BIOL 263 Fall 2023

Syllabus

Fall Semester 2023

ALWAYS UNDER CONSTRUCTION

October 19, 2023
(Latest update overrides all previous versions, electronic and print.)

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

Dr. Wade Powell
Proper Nouns: "Wade," "Professor Powell," "Dr. Powell" are all appropriate
Pronouns: he/him/his
FSH 202/204, (740) 427-5396
powellw[a]kenyon.edu

Office hours:

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 (CHEM 121+124 or CHEM 122); or permission of the instructor. Organic Chemistry is not required (although many students take this course at the same time).

Learning Goals:

To recall and explain the basic cellular and biochemical processes of molecular biology.
To recognize, identify, interpret, and illustrate the chemical structures and interactions of the macromolecular machines that perform these processes.
To develop a "mental toolbox" of molecular biology techniques that will enable comprehension and critical analysis of the field's primary literature.
To integrate content knowledge toward solving problems, designing experiments, and evaluating data in both familiar and novel situations.

Reading Materials and Resources:

Required text: Cox et al. Molecular Biology: Principles and Practice, 2nd ed. As in BIOL 115-116, students will read, annotate the text, and interact with each other using Perusall. Perusall access is by short-term rental or permanent license. Please establish access to your text directly via the class moodle site. A small number of purchase codes is available in the bookstore for students who must obtain their books through that channel. Hard copies of the textbook may be 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. Tablet devices and phones may be adequate, but they are rarely as effective as a computer.

Policies and Expectations:

Class attendance. This course operates on the assumption that every student attends every 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. 1.
- Do not come to class if you are ill. Please let me know as soon as possible 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 our frequent small group activities.
Faithful attendance is necessary but not sufficient for a top participation grade. Showing up regularly defines the standard 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 before midnight the night before class on the date indicated on syllabus.

Electronic devices. Full participation in class activities is crucial for success. Electronic devices are sometimes crucial for full 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 laptop, tablet, or phone.

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 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.
Please also read the course Policy on the Use of Artificial Intelligence Tools.

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 the office of Student Accessibility and Support Services (1-740-427-5453; sass@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 with SASS immediately, well in advance of the first assignments and exams.

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 maximum 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. 7 . The final version, with zero broken links, is due Thursday, Dec. 14 at 4:30 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 for your tutorial: PDB and NIH

Course Schedule

Day	Date	Topic	Primary Reading Assignment	Supporting Reading
*Part I: Molecular Interactions*
F	Aug 25	Course Introduction. Nucleic acid and nucleotide structure.	Cox pp. 62-64 and174-184.	DNA intro; B-DNA; A-DNA
M	Aug 28	Amino acid structure. Weak bonds in macromolecules.	Cox pp. 68-77 and 93-98 Iesp. Fig. 4-3)	Weak bonds. Amino Acids; CAP; Ident
W	Aug 30	Advanced DNA structure: B/A/Z-DNA structures; Base Tautomers, Supercoiling	Cox 185-189; 179-180; 304-317; FIg. 19.15 (p. 676)	Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topoisomerase
F	Sept 1	Protein Structure: Helices, strands, sheets, interactions between aa residues	Cox 102-119	AA2 in proteins.
M	Sept 4	Methods for Solving Macromolecular Structures. Intro to pdb and JMOL. RSCB Protein Data Bank	Protein Purification: Cox 100-101 (Highlight 4-1) Structure Determination: Cox 120-125 [no CryoEM :( ] 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 6	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 8	Transcription initiation, elongation, termination	Cox 519-536	Structures: RNAP open complex; RnaPol-Euk; movies!
M	Sept 11	Transcription Research: RNA polymerase "scrunching"	Kapanidis et al. 2006 Supporting Info Cox p. 533 (Fig. 15-15)	Background: Single-molecule techniques explained. DNA footprinting: Cox 700-701 (Highlight 20.1, Fig. 2)
W	Sept 13	Bacterial Transcription Regulation at level of transcription initiation.	Activators and repressors:Cox 665-675 Operons 693-703 Regulons: 705-707	CAP-CTD; Benoff 1999; Liu 2017 Lac repressor Cooperative binding
F	Sept 15	Bacterial transcription regulation, cont'd: Regulation of events after initiation: leader sequences, riboswitches, attenuation	Cox 704-705; 707-711	-Soukup 2004 review -Breaker Lab Riboswitch site (Yale) &movie -riboswitch methods/data
M	Sept 18	Unique mechanism of attenuation in Bacillus.	Paper: Antson 99 : trp RNA-binding attenuation protein.
W	Sept 20	Catch-up or review
F	Sept 22	Exam I (in class) .
M	Sept 25	Eukaryotic General Transcription Factors. DAB Pol II; TBP; TAF; solving the structure of RNA pol II.	Cox 537-548	Techniques: gel shifts: 700, FIg. 1 (Highlight 20.1) chromatography: 100-101(again).
W	Sept. 27	Cox 537-548	PIC assembly structures PIC assembly movie (download movie from supplementary info link in article)
F	Sept 29	Eukaryotic Basal Transcription Research:
M	Oct 2	Eukaryotic Transcriptional Regulation: Regulatory elements and transcription factors	Cox 730-737; Highlight 21-2 (738-739); 740-745
W	Oct 4	Nucleosomes & Transcriptional regulation; Nucleosome tutorial	Cox 331-343; 728-730 Histone binding sites: Nature N&V 2006
F	Oct 6	Fall Break; 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; cross-link chemistry PCR: Cox p. 221-226 Remember PCR?
W	Oct 11	Transcript Splicing; Splicing2; Spliceosome	Cox 553-565
F	Oct 13	[Wade Away]
M	Oct 16	Splicing conclusion Translation: Peptide bond formation; ribosome composition	Alternative splicing: Cox 561-562 Peptide bond formation: Cox 65, 644 Ribosome basics: 617-626	Due date: Molecular Tutorial Proposal (instructions and electronic submission page on moodle)
W	Oct 18	Translation basics; initiation. Initiation. PDB; ribosome structural primer	Cox 617-626; 626-630; 630-63
F	Oct 20	Translation elongation, termination. tRNA charging	Cox 639-649
M	Oct 23	Translation Research: Ribosome hybrid state	Dorner 2006
W	Oct 25	RNA Interference Animation from Nature Reviews Genetics.	Cox: 681; 774-781.	Wilson and Doudna 2013 (RNAi review paper)
F	Oct 27	Exam II (points to ponder)
*Part III: DNA Replication, Repair, Recombination*
M	Oct 30	DNA Replication; Beta ring ; DNA Rep; Replisome Web Project Workshop, 7-9 PM;	Cox 363-376
W	Nov 1	DNA Replication, cont'd.; Web Project Workshop, 7-9 PM;	Cox 377-393; 398
R	Nov 2	Web Project Workshop, 7-9 PM;
F	Nov 3	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 5	Web Project Workshop, 7-9 PM;
M	Nov 6	DNA Mutation and Repair	Cox 413-445
W	Nov 8	DNA Repair Research
F	Nov 10	Homologous Recombination;	Cox 449-466	Experiments; RuvA; PNAS; Tn;
M	Nov 13	Telomerase and telomeres. Telomerase structure.	Cox 399-405 Blackburn 2000 review
W	Nov 15	Paper: Ter, tert, and cancer	Li et al 2004
F	Nov 18	Generation of knockout mice by homologous recombination
M-F	Nov 20-24	Thanksgiving Break; no class
M	Nov 27	CRISPR Genome Editing	Cox 246-248 (esp. Fig. 7-33)
W	Nov 29	Paper: Application of CRISPR to characterize lncRNA function	Espinosa 2016 (News & Views piece) Paralkar 2016 (research article)
F	Dec 1	Exam III
M	Dec 4	In-class pdb work time
W	Dec 6	Student Project Presentations	.	Completed JMol Tutorial
F	Dec 8	Student Project Presentations	.
R	Dec 14	Revised Molecular Tutorials Due by 4:30 PM (corresponds with end of scheduled exam period)	Final Submission (via moodle)

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