Biology 14 (Cell Biology) Syllabus            Spring 2004

Instructors: Liz Vallen (328-8048) Martin 311/312 evallen1); Jocelyne Noveral (690-5760 Cornell 206 jnovera1).  Office hours for both Liz and Jocelyne are by appointment. 

Suggested Texts:

Alberts, et al. (2004).  Essential Cell Biology, 2nd edition.   Suggest readings are in bold below.

                        OR

Alberts, et al. (2002).  Molecular Biology of the Cell, 4th edition.   Suggested readings are in italics below.

 

Lectures: 11:30am, MWF in Martin 213

Laboratories: 1:15pm Tu or W, Martin 311

 

My expectations for what you should get out of this course include:

  1. A deeper understanding of the parts of a cell, how they work, and the limits of our current knowledge
  2. A sense of how cell biologists ask and answer questions experimentally
  3. Insight into how cell biology affects our lives
  4. Experience working productively in groups
  5. Practice keeping a laboratory notebook and interpreting data
  6. Experience speaking about science

 

Topics and suggested reading

I.               Introduction Chapters 1, 2, 3  and 7:258-263 or Chapter 1, 2 and 6:365-373 (you should read these Chapters, but you don’t need to STUDY them – most of Chapters 2 and 3 should be review)

What is cell biology?

What are cells made of? 

Where did cells come from?

II.             Protein folding and structure Chapter 4: 119-143; Chapter 7:256-257 or Chapter 3:129-156; Chapter 6:355-365

What do proteins look like and how do we know?

Protein domains

Structure determination and prediction

III.           Protein functions Chapter 4: 143-159 or Chapter 3:156-188

Catalysts, skeletons and machines

Regulation of protein levels and activity

IV.           Membrane structure and functions Chapter 11 or Chapter 10

The membrane is what makes a cell, a cell!

Components and characteristics of membranes

V.             Membrane Transport Chapter 12:389-410 or Chapter 11:615-637

Ways to move molecules across membranes

Carrier proteins

Ion channels

 

VI.           Using membranes Chapter 13, Chapter 14: 453-478; 487-493 or Chapter 2:91-108; Chapter14:767-793

How do mitochondria generate energy?

VII.         Protein sorting and intracellular compartments Chapter 15: 496-512 or Chapter 12

How are proteins targeted to subcellular compartments?  Part I

VIII.       Vesicular transport; protein modifications in the secretory pathway Chapter 15:512-531 or Chapter 13

How are proteins targeted to subcellular compartments?  Part II

What happens to proteins in those compartments?

How are proteins and other molecules moved into and out of the cell?           

IX.           Cytoskeleton, motors and movements Chapter 17 or Chapter 16

Structure and plasticity

How do cells swim and crawl?

Intracellular highways

X.             DNA packaging and gene expression Chapter 5:177-194, Chapter 7 and 8 or Chapter 4:207-216; Chapter 6:299-354; Chapter7

The structure of chromatin

From DNA to RNA to protein

Regulation of protein expression

XI.           Disease presentations/special topics

Note: disease presentations will take place on Wednesday April 28th and Friday April 30th.  Most likely, groups with lab on Tuesday will present on Wednesday and groups with lab on Wednesday will present on Friday.  On Wednesday, class may extend until 1:15.  On Friday, class may extend until 2:00.  PLEASE PLAN FOR THIS NOW.  If you do not tell me by the end of the first week of classes that you have a conflict, it will be inexcusable for you to miss these sessions.  We will know more precisely how much time will be required once we know how many groups and presentations there will be.  This can occur once course and lab enrollments are finalized.  If class extends past 12:20, I will provide lunch.     

 

Probable Assessments

 

Midterm quizzes 2@100pts (Mon. Feb. 16; Mon. March 29)          200

Final exam                                                                                           200

Disease project (week of April 26)                                                   100

Lab notebook/bioinformatics 5@50 pts, 1@75 pts                             325

Secretion lab question and answer period                                            100

Participation/ flowcharts/problem sets                                                 200

Total                                                                                                   1125

 

Late papers will be penalized 5% of their maximum original value per day (i.e., a 100 pt report will be penalized 5 points per day).

 

 

Week of        Lab Projects                                                  Assignments Due for the Week 

Jan 19              Microscopy and Math for Cell Biology                     

Jan 26              Bioinformatics I                                              Microscopy/math     

Feb 2               Subcellular fractionation I (Chloroplasts)        Bioinformatics I;

Chloroplast flow chart  

Feb 9              Subcellular fractionation II (Chloroplasts)                                         

Feb 16             Secretion I (sterile technique/minipreps)         EXAM in class                     

Feb 23             Secretion II (yeast transformations)                Overview of secretion flow chart;

                                                                                                             Chloroplast notebook       

Mar 1              Secretion III (mapping; streak transformants)            

Mar 8              Break!                                                                                                                        

Mar 15            Secretion IV (analysis; mapping discussion)                                                              

Mar 22            Bioinformatics II                                             Secretion Q and A period, notebook

Mar 29            Pigment granule migration I                            EXAM in class                     

Apr 5               Pigment granule migration II                           Bioinformatics II

Apr 12             Gene expression                                              Granule migration notebook

Apr 19             preparation for disease presentation                Gene expression notebook  

Apr 26             preparation for disease presentations               Disease presentations (in class) 

           

Lab rules and regulations

 

•     Be on time for lab.  We will give instructions, clarifications and changes in protocol at this time.  If there are exercises or lab reports due they must be handed in at the beginning of lab.   

•     You may NOT eat, drink, or smoke in the laboratory at any time.

•     Clean up after yourself.  There will be waste receptacles for trash and tubs for glassware  - please remove labels/tape from tubes and beakers before leaving them to be washed. 

•     Working with live organisms and performing experiments that require incubations may result in laboratories that take more than our allotted 3 hour time slot, or require you to come back later on that evening.  

•     Prepare for lab by following the format given in the lab notebook handout. Note any questions you have about the methods or experimental system, and do the calculations required before coming to lab.  For some labs, you will be required to turn in a flow chart diagramming out the procedure – make two copies, one to turn in and another to use in lab. Bring your notebook to lab each week to record data and observations.  Write in ink!  In research laboratories, one’s notebook stays in the laboratory, and is frequently used as a resource by others.  Your notes and data should be clear enough that someone could reproduce your experiment or analyze your results.   Your notebook will be assessed at least five times during the semester.

•     Material from the laboratory exercises may be used in the midterm quizzes and final exam.      

 

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