MCB II Syllabus. Spring 2020 PDF

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NEW YORK UNIVERSITY DEPARTMENT OF BIOLOGY  MOLECULAR AND CELL BIOLOGY II (BIOL-UA 22)  Course Syllabus — Spring 2020   Time: M  onday and Wednesday, 9:30 am – 10:45 pm Place: 1  9 West 4th Street, Room 101  Text: Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A and Scott MP. Molecular Cell Biology, either the 7th or 8th editions are fine. New York: W. H. Freeman and Company.  Instructors: Professor Lionel Christiaen, [email protected] Professor Carlos Carmona-Fontaine, [email protected]  Teaching Assistants: Joseph Koussa (coordinator) Dylan Iannitelli Jeremy Garcia  Welcome to Molecular and Cell Biology II. Our objective is to give you a firm and rigorous foundation in the principles of modern molecular and cellular biology. These concepts form the basis for the great advances now being made in biology and the medical sciences. In this second part of the course, we will discuss the fundamental processes that enable cells to grow, move, and communicate. The processes underlying tissue formation and cell death will also be introduced.  This document presents the course policies and schedule. Any updates will be posted to NYU Classes.  COURSEWORK AND POLICIES Exams There will be two midterm examinations and a final examination. Midterm 1 covers material through Meeting 9. Midterm 2 covers material through Meeting 17; it primarily covers material after Meeting 9 but is cumulative in the sense that you are expected not to forget fundamentals learned in the first part of the course. The final exam is cumulative; questions cover the entire course, with a slight emphasis on material after Meeting 17.

No notes, books or other materials will be allowed during the testing periods unless stated otherwise. ALL EXAMS ARE MANDATORY. If you have a schedule conflict involving other courses, religious observance, or personal matters, you MUST talk to Prof. Christiaen or Prof. Carmona-Fontaine at least ONE WEEK PRIOR TO THE EXAM. Policy on missed exams: Documents accepted if you miss an exam: -

Note from doctor Note from health center Note from wellness center Note from your academic advisor

You must present any of these documents to Joseph Koussa, Prof. Christiaen or Prof. Carmona-Fontaine the day after the exam or earlier. At the same time, you must contact Joseph Koussa to schedule a makeover exam. Makeovers will be scheduled for all students at the same time and will be about a week after the missed exam, most likely the following Friday at the same time as the exam this is subject to change. I t is your responsibility to contact Joseph Koussa, to find out the makeup exam’s exact date and to make sure you take the makeup exam. If you do not take the makeup exam, you will be marked with the average grade of the class on that exam or with the weighted average from your other two exams, whichever  is lowest. If you miss two makeup exams, this rule applies only to the first one and you will get a zero for the second exam. There will be no exceptions to this rule unless in extremely extenuating circumstances. In these extraordinary instances, we will require an official document from your doctor or from your academic advisor explicitly stating that you cannot (or could not) take both exams on the scheduled dates. We reserve the right to decide on these cases and excuses will be accepted only in extraordinary cases. In these rare cases, we will seek solutions on a case-by-case basis. Exam re-grading: If you are sure there is a mistake in how your exams were evaluated, you can request a regrade. Keep in mind that this process can also result in lowering your grade if the re-evaluation committee actually considers you deserve less points than originally received. If you want to ask for a regrade you must send  an email to Joseph Koussa within a week after receiving your marked exam. In this email you must include: 1) a scan of the page(s) in question and 2) a brief paragraph explaining why you consider you need a re-mark. Emails to other TAs, instructors, or without these two elements may be ignored. We will not consider re-grade requests outside of this one week time window.   

 Academic Integrity The professors instructing this course will not tolerate cheating or plagiarism. When academic dishonesty is suspected, it will be dealt with seriously in adherence to the official guidelines of New York University. The College of Arts & Science guidelines, which all students should read, are available online at http://cas.nyu.edu/page/ug.academicintegrity  Prerequisites You must have taken Molecular and Cellular Biology I (BIOL-UA 21) to register for this class.  Calculation of Final Grades The final course grades will be calculated as follows:  Midterm Exam I 25% Midterm Exam II  25% Final Exam 30% Recitation Participation 5% Recitation Paper 10% Recitation Presentation 5% Total 100%  Letter Grades After each midterm exam, the full distribution of scores for the entire class will be posted on NYU Classes. An indication will also be given of what score ranges would correspond to what letter grades, if that exam were representative of the student’s performance in the whole course. When the final course grade is calculated, it is the numerical scores (not the letter grades) that get combined and converted into a single letter grade for the entire course.  Class attendance and recording Class attendance is mandatory. I t is important to understand that meetings often present subject matter that is not introduced in the text. It therefore behooves you to attend class. To facilitate studying for exams we will do our best to record all classes. However, sometimes there may be unanticipated technical issues. Remember that these recordings are provided as a courtesy as an additional help, and should not be regarded as a substitute to attending class.  Reading Assignments The schedule of class meetings and associated readings are on the following pages. Reading assignments should be completed prior to each meeting. Readings not from the text will be linked on NYU Classes. Any changes to the readings or lecture schedule will be on NYU Classes as well.

NOTE:  Assigned  reading  should  be completed  prior to the  meeting.  A  s  the  meetings often present subject matter that is not introduced in the book, you must attend class!  Office Hours Office hours are to be used to ask specific questions about course material. Each instructor will explain office hour policies during their first lecture. As a general rule, office visits should be no longer than 15 minutes, which will allow other students to have access to the instructor. You should prepare for the meeting by making a list of specific questions. Those questions should be about the scientific content of the course, and not about what material will appear on an exam. If you need additional help, you will need to make an appointment with the instructor outside of office hours or to obtain a tutor. Tutoring is available through the University Learning Center: http://learning.cas.nyu.edu/  Recitations Contrary to the popular image of the lonely scientist toiling away in isolation, science is a collective activity that depends on the sharing of ideas. During recitation, you will discuss concepts learned in lecture, work in groups and solve problems. You will receive a grade for recitation based on participation and ability. Material from recitation may also appear on exams. DO NOT change your recitation section unless you do so officially in Albert. If you must attend another class for some personal reason, you MUST clear it with your section leader. A  ttendance to recitations is mandatory.  Accommodations for Students with Disabilities Academic accommodations are available to students with disabilities. Students should please register with the Moses Center for Students with Disabilities (http://www.nyu.edu/csd, 212-998-4980, [email protected]) as early as possible in the semester. Diversity and Inclusion The instructors of this course share NYU's commitment to “building a culture that respects and embraces diversity, inclusion, and equity” (see https://www.nyu.edu/life/diversity-nyu.html). We aim to create a learning environment in which every student feels included, supported, and respected. We will hold students (and ourselves) to the CAS Honor Code's pledge to "behave with decorum and civility, and with respectful regard" for others.  

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I. Intracellular organization and cell metabolism  Meeting 1: Monday January 27, 2020 Introduction and an overview of the cell and the plasma membrane (Carmona-Fontaine)  7th edition: Ch. 1; pp. 4-15;  Ch. 2; pp. 33-42; Ch. 9 Cell Organelles; pp. 424-430, Ch. 10; pp. 445-455.  8th edition: Ch. 1; pp. 5-19; Ch. 2; pp. 41-51; Ch. 4 Cell Organelles; pp. 161-164, Ch. 7; pp. 271-284.  Meeting 2: Wednesday January 29, 2020 An overview of membrane-bound proteins (Carmona-Fontaine)  7th edition: Chapter 10; membrane proteins; pp. 455–462;  8th edition: Chapter 7; membrane proteins; pp. 284–293;  Meeting 3: Monday February 3, 2020 Metabolism I: Photosynthesis (Carmona-Fontaine)  7th  edition:  Chapter  12  Photosynthesis,  Photosystems,  CO2  Metabolism during Photosynthesis; pp. 552-577  8th  edition:  Chapter  12  Photosynthesis,  Photosystems,  CO2  Metabolism during Photosynthesis; pp. 560-583  Meeting 4: Wednesday February 5, 2020 Metabolism II: Glycolysis (Carmona-Fontaine)  7th edition: Chapter 12 Glycolysis and the Citric Acid (aka Krebs) Cycle pp. 519–531  8th edition: Chapter 12 Glycolysis and the Citric Acid (aka Krebs) Cycle pp. 515–539  Meeting 5: Monday February 10, 2020 Metabolism III: Oxidative Phosphorylation and the Synthesis of ATP (Carmona-Fontaine)  7th edition: Chapter 12 Electron Transport Chain & Generation of the Proton-motive Force; pp. 532–552  8th edition: Chapter 12 Electron Transport Chain & Generation of the Proton-motive Force; pp. 539–560 

II. Cell trafficking, cytoskeleton, and cell movement  Meeting 6: Wednesday February 12, 2020 Cell  Compartments  I:  Synthesis  of  Secretory  and  Membrane-Bound  Proteins (Carmona-Fontaine)  7th edition: Chapter 13 Translocation and insertion of protein in ER Membrane;  pp.  577-592  8th edition: Chapter 13 Translocation and insertion of protein in ER Membrane;  pp.  583-601

 February 17, 2020 President's Day - NO CLASS  Meeting 7: Wednesday February 19, 2020 Cell  Compartments:  Vesicle  trafficking  and  introduction  to  the  secretory  pathway (Carmona-Fontaine)  7th edition: Chapter 14 Early Secretory Pathway & Vesicular Traffic; pp. 627-640  8th edition: Chapter 14 Early Secretory Pathway & Vesicular Traffic; pp. 631-645  Meeting 8: Monday February 24, 2020 Cell Compartments V: Early and Late stages of the secretory pathway (Carmona-Fontaine)  7th edition: Chapter 14 Early and late Stages of the Secretory Pathway; pp. 640-654  th  8 edition: Chapter 14 Early and late Stages of the Secretory Pathway; pp. 645-659  Meeting 9: Wednesday February 26, 2020 Cell Compartments VI: Endocytosis and lysosome targeting (Carmona-Fontaine)  7th edition: Chapter 14; pp. 654-664  8th edition: Chapter 14; pp. 659-673  Meeting 10: Monday March 2, 2020 Membrane  proteins,  Transport  and  Function  I  &  II:  Uniporters,  symporters  and  ATPase (Desplan)  7th edition: Chapter 11.1-11.3 Transmembrane Transport; pp. 473-494  8th edition: Chapter 11.1-11.3 Transmembrane Transport; pp. 473-494  Meeting 11: Wednesday March 4, 2020 Membrane Transport and Function III: The Resting Membrane Potential (Desplan)  7th edition: Chapter 11.4 The resting membrane potential. Pp 495-501  Chapter 22.1 Neurons and glia pp 1019-1023  8th edition: Chapter 11.4 The resting membrane potential. Pp 495-501  Chapter 22.1 Neurons and glia pp 1025-1033  Review Session Wed 4, 6:00 pm - 8:00 pm (Location and data TBA)  Midterm Evaluation I (Meetings 1-9) Date: Friday March 6, 2019, 2:00 pm–4:00 pm Room: TBA   

  Meeting 12: Monday March 9, 2020 Membrane  Transport  and  Function  IV:  Electrical  Signaling  and  Regulation  of  Channels (Desplan)  7th edition: Chapter 22.2 Voltage-gated ion channels; pp. 1025-1033  8th edition: Chapter 22.2 Voltage-gated ion channels; pp. 1034-1047  Meeting 13: Wednesday March 11, 2020 Membrane Transport and Function V: Propagation of action potential, The Synapse (Desplan)  7th edition: Chapter 22.3 Communication at Synapses; pp. 1036-1045  8th edition: Chapter 22.3 Communication at Synapses; pp. 1048-1060  March 16, 2020 Spring Recess NO CLASS March 18, 2020 Spring Recess NO CLASS  Meeting 14: Monday March 23, 2020 Cell Compartments II: Compartmental Targeting of Proteins  to  Mitochondria,  Chloroplasts, Peroxisomes, and the Nucleus (Christiaen)  7th edition:  Chapter  13  Protein Modifications, Folding,  and  Quality Control  in the ER; pp. 594-600;  Sorting  of  Proteins  to  Mitochondria  and  Chloroplasts;  pp.  601–610. Sorting Peroxisomal Proteins; pp. 612–613  8th edition:  Chapter  13  Protein Modifications, Folding,  and  Quality Control  in the ER; pp. 601-608;  Sorting  of  Proteins  to  Mitochondria  and  Chloroplasts;  pp.  608–619. Sorting Peroxisomal Proteins; pp. 619–622  Meeting 15: Wednesday March 25, 2020 Cell Compartments III: Nuclear transport. Lipid Synthesis and Traffic (Christiaen)  7th edition: Chapter 10 Phospholipids, Sphingolipids, and Cholesterol pp. 464-468  Chapter 13 Transport into and out of the Nucleus; pp. 615-619  8th edition: Chapter 7 Phospholipids, Sphingolipids, and Cholesterol pp. 293-301  Chapter 13 Transport into and out of the Nucleus; pp. 622-630

 III. Membrane transport and cell communication  Meeting 16: Monday March 30, 2020 Cytoskeleton I: Actin and Myosin (Christiaen)  7th edition: Chapter 17 Microfilaments and Actin Structures; pp. 776–778  Dynamics  of  Actin  Filaments;  pp.  779–783,  Mechanisms  of  Actin  Filament  Assembly; pp.784–789,  Myosins: Actin-based Motor Proteins; pp. 793–799  8th edition: Chapter 17 Microfilaments and Actin Structures; pp. 778–781

 Dynamics  of  Actin  Filaments;  pp.  781–786,  Mechanisms  of  Actin  Filament  Assembly; pp.786–793,  Myosins: Actin-based Motor Proteins; pp. 796–803  Meeting 17: Wednesday April 1, 2020 Cytoskeleton II: Microtubules and Intermediate Filaments (Christiaen)  7th  edition:  Chapter  18  Microtubule  Structure  and  Dynamics,  Kinesins  and  Dyneins;pp. 821–842  Intermediate Filaments; pp. 860–863   8thedition: Chapter 18  Microtubule Structure and Dynamics, Kinesins  and  Dyneins; pp. 821–842  Intermediate Filaments; pp. 861–866    Meeting 18: Monday April 6, 2020 Cell-Cell Adhesion and the Extracellular Matrix (Christiaen)  7th edition: Chapter 20.1-2 Cell-Cell and Cell-Matrix Adhesion pp 925-944. Chapter 20.3 Basal lamina pp. 945-950.  Chapter  20-4  Connective  tissue  pp  951-960 Chapter 20.5 Adhesive  interactions pp. 961-965  8th edition: Chapter 20.1-2 Cell-Cell and Cell-Matrix Adhesion pp 921-944. Chapter 20.3 Basal lamina pp. 945-950.  Chapter  20-4  Connective  tissue  pp  951-960 Chapter 20.5 Adhesive  interactions pp. 961-967  Meeting 19: Wednesday April 8, 2020 Cell polarity and migration (Christiaen)  7th edition: Chapter 17 Cell migration pp. 801-814  8th edition: Chapter 17 Cell migration pp. 803-820  Review session Midterm II XXX, 6:00 pm - 8:00 pm (Location and date TBA)  IV. Biochemical control of cell differentiation, division and communication  Meeting 20: Monday April 13, 2020 The Cell Cycle (Carmona-Fontaine)  7th edition: Chapter 19 Control of Mitosis by Cyclins and MPF; pp. 873–912  8th edition: Chapter 19 Control of Mitosis by Cyclins and MPF; pp. 873–910   Meeting 21: Wednesday April 15, 2020 Cell Death (Carmona-Fontaine)

Mid-April: Review Session   Midterm Evaluation II (Meetings 10-19) Date: Friday April 17th, 2019, 2:00 pm–4:00 pm Room: TBA  Meeting 22: Monday April 20, 2020  Cancer and the Tumor Microenvironment (Carmona-Fontaine)  7th edition: Chapter 24  8th edition: Chapter 24  Meeting 23: Wednesday April 22, 2020 Cellular Communication I: Introduction to cell signaling (Christiaen)  7th edition: Chapter 15.1  Signal transduction pp. 675-680, Chapter 15-2 Cell-surface Receptors; pp. 681-686  8th edition: Chapter 15.1  Signal transduction pp. 673-680, Chapter 15-2 Cell-surface Receptors; pp. 681-686  Meeting 24: Monday April 27, 2020 Cellular Communication II: G Protein-coupled Receptors (Christiaen)  7th edition: Chapter 15.3-6. G Protein-coupled Receptors; pp. 687-718  8th edition: Chapter 15.3-6. G Protein-coupled Receptors; pp. 686-718  Meeting 25: Wednesday April 29, 2020 Cellular Communication III: Extracellular control of gene expression I (Christiaen)  8th edition: Chapter 16.1-4, pp 719-748.   Meeting 26: Monday May 4, 2020 Cellular Communication IV: Extracellular control of gene expression II (Christiaen) 8th edition: Chapter 16.5-8, pp 748-772.   Meeting 27: Wednesday May 6, 2020  Cellular Communication V: TGFβ Morphogens and Cell Fate (Christiaen)  7th edition: Chapter 16.4 Receptor Serine Kinases, TGFβ Receptors; pp. 748-752  8th edition: Chapter 16.1 Receptor Serine Kinases, TGFβ Receptors; pp. 722-725  Meeting 28: Monday May 11, 2020 Optogenetics and synthetic cell biology (Christiaen)   FINAL EXAMINATION

(Meetings 1-28) Thurs May 14th 12pm-1:50pm Location: TBA...