BIOL 263: Molecular Biology and Genomics
Fall Semester 2011
Last modified Dec. 15, 2011
We are currently on schedule.
(Latest update overrides all previous versions, electronic and print.)
MWF 10:10 AM-11:00 AM (Period 3)
Tomsich Hall Room 101
(Owen York Lecture Hall)
Dr. Wade Powell
FSH 202, PBX 5396
powellw[a]kenyon.edu
Office hours: M 11-noon and 1:30 -3; W 11-noon; R noon-2; F 11-noon.
(or 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.
Recommended prerequisite or co-requisite: CHEM 231 and 232 (Organic Chemistry).
Reading Materials and Resources:
- Required text: Watson et al., (2008) Molecular Biology of the Gene, 6th 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 frequently need a laptop computer in class, either his/her own or one loaned by the Biology Department. A small number of loaner laptops are checked out for the entire semester and will be available after classes begin. Please the department laptop czar, Darcy Blankenhorn, for details.
- Rules for PC use during class:
- Stay on task. No email, facebook, IM, New York Times, etc. Misuse during class will result in loss of PC privileges.
- Access material presented by the professor, such as Jmol models, databases (Genbank, GEO, OMIM, metazome, etc.), or journal articles.
- You may Google a class topic, at your discretion. You are responsible for 100% of what the professor is presenting. Don't let it be a distraction.
- Departmental PCs: If any problem occurs, obtain replacement immediately from the professor.
- Rules for PC use during class:
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 (http://documents.kenyon.edu/provost/cas_athlet_sched.doc), all students with scheduled conflicts must meet with me to initiate resolution by Friday, Sept. 2.
- Class participation: To participate fully in class, you must thoughtfully read the assigned material before each meeting. Expect to be called on; better yet, raise your hand! Please feel free to ask questions, add insights, correct the instructor's innacuracies, etc. at any time during class.
- Phone policy: Cell phones that disrupt class (ringing, in-class texting, etc.) will be taken. Phones can be picked up after 4:00 PM from the Kokosing River. Look beneath the Laymon Road bridge.
- 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 situation are granted 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.
Assignments and Grades: Your grade is based on performance in the following areas:
- 10% Attendance and Participation. 100% attendance is expected. To participate fully in class, you must thoughtfully read and annotate the assigned material before each meeting. Active, vocal participation 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 will often be unannounced. 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. 7. The final version, with zero broken links, is due December 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: PDB and NIH
- Companion web site for Watson text (requires access code from textbook; see front matter).
Course Schedule
| Day | Date | Topic | Reading | Notes | Work Due |
Part I: Molecular Interactions |
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| F | Aug 26 | Course Introduction. DNA intro; B-DNA; A-RNA |
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| M | Aug 29 | Weak bonds. Amino Acids; CAP; FAB; Ident | Watson Ch 3; Ch 5, pp. 71-74 | Notes | |
| W | Aug 31 | Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topo | Watson Ch 6 | ||
| F | Sept 2 | AA2 in proteins. | Ch 5 p 73-93; | ||
| M | Sept 5 | Introduction to crystallography methods; basic X-Ray; |
Protein Purification: Ch. 21, pp. 764-769. basic X-ray; "Molecules of Life;" crystallography terminology; Fourier transform; FT applet;n`1 more advanced X-Ray (local version); another explanation (pdf). |
computers | How do you tell if a reported structure is correct? |
| W | Sept 7 | DNA-protein binding; Vocab; Human ADAR1; ADAR activity and consequence |
Schwartz 99; The famous Gillen guide to reading journal articles. |
computers | |
Part II: Gene Expression |
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| F | Sept 9 | Transcription initiation Structures: RNAP open complex; RnaPol-Euk |
Watson Ch 12, pp. 377-391; | ||
| M | Sept 12 | Transcription Elongation; transcriptional road blocks |
Epshtein & Nudler 2003 Watson Ch. 12, pp. 391-396; DNA footprinting: Watson Ch. 21, pp. 777-8] |
computers | |
| W | Sept 14 | Bacterial Gene Regulation at level of transcription initiation. CAP-CTD; Lac repressor; Benoff |
Watson Ch 16, pp. 547-567 | ||
| F | Sept 16 | Regulation of intiation, cont'd; Regulation of events after initiation: Attenuation in E. coli. |
Watson Ch 18, pp.639-640; |
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| M | Sept 19 | Attenuation in Bacillus. TRAP-RNA; |
Antson 99; |
computers | |
| W | Sept 21 | Regulation without regulatory proteins: Riboswitches. Breaker Lab Riboswitch site (Yale) &movie |
Watson Ch. 18, pp. 633-638; Soukup 2004 review riboswitch methods/data |
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| F | Sept 23 | Exam I (in class) Points to ponder for the exam. | |||
| M | Sept 26 | Eukaryotic Basal Transcription Factors. DAB Pol II; TBP; TAF; solving the structure of RNA pol II. |
Watson Ch. 12 pp.396-414; gel shifts: Ch. 21, pp. 776-778; chromatography: Ch. 21, pp. 764-769. |
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| W | Sept. 28 | Eukaryotic Transcriptional Regulation; Spec. TFs. Identify |
Watson Ch, 17, pp. 589-620 | ||
| F | Sept. 30 | Eukaryotic Transcription, cont'd. | . | . | |
| M | Oct 3 | Eukaryotic Transcription Research: Promoter Clearance | Pal et al. 2005 | computers | |
| W | Oct 5 | Nucleosomes & Transcriptional regulation; Histone Code. Nucleosome Nucleosome tutorial | Watson Ch. 7 pp. 156-191; Ch. 17 pp. 620-636. Histone binding sites: Nature N&V 2006 |
computers | |
| F | Oct 7 | October Reading Days; No Class | |||
| M | Oct 10 | Research in Eukaryotic Transcriptional Regulation: Histone acetyltransferase recruitment | Watson Ch. 21, pp. 751-752; 778-780. Sharma 2002 Chromatin IP; cross-link chemistry Remember PCR? |
computers | |
| W | Oct 12 | Transcript Splicing; Splicing2; Spliceosome | Watson Ch. 13: pp. 415-425, 430-4346, 439 (bottom)-445. | JMol Project: PDB Proposal | |
| F | Oct 14 | Translation basics; initiation. Initiation. PDB; ribosome structural primer | Watson Ch. 14, pp. 457-487. | Family Weekend; Summer Science Poster Presentation | |
| M | Oct 17 | Translation elongation, termination. | Watson Ch. 14. pp. 487-519. | ||
| W | Oct 19 | Translation Research: ribosome hybrid state | Dorner et al. 2006 | computers | |
| F | Oct 21 | Translation elongation, termination., cont'd | Watson Ch. 14. pp. 487-519. | ||
| M | Oct 24 | RNA Interference Animation from Nature Reviews Genetics . |
Meister
04 (RNAi review paper) Watson Ch. 18 pp. 641-660 |
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| W | Oct 26 | Exam II (points to ponder) | |||
Part III: DNA Replication, Repair, Recombination |
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| F | Oct. 28 | class cancelled | |||
| M | Oct. 31 | DNA Replication; Beta ring; DNA Rep; Replisome | Watson Ch. 8, pp. 195-238 |
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| W | Nov 2 | DNA Rep., cont'd.; | Watson Ch. 8, pp. 195-238 | ||
| F | Nov 4 | Mutation and repair. | Watson Ch. 9 | ||
| M | Nov 7 | MutS; MutS-DNA; Figs. | Obmolova 00 | In-Class activity: Student descriptions for mock tutorial | |
| T | Nov 8 | Web Project Workshop, FSH 009, 7-10 PM | |||
| W | Nov 9 | Recombination; Experiments; RuvA; PNAS; Tn; Web Project Workshop, FSH 009, 7-10 PM |
Watson Ch. 10: pp. 283-310 and 314-316 | ||
| R | Nov 10 | Web Project Workshop, FSH 009, 7-10 PM | |||
| F | Nov 11 | Knockout mice in molecular biology Knockout mice, cont'd
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H19 Gene; Generation of Transgenic animals; MIT core facility |
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| M | Nov 14 | Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1 | Watson Ch. 8 p. 247-254. |
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| T | Nov 15 | ||||
| W | Nov 16 | Telomerase research: telomeres and cancer cell proliferation. | |||
Part IV: Genomic-scale molecular biology |
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| F | Nov 18 | Sequencing: cycle; pyrosequencing (454); illumina video; another illumina video; cheap genomes personalized medicine; hepatitis drug; |
Watson Ch. 2, p. 39-40; Ch. 7, p. 133-138; Ch. 20, p. 703-715. |
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| Nov 21-25 | Thanksgiving Break | ||||
| M | Nov 28 | Genomes: Human Genome; Ensembl; Metazome; | Bring computers! In-class: Genome Exploration
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| W | Nov 30 | Intro to Microarrays; Gene Chip Manufacturing; Spotting arrays | Schulze 2001 review article Watson Ch. 19, p. 662 |
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| F | Dec 2 | Expression microarray research |
Andreasen et al. 2006 | Points to ponder | |
| M | Dec 5 | Exam III (points to ponder) | |||
| W | Dec 7 | Student Project Presentations | . | . | Completed JMol Tutorial |
| F | Dec 9 | Student Project Presentations | . |
. | |
| W | Dec 14 | Revised JMol Tutorials Due | No Broken Links | 4:30 PM | |
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