Syllabus

Fall Semester 2019

UNDER CONSTRUCTION

Oct. 22, 2019
(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. As in BIOL 115-116 last year, students will read and annotate the text and interact with each other using Perusall. Please follow my instructions in class to purchase a version of the text that works with Perusall.  Hard copies of the textbook are available for short-term loan in the library.
  
• Supplemental material. Resources on the Moodle site includes animations, activities, articles from the scientific literature and popular press, etc. Some links may also be found on this page.
• Journal Articles: Provided on moodle and/or in class. We will read one almost every week.
• Laptop Computers. Each student will occasionally 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 syllabus and my announcements about this.

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Policies and Expectations:

• Class attendance. This course operates on the assumption that every student attends class meeting. Absences will detract from one's learning and course performance.
  • 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.
  • Please let me know in advance if you must miss class due to illness.
  • In addition to regular course meetings, several help sessions for the Molecular Tutorial project (see below) will be held during evenings.
    
   
• Engagement. To participate fully in class, you must thoughtfully read and annotate the assigned material before each meeting. During class, expect to be called on; better yet, sing out or raise your hand! Every student is invited to ask questions, add insights, correct the instructor's inaccuracies, etc. at any time during class meetings. Pull your weight in small group activities. Faithful attendance is necessary but not sufficient for a top participation grade. Showing up regularly is necessary to earn a B. A's are awarded for excellent attendance plus active engagement. Participation can take many forms, including class discussion, strong contribution to small group work, attending course-relevant seminars, visiting office hours, etc.  Periodically, students may be asked to document and/or reflect on their participation in short assignments.


• Perusall.  All reading assignments/Perusall annotations must be completed by 10:00 PM the night before class on the date indicated on syllabus.

• 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 distracting and disrespectful to your classmates and to me. Note taking, calculations, 2-factor authentication, and accessing relevant databases or background information 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. Extensions will not ordinarily 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 and take-home quizzes, 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 arrangements should be initiated immediately, well in advance of the first assignments and exams.  Accommodation requests to SASS must be made at least one week prior to  an exam.
  

• Responsible Employee Syllabus Statement. 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 Discrimination and Harassment Policy is available at: http://www.kenyon.edu/titleix.  ADA/504 Student Grievance Procedures are defined at this URL:  www.kenyon.edu/directories/offices-services/ocr/discrimination/504-ada-grievance/student-grievance-procedure-resolving-complaints-under-ada-section-504/.

Assignments and Grades: Your letter grade is assigned at the end of the course based on performance in the following areas:

• 10% Course Engagement. Attendance is expected. Fully engaged students 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.
  
• 5% Perusall Annotations.  The Perusall system will score the quality of your annotations and interactions on a scale of 1-5.  Grades are assigned on a GPA-type scale:  A=4; B=3; etc.
  
• 10% Quizzes and assignments. Approximately 9-11 quizzes over the semester. Quizzes can be given in class (announced or unannounced) or (more commonly) as take-home assignments.  A perfect score for the semester is 90 points, and the quiz average will reflect the fraction of 85 points earned.  Make-up quizzes will not be possible.  However, "excess" points compensate for conflicts due to illness, busy schedule, athletics, performances, or any other reason.  Take-home quizzes can often be submitted remotely if you are traveling.  Please see me in advance to make arrangements.
• 55% Three Exams (Best two count 20% each; lowest score only 15%). 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. 11 . The final version, with zero broken links, is due Wednesday, December 18 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 for your tutorial: PDB and NIH

Day	Date	Topic	Primary Reading Assignment	Supporting Reading
Part I: Molecular Interactions
F	Aug 30	Course Introduction. Nucleic acid and nucleotide structure.		DNA intro; B-DNA; A-DNA
M	Sept 2	Amino acid structure.  Weak bonds in macromolecules.	Watson Ch 3, pp. 55-63; Ch. 6, pp. 121-122, especially Fig. 6-2.	Weak bonds. Amino Acids; CAP; Ident
W	Sept 4	Advanced DNA structure:  B/A/Z-DNA structures; Base Tautomers, Supercoiling	Watson Ch 4.	Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topoisomerase
F	Sept 6	Protein Structure: Helices, strands, sheets, interactions between aa residues	Ch 6, pp. 121-129.	AA2 in proteins. Ch. 6, pp. 130-144.
M	Sept 9	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. A summary of structural biology approaches NIH Structure Primer Protein purification by liquid chromatography	Critical Thinking: How do you tell if a reported structure is correct? Biochemistry vs. structural biology
W	Sept 11	Structure of a DNA binding protein, ADAR1	Schwartz 99; ADAR1 structures in rcsbPDB ADAR activity and consequence	The famous Gillen guide to reading journal articles. Vocab;
Part II: Gene Expression
F	Sept 13	Transcription initiation, elongation, termination	Watson Ch 13, pp. 429-447.	Structures: RNAP open complex; RnaPol-Euk; movies!
M	Sept 16	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 18	Bacterial Transcription Regulation at level of transcription initiation.	Watson Ch 18, pp. 615-636	CAP-CTD; Benoff 1999; Liu 2017 Lac repressor Cooperative binding
F	Sept 20	Bacterial transcription 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 23	Unique mechanism of attenuation in Bacillus.	Paper:  Antson 99 :  trp RNA-binding attenuation protein.
W	Sept 25	Catch-up or review
F	Sept 27	Exam I (in class) .
M	Sept 30	Eukaryotic General Transcription Factors. DAB Pol II; TBP; TAF; solving the structure of RNA pol II.	Watson Ch. 13 pp.448-464	Techniques: gel shifts: Watson Ch. 7, pp. 183-184 chromatography: Ch. 7, pp. 173-177.
W	Oct 2	Eukaryotic Transcription, cont'd.		PIC assembly structures PIC assembly movie
F	Oct 4	Eukaryotic Basal Transcription Research:
M	Oct 7	Eukaryotic Transcriptional Regulation:  Regulatory elements and transcription factors	Watson Ch, 19, pp. 657-665 + 669-686
W	Oct 9	Nucleosomes & Transcriptional regulation;  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	CORRECTED SCHEDULE FOLLOWS FROM HERE		ChIP:Watson Ch. 21, pp. 751-752; 778-780. cross-link chemistry PCR: Watson Ch. 21, pp. 751-752 Remember PCR?
W	Oct 16	Research in Eukaryotic Transcriptional Regulation: Chromatin Immunoprecipitation; Histone acetyltransferase recruitment	Sharma 2002 See moodle for guided meditation assignment.
F	Oct 18	Transcript Splicing; Splicing2; Spliceosome	Watson Ch. 14: pp. 467-477, 480-487, 491-496.	Family Weekend; Summer Science Posters!
M	Oct 21	Splicing conclusion Translation: Peptide bond formation; ribosome size	Watson Ch. 15, pp. 509-515; 521-528	Revised Due date: Molecular Tutorial Proposal (instructions and electronic submission page on moodle)
W	Oct 23	Translation basics; initiation. Initiation. PDB; ribosome structural primer	Watson Ch. 15, pp. 528-535
F	Oct 25	Translation elongation, termination. tRNA charging	Watson Ch. 15. pp. 535-549; 515-520	Watson Ch. 15: pp. 552-553
M	Oct 28	Translation Research: Ribosome hybrid state	Dorner et al. 2006 See moodle for guided meditaton
W	Oct 30	RNA Interference Animation from Nature Reviews Genetics .	Wilson and Doudna 2013 (RNAi review paper) Watson Ch. 20, pp. 711-727.
F	Nov 1	Exam II (points to ponder)
Part III: DNA Replication, Repair, Recombination
M	Nov 4	DNA Replication; Beta ring ; DNA Rep; Replisome Web Project Workshop, 7-10 PM; TOM 101	Watson Ch. 9, pp. 257-277
W	Nov 6	DNA Replication, cont'd.; Web Project Workshop, 7-10 PM; TOM 101	Watson Ch. 9, pp. 277-288; 293-296
R	Nov 7	Web Project Workshop, 7-10 PM; SMA 201
F	Nov 8	Replication Paper--Single-molecule replisome study: Are leading and lagging strand polymerases really coordinated?	Graham et al. 2017 Guided meditation on moodle due at beginning of class	Don't ignore the supplemental information figures!
Sun	Nov 10	Web Project Workshop, 7-10 PM; SMA 201
M	Nov 11	DNA Mutation and Repair	Watson Ch. 10
W	Nov 13	DNA Repair Research
F	Nov 15	Homologous Recombination;	Watson Ch. 11: pp. 341-368 and 371-375	Experiments; RuvA; PNAS; Tn;
M	Nov 18	Telomerase and telomeres. Telomerase structure.	Watson Ch. 9 p. 302-310. Blackburn 2000 review
W	Nov 20	Paper:  Ter, tert, and cancer	Li et al 2004
F	Nov 22	CRISPR Genome Editing	Ch. 20: 706; 709-711
M-F	Nov 25-29	Thanksgiving Break; no class
M	Dec 2	Generation of knockout mice by homologous recombination
W	Dec 4	Paper:  Application of CRISPR to characterize lncRNA function	Espinosa 2016 (News & Views piece) Paralkar 2016 (research article)
F	Dec 6	Exam III
M	Dec 9	In-class pdb time
W	Dec 11	Student Project Presentations	.	Completed JMol Tutorial
F	Dec 13	Student Project Presentations	.
W	Dec 18	Revised Molecular Tutorials Due 9:30 PM (corresponds with end of scheduled exam period)	Final Submission (via moodle)

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