SONOMA STATE UNIVERSITY DEPARTMENT OF BIOLOGY BIOLOGY 344: CELL BIOLOGY Fall 2013

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1 SONOMA STATE UNIVERSITY DEPARTMENT OF BIOLOGY BIOLOGY 344: CELL BIOLOGY Fall 2013 Instructor Murali C. Pillai, PhD Office 214 Darwin Hall Telephone (707) Website Office Hours Tues & Fri. 10:00 AM 11:30 AM Lecture Mon. & Wed. 1:00 PM 2:15 PM, DARWIN HALL- ROOM 38 Laboratory DARWIN HALL- ROOM 204 SECTION 1: Mon. 2:25 PM - 5:15 PM SECTION 2: Wed. 2:25 PM - 5:15 PM Course goals and objectives: An introduction to structural and molecular organization of eukaryotic cells and tissues. Specific topics will represent the central core of modern cell biology and are concerned mainly with those properties that are common to most eukaryotic cells. These include membrane structure and function, intracellular compartments and protein sorting, protein trafficking, cell signaling, structure and dynamics of cytoskeletal elements, molecular mechanisms of cell division and, extracellular matrix molecules and their roles in cell functions. Laboratory experience involving modern cell biological techniques are designed to demonstrate lecture concepts. Text Book: Molecular Biology of the Cell, Bruce Alberts et al., 5 th ed., Garland Science, NY. For the lab portion of the course, a Lab Manual needs to be purchased. Examinations: There will be two (2) lecture midterm exams, two (2) laboratory exams and a cumulative final exam. SOME IMPORTANT ACTIVITIES AND DATES DATE ACTIVITY POINTS Sept. 23 First Lecture Midterm Examination 100 Oct. 09/14 First Laboratory Examination 40 Oct. 09/14 Laboratory Notebook Due 20 Oct. 23 Second Lecture Midterm Examination 100 Nov. 25 Library Research Report Due 25 Dec. 02/04 Second Laboratory Examination 40 Dec. 02/04 Laboratory Notebook Due 20 Dec. 11 Cumulative Final Examination 100 TOTAL POINTS 445 1

2 Library Research Report: As part of the laboratory portion of the course, you are required to prepare and submit a Library Research Report. This report is due no later than November 25, :00 PM (PST), and it is worth a maximum of 25 points. Late and/or electronic submissions will not be accepted. For details of this assignment, please see the Lab Manual. Optional Review Paper: For 10 bonus points, you may submit a review paper on a specific topic of your interest in contemporary cell biology. The paper should be 4 pages long (type-written, double spaced), and represent a thorough review of recent literature published during the last 2 years on the topic you choose. If you choose to do this assignment for bonus points, AT LEAST BY Friday, Nov. 15 th, you must meet with your instructor during his office hours for approval of the review topic and for specific instructions on how to organize the paper- no exceptions!- And this approval process cannot be done via . The paper is due no later than Friday, December 6 th 11:00 AM (PST)- early submission is encouraged so that it won t conflict with other assignments due around that time. Late and/or electronic submissions will not be accepted. Grading: Your final course grade will be determined based on the total number of points earned. It is expected that letter grades will be assigned on the basis of the following scale: 90 % and above: A (A _, A): %: B (B _, B, B + ) %: C (C _, C, C + ) %: D (D _, D, D + ) Less than 60%: Regarding Exams: If you have questions and concerns regarding your answers on exams, they must be submitted to the instructor in writing within one week after receiving the graded exam. Upon your written request, the entire exam may be re-graded. Attendance and "serious/active participation" in lecture and lab are strongly encouraged since history has shown a strong correlation with course grade. Unexcused absence from the lab will cost you 5 points! Poor attendance at lecture can result in deduction of points from your test scores. Late arrivals and early departures from lecture or lab for no documented reasons will be counted as absence. Late arriving students disrupt the class, so do those who leave early!! Late students will not be given extra time to complete tests. Learning Disabilities: If you have a learning disability and may have need for some type of accommodation(s) in order to participate fully in this class, please feel free to discuss your concerns in private with me AND BE SURE TO CONTACT the SSU Disability Student Services office. As a student at Sonoma State University, it is important that you know the policies and procedures that affect you. These policies and procedures, approved by the SSU Academic Senate and the President, may be found at the following web sites. Add/Drop Policy Cheating and Plagiarism Policy Grade Appeal Policy Access to Programs for Students with Disabilities Policy Diversity Statement 2

3 COURSE OUTLINE Date: Lecture Topic Reading Aug. 21 Introduction to Course Plasma Membrane Structure and Properties Chapter The Lipid Bilayer: Properties and Dynamics 28 Membrane Proteins: Structure and Properties Sept. 02 Labor Day: No Class 04 Membrane Proteins: Carbohydrate Interaction Intracellular Compartments and Protein Sorting Chapter Compartmentalization of Cells 11 Transport of Molecules Between Cytosol and Nucleus 16 Transport of Molecules into Mitochondria and Chloroplast 18 Endoplasmic Reticulum and Protein Integration 23 FIRST MIDTERM EXAMINATION (100 PTS.) Intracellular Vesicular Traffic Chapter Molecular Mechanism of Membrane Transport 30 Transport from the ER Through the Golgi Apparatus Oct. 02 Transport from the Trans Golgi Network to Lysosomes 07 Endocytosis and Exocytosis Date: Lecture Topic Reading Cell-Cell Communication Chapter General Principles of Cell Communication 14 Cell Surface Receptors and Cell Communication 16 Signaling via G-protein Linked Cell Surface Receptors. 21 Intracellular Ca ++ Oscillations: Membrane Lipid Messengers 3

4 23 SECOND MIDTERM EXAMINATION (100 PTS.) The Cytoskeleton Chapter Nature and Dynamics of Cytoskeletal Elements 30 Microtubule and Microtubule Dynamics Nov. 04 Cytoskeleton and Cell Behavior The Mechanics of Cell Division Chapter An Overview of Cell Cycle/ M-phase 11 Veterans Day Observed: No Class 13 Mitosis: Molecular Regulators 18 Cytokinesis in Plants and Animals Cell Junctions, Cell Adhesions and Extra-cellular Matrix Chapter Cell Junctions: Structure and General Functions 25 Cell-Cell Adhesion: Molecular Mechanisms 27 Thanksgiving Holiday: No Class Dec. 02 Extra-Cellular Matrix Molecules and Cell Functions 04 Tissue Formation: General Principles and Mechanisms 11 CUMULATIVE FINAL EXAMINATION (100 PTS.): 2:00 PM - 3:50 PM 4

5 TENTATIVE LABORATORY SCHEDULE: [MONDAY GROUP] WEEK WEEK 1 [AUG. 26] WEEK 2 [SEPT. 02] WEEK 3 [SEPT. 09] WEEK 4 [SEPT. 16] WEEK 5 [SEPT. 23] WEEK 6 [SEPT. 30] WEEK 7 [OCT. 07] WEEK 8 [OCT. 14] LABORATORY ACTIVITY Laboratory Orientation and Preparation for SDS-PAGE The Do s and Don ts in the lab- Discussion of Lab Safety Discussion of various laboratory techniques used for the study of cell biology Discussion of how to prepare lab notebook and library research report LABOR DAY HOLIDAY: NO LAB SDS-PAGE for Protein Electroelution: Review of the theory and principles of protein electrophoresis (SDS-PAGE). Preparation of SDS-PAGE samples for Protein Electroelution Protein Electroelution-I applications of protein electroelution Preparation for electroelution of proteins Set up Protein Electroelution Protein Electroelution-II Completion of protein electroelution SDS-PAGE analysis of electroeluted protein(s) Coomassie brilliant blue staining of electro-eluted polypeptides and molecular weight estimation Light and Electron Microscopic Techniques Review and discussion of light (Biol. 123) and electron microscopic (SEM and TEM) techniques. Identification of cellular organelles and structures at the ultrastructural (TEM) level Cellular Fractionation Review and discussion of density gradient centrifugation Preparation of HEK 293T or HeLa cells for cellular fractionation Preparation of nuclear, mitochondrial, cytosolic and membrane fractions Histochemical staining and examination of isolated fractions Preparation of cytosolic and nuclear fractions for SDS- PAGE FIRST LABORATORY EXAM (40 PTS.) SUBMIT LAB NOTEBOOK (20 PTS.) 5

6 WEEK 9 [OCT. 21] WEEK 10 [OCT. 28] WEEK 11 [NOV. 04] WEEK 12 [NOV. 11] WEEK 13 [NOV. 18] WEEK 14 [NOV. 25] WEEK 15 [DEC. 02] Western Blotting and Immunostaining-I Demonstration of Western blotting Electrophoresis AND Western blotting of HEK 293T/HeLa cell lysate polypeptides. Detection of polypeptides on Western blots by Ponceau-S staining Western Blotting and Immunostaining-II applications of Western blotting Immunodetection of polypeptides on Western blots and its digital imaging (NIH 3T6) -I Review of fluorescence (Biol. 123) and confocal microscopy. Anti-tubulin staining of mouse embryonic fibroblasts, fixation, blocking and antibody treatments applications of indirect immunofluorescent staining cells and tissues VETERANS DAY OBSERVED: NO LAB (NIH 3T6)-II Preparation of permanent slides of stained cells Epifluorescence and/or Confocal Imaging of Immunostained Cells [refer to the schedule] Cytoplasmic Streaming and Amoeboid Motion Studies of cytoplasmic streaming and contraction. Effect of cytoskeletal drugs in cytoplasmic streaming. SECOND LABORATORY EXAM (40 PTS.) SUBMIT LAB NOTEBOOK (20 PTS.) 6

7 TENTATIVE LABORATORY SCHEDULE: [WEDNESDAY GROUP] WEEK WEEK 1 (AUG. 21) WEEK 2 [AUG. 28] WEEK 3 [SEPT. 04] WEEK 4 [SEPT. 11] WEEK 5 [SEPT. 18] WEEK 6 [SEPT. 25] WEEK 7 [OCT. 02] WEEK 8 [OCT. 09] LABORATORY ACTIVITY NO LAB Laboratory Orientation and Preparation for SDS-PAGE The Do s and Don ts in the lab- Discussion of Lab Safety Discussion of various laboratory techniques used for the study of cell biology Discussion of how to prepare lab notebook and library research report SDS-PAGE for Protein Electroelution: Review of the theory and principles of protein electrophoresis (SDS-PAGE). Preparation of SDS-PAGE samples for Protein Electroelution Protein Electroelution-I applications of protein electroelution Preparation for electroelution of proteins Set up Protein Electroelution Protein Electroelution-II Completion of protein electroelution SDS-PAGE analysis of electroeluted protein(s) Coomassie brilliant blue staining of electro-eluted polypeptides and molecular weight estimation Light and Electron Microscopic Techniques Review and discussion of light (Biol. 123) and electron microscopic (SEM and TEM) techniques. Identification of cellular organelles and structures at the ultrastructural (TEM) level Cellular Fractionation Review and discussion of density gradient centrifugation Preparation of HEK 293T or HeLa cells for cellular fractionation Preparation of nuclear, mitochondrial, cytosolic and membrane fractions Histochemical staining and examination of isolated fractions Preparation of cytosolic and nuclear fractions for SDS-PAGE FIRST LABORATORY EXAM (40 PTS.) SUBMIT LAB NOTEBOOK (20 PTS.) 7

8 WEEK 9 [OCT. 16] WEEK 10 [OCT. 23] WEEK 11 [OCT. 30] WEEK 12 [NOV. 06] WEEK 13 [NOV. 13] WEEK 14 [NOV. 20] WEEK 15 [NOV. 27] WEEK 16 [DEC. 04] Western Blotting and Immunostaining-I Demonstration of Western blotting Electrophoresis AND Western blotting of HEK 293T/HeLa cell lysate polypeptides. Detection of polypeptides on Western blots by Ponceau-S staining Western Blotting and Immunostaining-II applications of Western blotting Immunodetection of polypeptides on Western blots and its digital imaging (NIH 3T6) -I Review of fluorescence (Biol. 123) and confocal microscopy. Anti-tubulin staining of mouse embryonic fibroblasts, fixation, blocking and antibody treatments applications of indirect immunofluorescent staining cells and tissues (NIH 3T6)-II Preparation of permanent slides of stained cells Epifluorescence and/or Confocal Imaging of Immunostained Cells [refer to the schedule] (NIH 3T6)-II- CONTD.. Epifluorescence and/or Confocal Imaging of Immunostained Cells [refer to the schedule] Cytoplasmic Streaming and Amoeboid Motion Studies of cytoplasmic streaming and contraction. Effect of cytoskeletal drugs in cytoplasmic streaming. THANKSGIVING HOLIDAY: NO LAB SECOND LABORATORY EXAM (40 PTS.) SUBMIT LAB NOTEBOOK (20 PTS.) 8

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