Instructor: Dr. Alison Crowe 426A Hitchcock Hall 616.6945 Course: Biol 401 Instructor: Dr. Alison Crowe 426A Hitchcock Hall 616.6945 acrowe@u.washington.edu Office Hours: Wed 4:30-5:30 PM HCK 426A or by arrangement Teaching Assistant: Qing Feng qingf@u.washington.edu Office Hours: TBA NOTE: CHANGE OF ROOM FOR AB TO LOW 216 Loew Hall

You will need the following info to access Required Text: Lodish et al., 2013, 7th edition, Molecular Cell Biology Required Course Manual: Professional Copy’n Print 4200 Univ. Way NE Course website: http://mesh.biology.washington.edu/biol401-spr13/index.html You will need the following info to access the readings folder on the course website: Login: biol401 Password: cell New web site

Schedule in course manual: Topics, Assignments, Due dates Important dates: Midterm: April 30 10:30-11:20 AM MGH 231 Final: June 10:30AM-12:20 PM MGH 231 Discussion sections are mandatory Readings: To be completed each week BEFORE lecture and 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)

W.A. #1 - nuclear transport I 15* W.A. #2 – nuclear transport II 10 POINTS AVAILABLE IN CLASS Individual Points Diagnostic Test 3 W.A. #1 - nuclear transport I 15* W.A. #2 – nuclear transport II 10 W.A. #3 – critical analysis 10 W.A. #4 – figure analysis 5 MCQ answers 5 Practice Midterm 5 Midterm Exam 60 Final Exam 90 pts Subtotal 203 pts (70%) WA#1 based on this week’s discussion, due in lecture next week * Due in Lecture Next Week

Group Points Reading Quiz #1 (group) 5 Reading Quiz #2 (group) 5 Nuclear Transport Experiment 5 Group presentation of figures 10 W.A. # 5 – Critical Analysis 20 pts Subtotal 45 pts (16%) Group Participation Score Group Assessment #1 20 Group 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.

How People Learn Imagination Expertise Rudderless learners Adaptive experts synthesis evaluation analysis Imagination application knowledge comprehension Routine experts Expertise John Bransford

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

What are the advantages and challenges of eukaryotic and prokaryotic cells? Review organelles in readings: know primary function of cell organelles Fig. 1-11, 1-12. Lodish et al. 2013

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 lamina Nucleolus Chromatin (heterochromatin and euchromatin)

Overview of Protein Trafficking Signal sequences on proteins target them to locations within the cell Protein Sorting Animation

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

Signal Sequences Have Been Identified Which Target Proteins to Locations Within the Cell Ended here – asked students to think about location of signal sequence when designing an experiment Start next lecture: What conclusion could you draw from this experiment? Use the word SUFFICIENT