NEW YORK UNIVERSITY 

DEPARTMENT OF BIOLOGY 
  
MOLECULAR AND CELL BIOLOGY II 
(BIOL-UA 22) 
  
Course Syllabus — Spring 2019 
  
  
Time:​ Monday and Wednesday, 9:30 am – 10:45 pm 
​ 9 West 4​th​ Street auditorium 101 
Place: 1
  
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, lc121@nyu.edu 
Professor Carlos Carmona-Fontaine, cf97@nyu.edu 
  
Teaching Assistants (TA): 
Joseph Koussa (leading TA) 
Federica Sartori 
Dylan Iannitelli 
  
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 15; 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 truly cumulative; questions cover the 
entire course, with a slight emphasis on material after Meeting 15. 
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. Any missed exam will result in a 
grade of 0 for that exam, unless there are serious extenuating personal circumstances that are 
immediately brought to the attention of the course instructors. Illness will be accepted as a 
justification for absence from a scheduled test if a doctor’s excuse is presented. The excuse 
must be dated on or immediately prior to the exam date, AND you MUST contact Prof. 
Christiaen or Prof. Carmona-Fontaine prior to the exam in order to be excused. If either of these 
conditions is not met, you will be given a grade of 0. If you miss a midterm exam and present a 
legitimate excuse, then, at the discretion of the instructors, either a make-up test will be made 
available to you or the final exam will count more toward your grade. A grade of “Incomplete” (I) 
will not be given unless it is warranted by circumstances like those described above. If you miss 
the final exam and present a legitimate excuse, then a grade of I will be given, and a make-up 
exam will be scheduled for the Fall 2018 semester. NO ALTERNATIVE DATES for the final exam 
will be offered, so avoid making travel plans to leave NYU before the date of the final exam. 
  
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 f​ inal 
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.  ​As  the  meetings  often 
present subject matter that is not introduced in the book, you must to 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. 
  
I. Intracellular organization and cell metabolism 
  
Meeting 1: Monday January 28, 2018 
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 30, 2018 
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 4, 2018 
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 6, 2018 
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 11, 2018 
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 13, 2018 
Cell Compartments I: Synthesis of Secretory and Membrane-Bound Proteins (​Christiaen​) 
  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 18, 2018 President's Day - NO CLASS 
Meeting 7: Wednesday February 20, 2018 
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 8: Monday February 25, 2018 
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 
  
Meeting 9: Wednesday February 27, 2018 
Cell  Compartments  IV:  Vesicle  trafficking  and  introduction  to  the  secretory  pathway 
(​Christiaen​) 
  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 10: Monday March 4, 2018 
Cell Compartments V: Early and Late stages of the secretory pathway (​Christiaen​) 
  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 11: Wednesday March 6, 2018 
Cell Compartments VI: Endocytosis and lysosome targeting (​Christiaen​) 
  7​th​ edition: Chapter 14; pp. 654-664 
  8​th​ edition: Chapter 14; pp. 659-673 
  
Review Session  
Wednesday March 5th, 6:00 pm - 8:00 pm 
(Location TBA) 
  
Midterm Evaluation I​ ​(Meetings 1-9) 
Date: Friday March 8, 2019, 2:00 pm–4:00 pm 
Room: X 
  
Meeting 12: Monday March 11, 2018 
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 13: Wednesday March 13, 2018 
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 
  
March 18, 2018 Spring Recess NO CLASS 
March 20, 2018 Spring Recess NO CLASS 
  
Meeting 14: Monday March 25, 2018 
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 15: Wednesday March 27 
Cell polarity (​Christiaen​) 
  7​th​ edition: Chapter 17​ C​ ell migration pp. 801-814 
th​
  8​ edition: Chapter 17​ C ​ ell migration pp. 803-820 
  
III. Biophysics of membrane transport and cell communication 
  
Meeting 16: Monday April 1 
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 17: Wednesday April 3 
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 
 
Mid-April: Review Session 
Wednesday April 3rd, 6:00 pm - 8:00 pm  
location TBA 
  
Midterm Evaluation II (Meetings 1-15) 
Date: Friday April 5th, 2019, 2:00 pm–4:00 pm  
Room: TBD 
  
Meeting 18: Monday April 8 
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 19: Wednesday April 10 
Desplan  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 
 
IV. Biochemical control of cell differentiation, division and communication 
 
Meeting 20: Monday April 15 
Cell migration (​Christiaen​) 
  
Meeting 21: Wednesday April 17 
Optogenetics and synthetic cell biology (​Christiaen​) 
   
Meeting 22:​ M ​ onday April 22 
Carmona-Fontaine  Cellular  Communication  I:  Signaling  Molecules,  Receptors,  and  Second 
Messengers 
  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 23: Wednesday April 24 
Cellular Communication II: G Protein-coupled Receptors (​Carmona-Fontaine​) 
  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 24: Monday April 29 
Cellular Communication III: Receptor Kinases I (​Carmona-Fontaine​) 
  7​th  edition:  Chapter  16.1  RTKs,  JAK/STAT;  pp  723-733,  16.2  The  Ras/MAP  Kinase 
pathway; pp 734-744 
  Chapter 16.3 PLC and PI3K, pp 745-747 
  8​th  edition:  Chapter  16.2-4.  RTKs,  pp  734-739;  JAK/STAT,  pp  726-733;  The  Ras/MAP, pp 
739-747 
  Chapter 16.5 PLC and PI3K, pp 748-751 
  
Meeting 25:​ W ​ ednesday May 1 
Cellular Communication IV: Notch, Hedgehog, and Wnt Receptors (​Carmona-Fontaine​) 
  7​th  edition:  Chapter  16.5-7  Signaling  pathways  in  development,  Wnt,  Notch,  Shh;  pp. 
752-769 
  8​th  edition:  Chapter  16.6-8  Signaling  pathways  in  development,  Wnt,  Notch,  Shh;  pp. 
751-770 
  
Meeting 26: Monday May 6 
Cellular Communication V: TGFβ Morphogens and Cell Fate (​Carmona-Fontaine​) 
  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 27: Wednesday May 8   
The Cell Cycle (​Carmona-Fontaine​) 
  7​th​ edition: Chapter 19 Control of Mitosis by Cyclins and MPF 873–912 
  8​th​ edition: Chapter 19 Control of Mitosis by Cyclins and MPF 873–910 
  
Meeting 28: Monday May 13 
Cancer and the Tumor Microenvironment (​Carmona-Fontaine​) 
  7​th​ edition: Chapter 24 
  8​th​ edition: Chapter 24 
  
Review Session: TBD (Wednesday before, 6-8pm) 
  
FINAL EXAMINATION 
(Meetings 1-28) 
Monday May TBD, 4-6pm 
Location: TBD