oct 12	Biology/BMB Seminar: Heidi Andersen, MD Pediatric Infectious Disease, Cincinnati Children's Hospital	Metagneomic shotgun sequencing for detection of colonization, transmission, and invasion with multidrug resistant pathogens in high risk children	4:00 PM, HIG AUD
F	Oct 13	Transcript Splicing; Splicing2; Spliceosome	Watson Ch. 14: pp. 467-477, 480-487, 491-496.	Family Weekend; Summer Science Posters
M	Oct 16	Splicing conclusion; Peptide bond formation; ribosome size	Watson Ch. 15, pp. 509-535.
W	Oct 18	Translation basics; initiation. Initiation. PDB; ribosome structural primer
F	Oct 20	Translation elongation, termination.	Watson Ch. 15. pp. 535-549.
M	Oct 23	Translation Research: Ribosome hybrid state	Dorner et al. 2006	Watson Ch. 15: pp. 552-553
T	Oct 24	Chemistry/BMB Seminar:  Chris Neale, Center for Nonlinear Studies, Los Alamos National Laboratory	Structure/function of G-protein coupled-receptors
W	Oct 25	RNA Interference Animation from Nature Reviews Genetics .	Wilson and Doudna 2013 (RNAi review paper) Watson Ch. 20, pp. 710-727.
F	Oct 27	Exam II (points to ponder)
M	Oct 30	DNA Replication; Beta ring; DNA Rep; Replisome	Watson Ch. 9, pp. 257-287
Part III: DNA Replication, Repair, Recombination
W	Nov 1	DNA Replication, cont'd.; Web Project Workshop, 7-10 PM	Watson Ch. 9, pp. 288-296
R	Nov 2	Biology/BMB Seminar: Ann Miller, Dept. of Molecular, Cellular, and Developmental Biology, University of Michigan Web Project Workshop, 7-10 PM	Regulation and localization of RhoA GTPase in cytokinesis
F	Nov 3	Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1	Watson Ch. 9 p. 302-310. Blackburn 2000 review
S	Nov 5	Web Project Workshop, 4-6 PM
M	Nov 6	Replication Paper--Single-molecules replisome study: Are leading and lagging strad polymerases really coordinated? Web Project Workshop, 7-10 PM	Graham et al. 2017 Guided meditation on moodle due at beginning of class	Don't ignore the supplemental information figures!
W	Nov 8	DNA Sequencing, RNAseq Web Project Workshop, 7-10 PM	Watson Ch. 2, p. 40-41; Ch. 8, p. 199-208; Ch. 7, p. 158-171.	cycle; pyrosequencing (454); illumina video; another illumina video; cheap genomes
R	Nov 9	Web Project Workshop, 7-10 PM
F	Nov 10	Research:  ChiPseq Estrogen Receptor Binding throughout the Genome	Hurtado, et al. 2011. Supplementary info.	Integrates: Eukaryotic transcription factors, enhancer elements ChIP, NextGen sequencing, PCR, westerns, siRNAs, cell cycle, cancer
M	Nov 13	Mutation and repair	Watson Ch. 10
W	Nov 15	Homologous Recombination;	Watson Ch. 11: pp. 341-368 and 371-375	Experiments; RuvA; PNAS; Tn;
F	Nov 17	Knockout mice in molecular biology Knockout mice, cont'd	H19 Gene; Generation of Transgenic animals; MIT core facility
Nov. 20 - Nov 24: Thanksgiving Break
M	Nov 27	CRISPR Genome Editing
W	Nov 29	Catch-up
F	Dec 1	Exam III
M	Dec 4	In-class pdb time
W	Dec 16	Student Project Presentations	.	Completed JMol Tutorial
F	Dec 8	Student Project Presentations	.
R	Dec 14	Revised Molecular Tutorials Due (corresponds with end of scheduled exam period)	No Broken Links	9:30 PM

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