BIOL 263 Fall 2018

Syllabus

Fall Semester 2018

December 18, 2018
(Latest update overrides all previous versions, electronic and print.)

MWF 10:10 AM-11:00 AM (Period 3)
TOM 101

Dr. Wade Powell
FSH 202, (740) 427-5396
powellw[a]kenyon.edu
Office hours:
Tuesdays 12:30-2:30 PM (open) + 7:30-8:30 PM (by appointment)
Wednesdays 11:00 AM - 1:00 PM
Thursdays 9:30 AM - 10:30 AM
(and by appointment)

Introduction:

The molecular and genomic basis of life is at the heart of modern biology. In BIOL 263, we will learn techniques and explore research questions at the forefront of molecular biology, focusing on the mechanisms by which the information of the genome is expressed to form the functional molecules of living cells and organisms. The processes of DNA replication, recombination and repair, transcription of RNA from DNA templates, and translation of RNA into protein are discussed in the context of current research, frequently using primary literature. The function of genes and regulation and measurement of gene expression are treated in depth. Students analyze and publish interactive tutorials on the structure and function of key macromolecules. This intermediate-level course presumes a strong background in the basics of protein structure/function, central dogma processes, fundamental molecular techniques for manipulating nucleic acids and proteins, and general chemistry.
Required prerequisites: BIOL 115, 116; one year of chemistry (Intro or Honors Intro); or permission of the instructor.

Learning Goals:

To understand the basic processes of molecular biology.
To understand the chemical structure of the macromolecular machines that perform these processes.
To develop a "mental toolbox" of molecular biology techniques that will enable understanding of the field's primary literature and the design of experiments.
To apply content knowledge to higher-level thinking, problem solving, experimental design, and data analysis.

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 sylallabus and my announcements about this.

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

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. 7.
- 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 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, annotations of assigned journal articles using Perusall, strong contribution to small group work, attending course-relevant seminars, 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 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 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 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

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 9-11 quizzes over the semester. Quizzes can be given in class (announced or unannounced) or (more commonly) as take-home assignments that include Perusall annotations. 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, students will have the opportunity to earn at least 100 points through quizzes. These "excess" points compensate for conflicts due to illness, busy schedule, athletics, performances, or any other reason.
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. 12. The final version, with zero broken links, is due Thursday, December 18 at 9:30 pm. Both partners share full responsibility for the completed project.

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).

Course Schedule

Day	Date	Topic; interesting links	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 3	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 5	Advanced DNA structure: Base Tautomers, Supercoiling	Watson Ch 4.	Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topoisomerase
R	Sept 6	Biology/BMB Seminar: Harry Itagaki, Kenyon College
F	Sept 7	Protein Structure: Helices, strands, sheets, interactions between aa residues	Ch 6, pp. 121-129.	AA2 in proteins. Ch. 6, pp. 130-144.
M	Sept 10	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 (newly added) NIH Structure Primer basic X-ray; Amore complicated X-ray 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 12	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 14	Transcription initiation, elongation, termination	Watson Ch 13, pp. 429-447.	Structures: RNAP open complex; RnaPol-Euk; movies!
M	Sept 17	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 19	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 21	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 24	Unique mechanism of attenuation in Bacillus.	Paper: Antson 99: trp RNA-binding attenuation protein.
W	Sept 26	Catch-up
R	Sept 27	Biology/BMB Seminar: Priscilla Erickson '09 Biology Department, University of Virginia
F	Sept 28	Exam I (in class).		score distribution
M	Oct 1	Eukaryotic General 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 3	Eukaryotic Transcription, cont'd.		PIC assembly structures PIC assembly movie
R	Oct 4	Biology/BMB Seminar: Courtney Sulentic Dept. of Pharmacology and Toxicology, Wright State University	A genetic polymorphism + chemical exposure = Autoimmunity??
F	Oct 5	Eukaryotic Transcription Research: GTFs and promoter clearance	Pal et al. 2005	Background Review: Luse 2013
M	Oct 8	Eukaryotic Transcriptional Regulation	Watson Ch, 19, pp. 657-665 + 669-686
W	Oct 10	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 12	October Reading Days; No Class
M	Oct 15	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 17	Transcript Splicing; Splicing2; Spliceosome	Watson Ch. 14: pp. 467-477, 480-487, 491-496.	Due date: Molecular Tutorial Proposal (instructions and electronic submission page on moodle)
F	Oct 19	Splicing conclusion; Peptide bond formation; ribosome size	Watson Ch. 15, pp. 509-528.	Family Weekend; Summer Science Posters!
M	Oct 22	Translation basics; initiation. Initiation. PDB; ribosome structural primer	Watson Ch. 15, pp. 528-535
W	Oct 24	Translation elongation, termination.	Watson Ch. 15. pp. 535-549.
F	Oct 26	Translation Research: Ribosome hybrid state	Dorner et al. 2006	Watson Ch. 15: pp. 552-553
M	Oct 29	RNA Interference Animation from Nature Reviews Genetics .	Wilson and Doudna 2013 (RNAi review paper) Watson Ch. 20, pp. 710-727.
W	Oct 31	Catch-up Day
F	Nov 2	Exam II (points to ponder)
*Part III: DNA Replication, Repair, Recombination*
M	Nov 5	DNA Replication; Beta ring; DNA Rep; Replisome Web Project Workshop, 7-10 PM; TOM 201	Watson Ch. 9, pp. 257-287
W	Nov 7	DNA Replication, cont'd.; Web Project Workshop, 7-10 PM; TOM 101	Watson Ch. 9, pp. 288-296
R	Nov 8	Web Project Workshop, 7-10 PM; SMA 201
F	Nov 9	Replication Paper--Single-molecules 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 11	Web Project Workshop, 7-10 PM; SMA 201
M	Nov 12	Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1	Watson Ch. 9 p. 302-310. Blackburn 2000 review
W	Nov 14	Paper: Ter, tert, and cancer	Li et al 2004
F	Nov 16	Homologous Recombination;	Watson Ch. 11: pp. 341-368 and 371-375	Experiments; RuvA; PNAS; Tn;
Nov 17-25		Thanksgiving Break
M	Nov 26	Knockout mice in molecular biology	H19 Gene; MIT core facility
W	Nov 28	Mutation and repair	Watson Ch. 10
F	Nov 30	CRISPR Genome Editing
M	Dec 3	Paper: Application of CRISPR to characterize lncRNA function	Espinosa 2016 (News & Views piece) Paralkar 2016 (research article)
W	Dec 5	Catch-up
F	Dec 7	Exam III
M	Dec 10	In-class pdb time
W	Dec 12	Student Project Presentations	.	Completed JMol Tutorial
F	Dec 14	Student Project Presentations	.
R	Dec 18	Revised Molecular Tutorials Due (corresponds with end of scheduled exam period)	No Broken Links	9:30 PM

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