Biol 350 Cellular Biology

Biol 350 Cellular Biology

Sample lecture and lab syllabus from Fall 2008

ALL MATERIAL FOR THIS COURSE IS AVAILABLE FOR DOWNLOAD ON ANGEL

Instructor:George GomezOffice Hours: Mondays & Thursdays, 10:30-11:30

Loyola Hall 118Ph. 941-6355 (office)

E-mail: gomezg2@scranton.edu

Goals and Objectives for Biology 350 (lecture and lab)

Cell Biology is a discipline by which we attempt to gain an understanding of the structure and function of eukaryotic cells.This increasingly means studying the molecular mechanisms by which organelles and macromolecules interact to perform specific functions within and around each cell.Upon completion of both the lecture and laboratory portions of this course, students will be expected to:

1.Identify the major eukaryotic organelles, describe the function of each

2.Outline the processes of macromolecule synthesis and traffic.

3.Describe the steps involved in energy production and consumption, and how they pertain to organismal function

4.Describe the components of the cytoskeleton and extracellular matrix, and explain how their interrelationship affects cell shape, growth, function, and division.

5.Discuss how cells receive signals from the extracellular environment, and how these signals cause changes in cell structure or function.

6.Design and execute novel experiments using important techniques used by cell biologists to probe cell structure and function.

7.Read primary journal articles within the field of cell biology, interpret the author’s findings, and communicate your insights in writing.

8.Maintain a detailed and accurate laboratory notebook, and communicate your lab results in the format of a scientific paper.

Course Information

Grading Policy: Independent grades will be assessed for the lecture and the laboratory portions of the course, as outlined in the description of each course component below.Final grades will be based on the total number of points accumulated by each individual over the course of the semester.Approximate letter grades will be posted for each examination in order to aid students in determining their relative performance on the exam.

The grade for the lecture portion of the course will be derived from FOUR unit exams worth 100 points each.Unit exams will cover material presented in thelectures AND labsas indicated on the course syllabus.Each exam will involve both objective and essay-type questions.Expect at least ONE essay question to require you to integrate basic concepts from the matter covered in the previous exam (don’t worry – I will only ask about general concepts and things you SHOULD know, and not specific details).The fourth unit exam will be given during the final examination period. Examswillrequire you to apply the concepts and techniques you have learned to situations not covered directly in class.

If there is a current “Cell Biology” topic in the news, I will dedicate lecture time to discussing this topic.Whether or not we have discussion will depend upon you - ideas for discussion topics may be emailed to meMost topics will likely be health-related, but any current newsworthy event is open for discussion.

Textbook

Molecular Biology of the Cell(5thEdition) by B. Alberts: It is a complete and comprehensive textbook for cell biology and is a useful one to have as a desktop reference.This is also the textbook you ought to own (and read!) if you want to score well on an MCAT or if you want to go to Graduate School.Nearly all figures in the lecture come from the book.

Attendance Policy

Attendance will not be taken for lecture, but it is important that you remember that class participation and open discussion are important parts of the learning process this course.However, consistent absenteeism will not be acceptable, especially if you are begging me not to fail you for the course.Attendance at all lectures certainly works to your benefit, as exam questions will be based primarily on material covered in lecture.

If you miss a quiz and your absence is unexcused, you LOSE all points for your quiz.

Quizzes

Quizzes will constitute approximately 1/5 of your grade.Quizzes will be given almost every Monday and will consist of straightforward objective questions.The content of each quiz will be derived from lecture notes posted on-line and announced previous to the quiz, but will often contain material that has not yet been covered in the lecture.It is your duty to come to class prepared (by reading lecture notes), and the quizzes are a way of forcing you to study.These will also help you retain the material that you study

Exam Format and Policies

Exams will constitute 4/5 of your grade.All exams will follow roughly the same format.Most of the test will consist of short-answer questions requiring two to five sentences to complete, and a longer essay questions requiring up to a full page to answer thoroughly.The exact point value of all questions will be clearly indicated on the exam so that you can determine which questions to spend the most time answering.Exams will often contain application questions, where you will be given new information, and it will be up to you to apply your knowledge from the lecture.

Review sessions for each exam will be conducted only if at least one half of the class (ten students) requests it.The review sessions will be scheduled accordingly.Remember, however, that I am always available for personal consultation

Students missing an exam must contact Dr. Gomez within 48 hours of the exam period or receive a failing grade for the exam.In order for an absence to be excused, the student must provide a written excuse from the Student Health Service or a parent or guardian, andthe excuse must contain a phone number for contacting the person who authored it.Each case involving an excused absence will be dealt with on an individual basis.

In addition, you are reminded of the Academic Code of Honesty in place at the University of Scranton.All tests and other graded assignments fall under the auspices of this policy.All graded materials (including laboratory notes and write-ups) must contain only work that you have completed yourself.

I HAVE A ZERO TOLERANCE POLICY FOR ACADEMIC DISHONESTY!That means that if you are caught violating the Academic Code (cheating, plagiarism, false reporting),YOU AUTOMATICALLY FAIL THE COURSE.

Grading Scale

Final grades will be assigned using the following percentage scale:

94-100%A74-76.99C

90-93.99A-70-73.99C-

87-90.99B+66-69.99D+

84-86.99B60-65.99D

80-83.99B-<60F

77-79.99C+




Day

Date

Topic

Chapter

Quiz?

M

Aug 25

Course introduction

1

 

W

Aug 27

Review of Cellular Chemistry

2

 

M

Sep 1

LABOR DAY

   

W

Sep 3

Proteins: structure and function

3

 

M

Sep 8

Nuclear Structures, Metabolism and Transport

6

Y

W

Sep 10

Protein Synthesis and Processing

 

M

Sep 15

Golgi and vesicular transport

12 &13

Y

W

Sep 17

Lysosomes, Endocytosis and Exocytosis

 

M

Sep 22

EXAM I

   

W

Sep 24

Cytoskeleton

16

 

M

Sep 29

Y

W

Oct 1

 

M

Oct 6

Energy transfer in cells: Photosynthesis and Bioenergetics

14

Y

W

Oct 8

 

M

Oct 13

FALL BREAK

   

W

Oct 15

Integration Lecture: Putting it all together

 

Y

M

Oct 20

EXAM II

   

W

Oct 22

Cell surface: Structure and Transport

11

 

M

Oct 27

Cell Signaling: Ligands and Receptors

15

Y

W

Oct 29

Second Messenger Signaling I

 

M

Nov 3

Y

W

Nov 5

Receptor Kinases and Phosphatases

 

M

Nov 10

Y

W

Nov 12

Cell Signaling: Extracellular Matrix

19

 

M

Nov 17

EXAM III

   

W

Nov 19

Cell Signaling: Long Distance Communication

   

M

Nov 24

Cell Cycle

17

Y

W

Nov 26

THANKSGIVING

   

M

Dec 1

Cell Growth and Differentiation

   

W

Dec 3

Cancer

20

 

M

Dec 8

Cell Death and Senescence

   

FINALS WEEK

EXAM IV

   

Bio 350 Lab Policies and Assignments

ALL MATERIAL COVERED IN THE LABORATORY IS AVAILABLE FOR DOWNLOAD FROM ANGEL

Reminder: This laboratory course is awriting-intensivecourse.

As described in the course syllabus, your lab grade will be based upon four criteria:

I.Lab Notebook50 pts

II.Scientific Writing Exercises50pts

III.Lab Reports250 pts

IV.Lab Conductdeductions only

V.AttendanceSee “Attendance Policy”

Total100 %.

Below is a description of each of these criteria, and what is demanded in order for you to receive the highest score possible.Final grades will be assigned using the following percentage scale:

95-100%A73-77.99C

91-94.99A-70-72.99C-

88-90.99B+66-69.99D+

84-87.99B60-65.99D

81-83.99B-<60F

78-80.99C+

All laboratory exercises are custom-made for the course and are available for download on Angel.

I. Lab Notebook Assessment

During each laboratory exercise that is numbered on your syllabus (except for the first laboratory), students will be asked to keep a detailed record ofallactivities and observations occurring during that lab period.

The purpose of this exercise is:

1.To provide you with a detailed account of your activities, allowing for greater ease in composing the required lab reports.

2.To prepare you for the detailed, accurate note-taking required while performing independent research or working in a clinical or laboratory setting.

It is important to remember that the reason for taking notes is so that you (or someone else) can return to them at a later date, and recall exactly what you did, what the results of the experiment were, and what conclusions were drawn from the data you accumulated.

Your notes will include three essential components for each exercise:

1.Introduction:(Due at the beginning of lab.) A two or three paragraph description of the experiment or exercise to be performed,written prior to arriving in lab.The purpose of this introductory paragraph is to get you thinking in advance about why you are undertaking the exercise and what techniques you will be using.It will also serve as a reminder of what experiment was performed when you glance back at your notes at a later date.

2.Procedure:(Dueon or before10 am sharp on the Friday following lab, but wait for my announcements)Accurate notes detailingeverythingdone during the lab period.These notes need not be written out in sentence form, but need to be clear enough and contain enough information that another cell biologist could read them at a later date and understand exactly what you have done.This means that all numerical data and sketches should be clearly labeled, andalltechniques described in detail. Do not simply write, “Followed lab handout.”Write whatyoudid.

It is also helpful to write down THINGS THAT YOU SEE while you do your procedure.For example, is your solution turning bright pink?That may be important.Later, if you repeat your procedure and your solution DOESN’T turn bright pink, then you know something different is happening.

3.Results:(Dueon or before10 am sharp on the Friday following lab.) A paragraph or two summarizing the results of your experiments, and any conclusions you may have drawn from these results.Be sure to include any observations that you think are important, even if they were already jotted down in your notes.You are more likely to find these important data when reviewing your notebook at a later date if they are included in the conclusions at the end of the exercise than if they are buried in with the rest of your notes for the experiment.

Completed lab notebooks are awarded 10 points per exercise.

If you are late in submitting ANY PART your lab notebook (intro, procedure, etc.), you will NOT receive any credit for the lab exercise. I will make every reasonable attempt to return the lab notebooks to you on Monday morning or Monday afternoon during the lecture.

All entries in the lab notebook should be made in permanent ink (black or blue ball point pen, preferably).If you realize you made a mistake or recorded some data incorrectly, put a single line through what you have written, and clearly write in the correction.This is done to prevent alteration of data that has already been entered in a notebook.Ideally, if you use your lab notebook properly, you need not do too much additional work to submit your lab notebooks for grading

**Absolute adherence to the lab manual handouts and obtaining the results you are “supposed to” obtain arenot necessitiesfor getting full credit.Write downexactlyhow YOU performed the experiment, even if it was altered from the protocol in the lab manual.And describe the results that YOU actually observe, not what someone else says they see or what you expect to see.Your lab notebooks must be turned in to my office by 10:00 a.m. on the Friday following the lab period (wait for detailed instructions) in order to receive credit.Notebook submitted late will NOT receive any credit for the exercise.

II. Scientific Writing Exercises

Throughout the semester, I will be asking you to complete some writing exercises.The goal of these exercises is to teach you how to write in a style that is suitable for scientific manuscripts.Each exercise will be posted on Angel; the point value differs for each exercise.These exercises will focus on the writing of the areas that are often problematic, including abstracts, methods, and figure legends.

The writing exercises will force you to learn how to write concise sentences and how to condense text.This will also help you understand how to read primary research articles and how to write your final lab report.

III. Lab Reports:

Equally important to maintaining an accurate lab notebook is the having the ability to write a report describing the experiments you performed, the results of those experiments, and the conclusions you have drawn from those results.The ultimate goal of performing a scientific experiment is to disseminate any new findings you make in report published in a scientific journal. Primary journal articles published in scientific journals usually contain seven distinct sections:

1. Title

2. Abstract

3. Introduction

4. Materials and Methods

5. Results

6. Discussion

7. References

During the semester, you will be asked to complete three lab write-ups in the format of a primary journal article.Each report will be increasingly complex, and as a result will have a greater point value.Lab Report 1 will include only title, a brief introduction, results, discussion, and references sections, and will be based upon your work in labs 2 to 3.Lab Report 2 (Labs 4-7) will include each of the sections from Lab Report 1, plus a description of materials and methods.The Final Lab Report will be written as though the paper was being submitted for publication, and thus will include all seven sections listed above.This final report will be based on experiments never before performed, and thus should include original data.Lab Reports that are submitted late willNOT RECEIVE ANY CREDIT.Further descriptions of these assignments will be available on Angel.

IV Digital Submissions

A. General Instructions for Digital Submissions

You may use any common word processing format for your work, but MS Word, Rich Text Format, or Adobe Acrobat (PDF) are preferred. Other word processing formats are acceptable, but bear in mind that embedded graphics and text formatting do not always import properly into MS Word. If you do not have a copy of MS Word, feel free to use any word processor (such as WordPad, which is included with every copy of Windows, or a Macintosh word processor). Nowadays, most file formats are readable in all computing platforms. If you are having trouble incorporating your illustrations into your document, you may opt to submit your written text digitally and then hand in your appropriately labeled figures separately.

B. Specific instructions on digital submissions

All submissions MUST be done via Angel.

·            Under the “Lessons” Tab, go to the appropriate folder: either the “Writing Assignments” folder or the “Lab Reports” folder.

·            Each assignment or lab report has a Drop Box associated with it.If you run your mouse over the icon and leave it there for a second or two, the “Drop Box” information pop-up should appear.

·            Click on the Drop Box

·            You can enter or paste your written work directly in the message box, or you can upload your file by clicking on the “Attachments” button.This will bring up a pop-up window/dialog box that will allow you to browse for a file (don’t forget to Upload it once you select it), or you can use the “Drag-n-Drop” tool of Angel.

·            Once you are done selecting your files, click “Upload File” to upload the file.It should then appear in the “Uploaded Files” box.

·            Click “Finished” to close the pop-up window.Once you do this, your file is stored on the Angel server.You can access this file any time/anywhere you have access to Angel.You can upload multiple versions, multiple files, etc.

·            Once you are COMPLETELY DONE and ready to submit your work, click on the “Submit” button.DON’T FORGET TO DO THIS!!!If you don’t, the work does not get submitted.

·            You may make multiple submissions on or before the deadline.Once the deadline is passed, you will no longer be able to access your submissions.The next time you see it is when it is corrected and graded (which you can access using the Gradebook).

C. Embedding graphics into your document
These instructions are written for MS Word, but I'm sure that other word processors are similar.
When you are editing your document, do not worry about formatting or making it look nice. All your formatting will probably be removed when I check the document, so focus on your content and writing.
To embed a picture into your file, go to the INSERT - - PICTURE - - FROM FILE command on the main menu. This will bring up a dialog box. Hit the BROWSE button, then use the file manager to select the file that you want to insert. The file must be saved on your hard drive or floppy disc.
If you want to make the document look nicer, you can insert a graphic using the INSERT - - TEXT BOX command. You can draw a text box and resize it to your liking. Then click inside the text box (so that the cursor is blinking inside the box). When you use the INSERT - - PICTURE - - FROM FILE command, your picture will appear inside the text box. Right click on the text box, then select PROPERTIES to control the position of text flow around your picture

V. Attendance Policy

Attendance isrequiredfor every laboratory exercise.Attendance will be taken!Eachunexcused absence will result in the lowering of your course grade by 1/2 a letter grade (i.e. A to A-, B- to C+, etc.), as well as the loss of all potential points for assignments pertaining to that lab.For an absence to be excused,it must be approved by the instructorpriorto the laboratory period, OR approval must be sought through the submission of awritten excuse signed by a physician, parent, psychiatrist, or other person of authority.The written excuse must contain a phone number for contacting the person.If an excused absence occurs, a writing project will be assigned as a lab make-up.The assignment must be completed in order the absence to be considered excused, and for no grading penalty to occur.

VI. Lab Conduct

As part of proper laboratory practice, it is absolutely necessary for a student to demonstrate appropriate conduct.Although most of the laboratory etiquette involves common sense (such as no eating or drinking during the lab period, no loud music, etc.), there are certain rules that absolutely cannot be broken:

1. Keep a clean labspace.Accidents are inevitable; however, you must deal with any accidental spills, breakage, etc. appropriately.Workspaces can get dirty as the laboratory period progresses (that is part of science); however, you must leave your work space as clean as (or cleaner than) you found it.This includes all common areas.

2. Do not disturb other lab groups – this includes taking implements without permission, disrupting their progress, etc.

3. You MUST collaborate!You will be working in pairs, and you will be required to change lab partners for every lab.Some laboratory exercises require multiple aspects of a large project to be subdivided among the lab pairs.The inability to cooperate and collaborate with your classmates (no matter how much you love or hate them) does not bode well for you.

Laboratory misconduct is purely a demerit system.You can lose up to 35 points (approx. 10% of your total grade) for inappropriate laboratory etiquette at the instructor’s or teaching assistant’s discretion; note that your instructors have itchy trigger fingers for giving deductions.

Reminder:

You MUST perform all graded work that you turn.This includes lab notebooks and lab reports.Performing each lab is a cooperative effort, with a significant amount of interaction, discussion, and collaboration within lab groups.These interactions are critical to having a productive lab experience.Butallwriting resulting from the lab is to be completed as an individual assignment.If duplicate notebooks or lab reports are submitted, both authors are considered in violation of the code of honesty

Beespeciallymindful of these rules thatABSOLUTELY CANNOT BE BROKEN:

-             PLAGIARISM.Plagiarism is a form of scientific misconduct that is unforgivable in any setting. This is especially pertinent to the laboratory reports.Plagiarism of published materials will not be tolerated.Any assignment that contains plagiarized material will be considered as violators of the academic code of honesty.

-             SCIENTIFIC FRAUD.In this context, fraud will primarily involve inventing of experimental results, or claiming in writing (in the lab notebook or lab report) that you did something when you obviously did not.In science, we all make mistakes, and experiments often do not work, so my emphasis for grading will NOT be on results but on scientific technique, accurate record keeping, and results interpretation.With this in mind, you really have not reason to make things up in your lab notebook.

I HAVE A ZERO TOLERANCE POLICY FOR ACADEMIC DISHONESTY!That means that if you are caught violating the Academic Code (cheating, plagiarism, false reporting),YOU AUTOMATICALLY FAIL THE COURSE.

VII. Sustainability

As part of our social responsibility, we will make every effort to reduce the amount of non-recyclable waste in our laboratory.These include:

·            All digital laboratories – data, lab reports, assignments, etc.If you decide to do print your lab manuals, so I encourage you to on recycled paper, on the back of previously-used paper, or print them on both sides of paper.Don’t forget to recycle the paper when you are done.

·            Reusing or recycling laboratory ware (6 well plates, microscope slides) whenever appropriate.See your instructor for details

·            Reduction in use of paper towels by the use of cloth wipes for laboratory clean-up

·            Other laboratory practices that you deem appropriate

I strongly encourage all of you to make every effort to make sustainability a part of your daily routine.I also encourage you to take the initiative and identify wasteful laboratory practices, inform the instructor of any ideas, etc.


Schedule of activities

 Lab #

Laboratory Exercise

1

Light Microscopy and Use of Pipettemen

2

Cell Fractionation and Protein electrophoresis

3

Western Blotting of protein fractions

4

Visualization of Living Cells: Vital Staining and Fluorescence Microscopy

5

Introduction to Immunocytochemistry

6

Immunocytochemistry II and Visualization

7

Cell Motility

 

FALL BREAK

8

Cell Culture and planning your individual experiments

9

Start Independent Experiments

10

Start Replicates, Start Assays

11

Complete Assays

12

13

Data analysis and discussion

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