BIOL 263: Molecular Biology and Genomics
Fall Semester 2009
Last modified Dec. 17, 2009
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: T,R 0845-1015; F1330-1530.
(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 research, 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 113, 114; 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 must bring a laptop computer to use in class, either their own or one loaned by the Biology Department. Loaner laptops are checked out for the entire semester and will be available during the first class meeting on August 31. Please the department laptop czar, Dr. Slonczewski, 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.
- H1N1 and other flu policy:If you are running a fever, stay in your room and notify the health and counseling center; do not come to class.
- 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.
- 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 (pp. 24-27 of the Course of Study) 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. Eight to 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 up to two quizzes without penalty or prior permission. If a student takes all quizzes, the two lowest scores will not be used in calculating the quiz average.
- 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. It is recommended that two partners share a project. Examples of past projects and instructions for creating new onew 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 December 18 at 4:30 pm (time corresponds to the scheduled time for the final exam). 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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| M | Aug 31 | Course Introduction. DNA intro; B-DNA; A-RNA; DNA & RNA |
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| W | Sept 2 | Weak bonds. Amino Acids; CAP; FAB; Ident | Watson Ch 3; Ch 5, pp. 69-73 | Notes | |
| F | Sept 4 | Adv DNA; Z-DNA ; HIV; Triplex; Quad; base tautomers; supercoiling; Topo | Watson Ch 6 | ||
| M | Sept 7 | AA2 in proteins. | Ch 5 p 73-93; | ||
| W | Sept 9 | 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; more advanced X-Ray (local version); another explanation (pdf). |
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| F | Sept 11 | DNA-protein binding; Vocab; Human ADAR1; ADAR activity and consequence |
Schwartz 99; The famous Gillen guide to reading journal articles. |
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Part II: Gene Expression |
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| M | Sept 14 | Transcription initiation Structures: RnaPol-Bact; RnaPol-Euk |
Watson Ch 12, pp. 377-391; | ||
| W | Sept 16 | Transcription Elongation; transcriptional road blocks |
Epshtein & Nudler 2003 [Background: Conaway et al. 2003 (2nd and 3rd paragraphs); DNA footprinting: Watson Ch. 21, pp. 777-8] |
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| F | Sept 18 | Bacterial Gene Regulation at level of transcription initiation. CAP-CTD; Lac repressor; Benoff |
Watson Ch 16, pp. 547-567 | ||
| M | Sept 21 | Regulation of intiation, cont'd; Regulation of events after initiation: Attenuation in E. coli. |
Watson Ch 18, pp.639-640; |
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| W | Sept 23 | Attenuation in Bacillus. TRAP-RNA; |
Antson 99; |
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| F | Sept 25 | 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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| M | Sept 28 | Exam I (in class) Points to ponder for the exam. | |||
| W | Sept 30 | 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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| F | Oct 2 | Eukaryotic Transcriptional Regulation; Spec. TFs. Identify |
Watson Ch, 17, pp. 589-620 | ||
| M | Oct 5 | Eukaryotic Transcription, cont'd. | . | . | |
| W | Oct 7 | Eukaryotic Transcription Research: Promoter Clearance | Pal et al. 2005 | ||
| F | Oct 9 | 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 |
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| M | Oct 12 | October Reading Days; No Class | |||
| W | Oct 14 | 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? |
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| F | Oct 16 | Submit PDB tutorial proposals to Wendy Busenburg-Taylor in TOM 101, 10:10 AM. Class is otherwise cancelled. | JMol Project: PDB Proposal | ||
| M | Oct 19 | Transcript Splicing; Lupus; Splicing2; Spliceosome (family weekend) | Watson Ch. 13 | ||
| W | Oct 21 | Translation basics; initiation. Initiation. PDB; ribosome structural primer | Watson Ch. 14, pp. 457-487. | ||
| F | Oct 23 | Translation elongation, termination. | Watson Ch. 14. pp. 487-519. | ||
| M | Oct 26 | Translation in the Nucleus? Notes Nonsense-mediated decay |
Iborra 01 | ||
| W | Oct 28 | RNA Interference Animation from Nature Reviews Genetics . |
Meister
04 (RNAi review paper) Watson Ch. 18 pp. 641-660 |
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| F | Oct 30 | RNAi, cont'd. | RNAi research article | ||
| M | Nov 2 | Exam II (points to ponder) | |||
Part III: DNA Replication, Repair, Recombination |
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| W | Nov 4 | DNA Replication; Beta ring; DNA Rep; Replisome | Watson Ch. 8 | ||
| F | Nov 6 | DNA Rep., cont'd.; | Watson Ch. 8 |
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| M | Nov 9 | Mutation and repair. | Watson Ch. 9 | ||
| T | Nov 10 | Web Project Workshop, FSH 009, 7-10 PM | |||
| W | Nov 11 | MutS; MutS-DNA; Figs. | Obmolova 00 | In-Class activity: Student descriptions for mock tutorial | |
| R | Nov 12 | Web Project Workshop, FSH 009, 7-10 PM | |||
| F | Nov 13 | Recombination; Experiments; RuvA; PNAS; Tn; | Watson Ch. 10 | ||
| M | Nov 16 | Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1 | Watson Ch. 8 p. 247-254. Blackburn 2000 review |
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| W | Nov 18 | Telomerase research: telomeres and cancer cell proliferation. | Li et al. 2004 | ||
| F | Nov 20 | Knockout mice in molecular biology | H19 Gene; Generation of Transgenic animals; MIT core facility |
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| Nov 21-29 | Thanksgiving Break | ||||
Part IV: Genomic-scale molecular biology |
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| M | Nov 30 | Genomes: Human Genome; Ensembl; Metazome; cheap genomes Black heart drug; hepatitis drug; Sequencing: cycle; next gen |
Watson Ch. 2, p. 39-40; Ch. 7, p. 133-138; Ch. 20, p. 703-715. | In-class: Genome Exploration
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| W | Dec 2 | Intro to Microarrays; Gene Chip Manufacturing; Spotting arrays |
Schulze 2001 review article Watson Ch. 19, p. 662 |
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| F | Dec 4 | Microarray research article | Schaffer et al. 2001; supplemental materials | Guided meditation | |
| M | Dec 7 | Catch up and review | . | . | . |
| W | Dec 9 | Exam III (points to ponder) | . | . | . |
| F | Dec 11 | Student Project Presentations | . |
. | Completed JMol Tutorial |
| M | Dec 14 | Student Project Presentations | . | . | . |
| M | Dec 18 | Revised JMol Tutorials Due | No Broken Links | 4:30 PM | |
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