BIOL 263: Molecular Biology and Genomics
Fall Semester 2013
August 12, 2013
Syllabus under construction.
(Latest update overrides all previous versions, electronic and print.)
MWF 10:10 AM-11:00 AM (Period 3)
Tomsich Hall, room 101
Dr. Wade Powell
FSH 202, PBX 5396
powellw[a]kenyon.edu
Office hours:
(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., (2014) Molecular Biology of the Gene, 7th 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 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 if they support Java (i.e. not ipads or iphones). Please pay attention to the syallabus 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. 6.
- Participation and preparation: 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 innacuracies, etc. at any time during class.
- Electronic device policy: Full participation in class activities is crucial for success. Electronic devices can enhance particiatipation, but they can also become a distraction. Texting, phone calls, social media, and unrelated web surfing are not appropriate. Note taking, calculations, and accessing relevant databases are encouraged on your laptop, tablet, or smart phone.
- 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 only 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% 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 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 can be given in class (announced or unannounced) or as take-home assignments. 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. 12. The final version, with zero broken links, is due December 18 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 | Technical Notes |
Part I: Molecular Interactions |
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| F | Aug 30 |
Course Introduction. DNA intro; B-DNA; A-RNA |
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| M | Sept 2 |
Weak bonds. Amino Acids; CAP; FAB; Ident | Watson Ch 3; Ch 5, pp. 71-74 | ||
| W | Sept 4 |
Adv DNA; Z-DNA ; Triplex; Quad; base tautomers; supercoiling; Topo | Watson Ch 6 | ||
| F | Sept 6 |
AA2 in proteins. | Ch 5 p 73-93; | ||
| M | 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;n`1 more advanced X-Ray (local version); another explanation (pdf). |
||
| W | 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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| F | Sept 13 |
Transcription initiation Structures: RNAP open complex; RnaPol-Euk; movies! |
Watson Ch 12, pp. 377-391; | ||
| M | Sept 16 |
Transcription Elongation; transcriptional road blocks |
Epshtein & Nudler 2003 Watson Ch. 12, pp. 391-396; |
Electrophoresis: Watson Ch 21, pp. 740-1. DNA footprinting: Watson Ch. 21, pp. 777-8 |
|
| W | Sept 18 |
Bacterial Gene Regulation at level of transcription initiation. CAP-CTD; Lac repressor; Benoff |
Watson Ch 16, pp. 547-567 | ||
| F | Sept 20 |
Regulation of intiation, cont'd; Regulation of events after initiation: Attenuation in E. coli. |
Watson Ch 18, pp.639-640; |
||
| M | Sept 23 |
Attenuation in Bacillus. TRAP-RNA; |
Antson 99; |
||
| W | 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 |
||
| F | Sept 27 |
Exam I (in class) Points to ponder for the exam. | |||
| M | 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: Watson Ch. 21, pp. 776-778; chromatography: Ch. 21, pp. 764-769. |
|
| W | Oct 2 |
Eukaryotic Transcriptional Regulation; Spec. TFs. Identify |
Watson Ch, 17, pp. 589-620 . | ||
| F | Oct 4 |
Eukaryotic Transcription, cont'd. | |||
| M | Oct 7 |
Eukaryotic Transcription Research: Promoter Clearance | Pal et al. 2005 | ||
| W | 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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| F | Oct 11 |
October Reading Days; No Class | |||
| M | Oct 14 |
Research in Eukaryotic Transcriptional Regulation: Histone acetyltransferase recruitment | Sharma 2002 |
ChIP:Watson Ch. 21, pp. 751-752; 778-780. Chromatin IP; cross-link chemistry PCR: Watson Ch. 21, pp. 751-752 Remember PCR? |
|
| W | Oct 16 |
Transcript Splicing; Splicing2; Spliceosome | Watson Ch. 13: pp. 415-425, 430-4346, 439 (bottom)-445. | Due date: JMol PDB Proposal | |
| F | Oct 18 |
Translation basics; initiation. Initiation. PDB; ribosome structural primer | Watson Ch. 14, pp. 457-487. | Family Weekend; Summer Science Poster Presentation | |
| M | Oct 21 |
Translation elongation, termination. | Watson Ch. 14. pp. 487-519. | ||
| W | Oct 23 |
Translation Research: ribosome hybrid state | Dorner et al. 2006 | ||
| F | Oct 25 |
Translation elongation, termination., cont'd | Watson Ch. 14. pp. 487-519. | ||
| M | Oct 28 |
RNA Interference Animation from Nature Reviews Genetics . |
Meister
04 (RNAi review paper) Watson Ch. 18 pp. 641-660 |
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| W | Oct 30 |
RNAi research | |||
Part III: DNA Replication, Repair, Recombination |
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| F | Nov 1 |
Exam II (points to ponder) | |||
| M | Nov 4 |
DNA Replication; Beta ring; DNA Rep; Replisome | Watson Ch. 8, pp. 195-238 |
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| T | Nov 5 |
Web Project Workshop, FSH 009, 7-10 PM | |||
| W | Nov 6 |
DNA Rep., cont'd.; |
Watson Ch. 8, pp. 195-238 | ||
| R | Nov 7 | Web Project Workshop, FSH 009, 7-10 PM | |||
| F | Nov 8 |
Mutation and repair. | Watson Ch. 9 | ||
| M | Nov 11 |
MutS; MutS-DNA; Figs. | Obmolova 00 | ||
| W | Nov 13 |
Recombination; Experiments; RuvA; PNAS; Tn;
|
Watson Ch. 10: pp. 283-310 and 314-316 | ||
| F | Nov 15 |
Knockout mice in molecular biology Knockout mice, cont'd
|
H19 Gene; Generation of Transgenic animals; MIT core facility |
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| M | Nov 18 |
Telomerase and telomeres. Telomerase structure. Telomeres 12-mer; 22-mer; Ten1, Stn1 | Watson Ch. 8 p. 247-254. |
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| W | Nov 20 |
Telomerase research: telomeres and cancer cell proliferation. | |||
Part IV: Genomic-scale molecular biology |
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| F | Nov 22 |
Sequencing: cycle; pyrosequencing (454); illumina video; another illumina video; cheap genomes | Watson Ch. 2, p. 39-40; Ch. 7, p. 133-138; Ch. 20, p. 703-715. | ||
| Nov. 23 - Dec. 1: Thanksgiving Break | |||||
| M | Dec 2 |
Intro to Microarrays; Gene Chip Manufacturing; Spotting arrays; RNAseq | Watson Ch. 19, p. 662 | ||
| W | Dec 4 |
Genomic scale gene expression research | Andreasen et al. 2006 | points to ponder | |
| F | Dec 6 |
Catch up | |||
| M | Dec 9 |
Exam III (points to ponder) | |||
| W | Dec 11 |
Student Project Presentations | . | Completed JMol Tutorial | |
| F | Dec 13 |
Student Project Presentations | . |
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| W | Dec 18 |
Revised JMol Tutorials Due | No Broken Links | 4:30 PM | |
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