course: biol 401 instructor: dr. alison crowe 426a hitchcock hall 616.6945

Course: Biol 401Instructor: Dr. Alison Crowe

426A Hitchcock Hall616.6945acrowe@u.washington.edu

Office Hours: Wed 4:30-5:30 PMHCK 426Aor by arrangement

Teaching Assistant: Qing Feng qingf@u.washington.edu Office Hours: TBA

NOTE: CHANGE OF ROOM FOR AB TO LOW 216

Required Text: Lodish et al., 2013, 7th edition, Molecular Cell Biology

Required Course Manual: Professional Copy’n Print4200 Univ. Way NE

Course website: http://mesh.biology.washington.edu/biol401-spr13/index.html

You will need the following info to accessthe readings folder on the course website:

Login: biol401 Password: cell

Schedule in course manual: Topics, Assignments, Due datesImportant dates:

Midterm: April 30 10:30-11:20 AM MGH 231Final: June 10:30AM-12:20 PM MGH 231

Discussion sections are mandatory

Readings: To be completed each week BEFORE lectureand discussion sections

This week: How we study cells & protein trafficking

Overview of cell biology approaches: Chp 1.2 p. 10-15 (Fig. 1-13, 1-14)Gene and protein tagging: Chp 5 pp. 203-205 (Fig. 5-34)Organelles of the eukaryotic cell: Chp. 9 pp. 424-427 (Fig. 9-32) Overview protein trafficking: Chp. 13 p. 577-579 (Fig. 13-1)

Individual PointsDiagnostic Test 3W.A. #1 - nuclear transport I 15* W.A. #2 – nuclear transport II 10W.A. #3 – critical analysis 10W.A. #4 – figure analysis 5MCQ answers 5Practice Midterm 5 Midterm Exam 60Final Exam 90 pts

Subtotal 203 pts (70%)

POINTS AVAILABLE IN CLASS

* Due in Lecture Next Week

Group PointsReading Quiz #1 (group) 5Reading Quiz #2 (group) 5Nuclear Transport Experiment 5Group presentation of figures 10 W.A. # 5 – Critical Analysis 20 pts

Subtotal 45 pts (16%)

Group Participation ScoreGroup Assessment #1 20Group Assessment #2 20 pts

Subtotal 40 pts (14%)

Total 288 pts*Access your scores on course web page: “scores” link on left-hand menu

Learning Goals for Course:• Evaluate the relative merit of using a particular molecular technique to address a specific research question • Interpret cellular and molecular data (e.g. gels, graphs)• Predict outcomes of future experiments based on existing data• Develop new hypotheses and design experiments to test those hypotheses• Draw a model for a molecular process based on existing data• Recognize assumptions inherent in a given molecular model• Evaluate the merits of a scientific study•Communicate scientific ideas and/or interpretations articulately, both in writing and orally.

Expertise

Imag

inat

ion

John Bransford

Routineexperts

Rudderlesslearners

Adaptiveexpertssynthesis

evaluation

application

analysis

knowledge comprehension

How People Learn

Course Outline•Protein Trafficking

•Nuclear transport•Nuclear environment

•Nuclear pore structure•Spatial and dynamic organization of nucleus

•Eukaryotic transcription regulation• Epigenetic regulation• Cell memory• Cell specialization

• Embryonic Stem Cells• Epigenetic modifications during differentiation• Maintenance of pluripotency

Review organelles in readings: know primary function of cell organelles

Fig. 1-11, 1-12. Lodish et al. 2013

What are the advantages and challenges of eukaryoticand prokaryotic cells?

To understand how genes are regulated, need to understand the nuclear environment: structure, spatial organization

Know these Terms:Nuclear envelope (NE)Nuclear pore complex (NPC)Nuclear laminaNucleolusChromatin (heterochromatin and euchromatin)

Protein Sorting Animation

Overview of Protein Trafficking

Signal sequences on proteins target them to locations within the cell

Protein Trafficking Workshop

You have the following tools:A cell into which you can introduce (tranfect) DNAA DNA plasmid into which you can clone any gene you likeA fluorescent-labeled antibody to any protein you want to detectA piece of double-stranded DNA encoding a potential mitochondrial signal sequence 

Signal Sequences Have Been Identified Which Target Proteins to Locations Within the Cell