Penn State Lehigh Valley BIOLOGY 110
 
BIOL 230W:
Biology Molecules & Cells
* Course Materials

* Course Objectives

* Organization & Policies

* Evaluation Methods

* Technical Requirements

*University Policies

* Class Syllabus

* Lab Syllabus


FALL 2013

Class Time: Monday, Wednesday, Friday: 10:00am to 10:50am
Class Room: 311 Saucon
Laboratory Time:

Wednesday 2:00pm to 3:50pm

Laboratory Room: 316 Saucon
Instructor: Jacqueline McLaughlin, Ph.D.
Associate Professor in Biology
Cell and Developmental Biologist
Office: 3N
Office Hours:

Monday and Friday 1:00 p.m. to 4:00 p.m.

Office Phone: 610/285.5109
E-mail: jshea@psu.edu
   
Laboratory Research Assistant: Mrs. Missy Coyle, M.S.
E-mail: msg110@psu.edu
   

On-Line Resources:

Biology Place
Cell & Molecular Biology On-Line
Cell Biology Animations
Cell Biology News
CHANCE
iBioseminars
Nature: Cell Biology
Working with Molecular Genetics

Show Class Tutoring Information

Credits, class periods, lab periods: 4, 3, 3

BIOL 230W (GN) Biology: Molecules and Cells (4) A study of cellular phenomena including molecular genetics and metabolic interactions. (BIOL 220W, 230W, and 240W each carry only 1 credit of "writing"; all three courses must be taken to meet the writing requirement.)


Course Materials

Textbook: Essential CellBiology (3rd Edition), Alberts et al., 2009
ISBN: 978-08153-4130-7

Laboratory Manual: Life Science Student Lab Notebook, Hayden-McNeil Pub., 2003
ISBN: 978-19308-8235-5


Course Objectives

  • Explore and examine the core disciplines of cell and molecular biology in order to gain a deeper understanding of, and appreciation for, the "living cell."
  • Marvel over, and unravel the machinery that sustains life at the cellular level and the molecules like proteins, DNA, and RNA that define it.
  • Evaluate and discuss the importance of cell biology in medical, industrial, ecological, and environmental issues that confront the world today.
  • Analyze and utilize real-scientific research questions, data, and interpretations in order to understandand appreciate how past and present-day cell and molecular biologists carry-out basic and medical research.
  • Recognize that the facts (concepts) presented in your cell biology textbook are really the accumulation of the conclusions of numerous experiments over the years, and that it's important to understand that those conclusions might change on the basis of new information. Key here is that this information can be revised over time, but the process by which knowledge is generated from scientific experiments will remain relatively constant.
  • Delve into laboratory investigations as a contemporary cell/molecular biologist by doing actual research, orally presenting this research, then writing-up a formal research paper.
  • Practice keeping a laboratory notebook and recording/interpreting data.
  • Foster technology in both the classroom and laboratory as both a means of learning and research aid.
  • Experience, and more importantly, value working in groups. Scientific research is rarely a solo experience.
  • Broaden your critical thinking skills as a biologist since cells are the essence of all living things! There are macro and micro worlds within the field of biology.

MY PROMISE: YOU WILL BE A WELL-ROUNDED, INDEPENDENT, BUDDING BIOLOGIST UPON COMPLETION OF THIS COURSE!


Organization and Policies

  • Classroom: This course physically meets three times a week to go over core concepts and scientific information  related to these concepts.  Class topics are outlined in the below schedule. Know that it is my personal quest to bring to my teaching the critical thinking, rigor, creativity, and spirit of experimentation that defines research itself. In short, you will not be memorizing; but instead, you will be practicing "scientific inquiry” by continually questioning, reasoning, hypothesizing, interpreting, and critically thinking about scientific data/information.

I expect that you to come to class prepared, work-hard, and actively participate in class. You are required to read all on-line and textbook assignments ahead of time, and to complete all web-based modules to your fullest potential. Hint: A good way to prepare for class is to make a list of questions (at least 10) on the topic that will be covered. Be ready to learn. Class time will be more engaging and productive if you participate in class by generating questions that bring about classroom discussions and opportunities for scientific thinking and peer-interactions.

  • Study groups: I strongly suggest that you participate in a study group, and use the group to assess your comprehension of the course material.
  • Laboratories: Laboratories will commence on the second week of classes and will meet as scheduled. Check pre-lab assignments carefully before attending lab. The laboratory exercises are designed to give you an opportunity to learn through experimentation (inquiry and experience) and to use your critical thinking skills. Laboratory staff and I will provide instruction in the nuts and bolts of appropriate experimental methods. I will also provide guidance into how an effective experiment is designed. Then, you and your selected lab partners will perform your own experiments. As researchers, you must formulate your own hypothesis, determine the data to be collected and how to collect it, and then carry-out your experiment. Student groups will be required write scientific protocols and a professional lab report.
  • Attendance and Make-up Exams: You will be responsible for all material covered in class. Please note the exam schedule which is entwined in your lab syllabus. All of the exams will be used to assess your performance in this course; none will be dropped. Only those individuals with legitimate and verifiable excuses will be allowed to schedule a make-up exam. If you cannot take the exam at a scheduled time, you need to contact me as soon as possible via email.

* It is stressed that if you are late for class or miss class because of dangerous weather conditions, your safety is more important. Always drive safely.

  • Missed Laboratories: Lab attendance is mandatory. If you miss a lab you must have a legitimate excuse (as above). If you fail to make up a missed lab you will lose 200 of your total laboratory points at the end of the semester. Missed labs will indeed affect your grade!

Evaluation Methods

Knowledge of class material will be evaluated by four semester exams, four readiness assessment tests (RATS), eight on-line assignments through Angel (TBA), and a comprehensive final exam. The class exams will cover material presented in the class, the assigned textbook readings, as well as interactive on-line assignments. Each exam will consist of multiple choice, fill-ins, short answers, and essays. The final exam will test your comprehensive knowledge of the entire semester's material.

The lab component will be judged on the following:
  • Group protocol on Vero cell culture research.
  • Individual research paper on Vero cell growth in cell culture.
  • Lab notebook showcasing all data and interpretations made; and, of course
    your overall lab preparation, organization, technique, and wortk-ethic.

Class (60% of grade):
4 Semester Exams (100 points each) = 400 points
4 Readiness Assessment Tests (RATS) (25 points each) = 100 points
8 On-Line Assessments (25 points each) = 200 points
1 Cumulative Final Exam = 200 points
Total = 900 points

Laboratory (40% of grade):
Group Protocol on Endosymbiosis = 100 points
Group Protocol on Vero Cell Growth = 100 points

2 Citation Chasing Assignments (50 points each)

= 100 points
Individual Lab Report on Vero Cell Growth in Cell Culture = 400 points
Lab Notebook including ALL lab data collected and interpretations = 200 points
Total = 900 points

Class grades will be determined by a percentage scale based upon the total number of points available (900 points). Lab grades will be determined by a percentage scale based upon the total number of points available (900 points). Class grade equals 60% of overall final grade; lab grade equals 40% of overall final grade.

Penn State University letter grade equivalents:
95-100 A
90-94 A-
87-89 B+
84-86 B
80-83 B-
75-79 C+
70-74 C
60-69 D
0-59 F

Technical Requirements

Operating System:

Windows 2000/XP, Vista, or Windows 7; Mac OS X 10.3 or higher (10.4 or higher recommended)

Processor:

1 GHz or higher

Memory:

256 MB of RAM

Hard Drive Space:

500 MB free disk space

Browser:

Mac OSX: Firefox (Current non-beta version)
Windows: Firefox (Current non-beta version)
Note: Cookies, Java, and JavaScript must be enabled.
Pop-up blockers should be configured to permit new windows
from Penn State web sites.
Due to nonstandard handling of CSS, JavaScript and caching,
older versions of Internet Explorer (such as IE 6 or earlier) do not work with our courses.

Plug-Ins:

Adobe Reader
Flash Player (v7.0 or Later)
Adobe Shockwave Player
Real Player

Additional Software:

Microsoft Office (2003 or Later)
iTunes
Quicktime

Internet Connection:

Broadband (cable or DSL) connection required

Printer:

Access to graphics-capable printer

DVD-ROM:

Required

Sound Card, Microphone, & Speakers:

Required

Monitor:

Monitor (Capable of at least 1024 x 768 resolution)

If you need technical assistance at any point during the course, please contact ANGEL Technical Support

University Policies

Academic Integrity Policy

Academic integrity is the pursuit of scholarly activity in an open, honest and responsible manner.

Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the University community are expected to act in accordance with this principle. Consistent with this expectation, the University's Code of Conduct states that all students should act with personal integrity, respect other students' dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts.

Academic integrity includes a commitment not to engage in or tolerate acts of falsification, misrepresentation or deception. Such acts of dishonesty violate the fundamental ethical principles of the University community and compromise the worth of work completed by others.

Penn State University Academic Policy 49-20

Academic dishonesty includes, but is not limited to cheating, plagiarism, fabrication of information or citation, prior possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students.

For further guidance on matching punishment with infractions, see "Sanctioning Guidelines for Academic Integrity Violations"

Disability Access Statement

Note to students with disabilities: Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact Disability Services located in 211 Saucon at 610-285-5124. For further information regarding the Office of Disability Services, please visit their web site at www.equity.psu.edu/ods/ . Instructors should be notified as early in the semester as possible regarding the need for reasonable academic adjustments.

Affirmative Action

Pennsylvania State University is committed to a policy that all persons shall have equal access to programs, facilities, admission, and employment without regard to personal characteristics not related to ability, performance, or qualifications as determined by University policy or by Commonwealth or Federal authorities. Penn State does not discriminate against any person because of age, ancestry, color, disability or handicap, national origin, race, religious creed, sex, sexual orientation, or veteran status. Direct all inquiries to the Affirmative Action Office.


Class Syllabus

Date
Class Content
Required Readings / Web Based Activities
M: 8/26
Introduction to Cells

Chapter 1 (pages 1–36; Panels 1.1 – 1. 3)

VIDEO: Inner Life of a Cell

W: 8/28
Continued

 

F: 8/30

No Class
Online Assessment #1

VIDEO LECTURE: Parts of the Cell

M: 9/2

Labor Day

No Class

W: 9/4
Continued
F: 9/6
Chemical Components of Cells

Chapter 2 (pages 39–78; panels 2.1 – 2.7);

 MODULE – The Biology Place: Properties of Biomolecules
M: 9/9
Continued

 

W: 9/11
Continued
F: 9/13
Continued
M: 9/16
Continued
W: 9/18
Energy, Catalysis, & Biosynthesis
F: 9/20

Energy, Catalysis, & Biosynthesis

Basic Review of Aerobic Cellular Respiration (ACR)

 

M: 9/23

RATS #1

Protein Structure & Function

Chapter 4 (pages 119-142; Panels 4.1, 4.2, 4.3, and 4.6 - Gel Electrophoresis Only); VIDEO: Protein Structure

W: 9/25

Continued

 

F: 9/27

Continued

M: 9/30

Continued

 

W: 10/2
Continued
F: 10/4

DNA and Chromosomes

Chapter 5 (pages 171-193)
VIDEO: Karyotype

M: 10/7
Continued

 

W: 10/9
Continued

 

F: 10/11

Continued

M: 10/14

DNA Replication, Repair, & Recombination

W: 10/16
Continued

 

F: 10/18
Continued

 

M: 10/21

RATS #2

Continued

 

W: 10/23

From DNA to Protein: How Cells Read the Genome

F: 10/25
Continued

 

M: 10/28
Continued
W: 10/30
Continued

 

F: 11/1
Continued
 
M: 11/4

Continued

Online Assessment #5
VIDEO LECTURE: Transcription

W: 11/6
Membrane Structure

F: 11/8

Continued

 

M: 11/11

RATS #3

Continued

 
W: 11/13 Continued

 

F: 11/15 Cytoskeleton

Chapter 17 (pages 572-592)

VIDEO: Cytoskeletal Microtubles

VIDEO: Intermediate Filaments
M: 11/18 Continued  
W: 11/20 Intracellular Compartments and Transport

No Class

MODULE: The Biology Place
Biomembranes II: Membrane Dynamics & Communication

F: 11/22  

No Class

Online Assessment #6

iBiologyEducation
Mysterious Membranes within the Cell

M: 11/25 Thanksgiving Break No Class
W: 11/27 Thanksgiving Break

No Class

F: 11/29 Thanksgiving Break No Class
M: 12/2

RATS #4

Continued

REVIEW SESSION
W: 12/4 The Cell Division Cycle

Chapter 18 (pages 609-619)

F: 12/6  

MODULE: The Biology Place:
Mitosis

M: 12/9 Continued

Online Assessment #7

Video: Cell Cycle, Mitosis, and Meiosis

iBiologyEducation
Cell Division

W: 12/11 Continued  
F: 12/13 Continued

Online Assessment #8

iBiologyEducation
Controlling the Cell Cycle 1: Introduction

Finals Week December 16th - 20th

Final Exam Date & Time To Be Announced


Lab Syllabus

Date
Topic
Assignment
W: 8/28
No Lab
W: 9/4

* Pre-lab assessment


Introduction to Lab: Microscopes & Cells

Handout

W: 9/11
Researching Endosymbioisis
W: 9/18

Researching Endosymbioisis

Continued

Protocols Due

 

W: 9/25

EXAM #1


Lab Recitation

 

W: 10/2

Agarose Gel Electrophoresis for DNA

Part 1: Technique

W: 10/9

Agarose Gel Electrophoresis for DNA:


Part 2: Run Gel

Part 3: Intro to Gel Analysis (during incubation)

W: 10/16

Agarose Gel Electrophoresis for DNA:
Part 4: Mutant Hb Gene Analysis (post incubation)

Vero Cell Culture Introduction (30 minutes):
Part 1: Finding Your Way Around our Cell Culture Lab

Handout -"Life and Death in Tissue Culture"-  
Cell Culture Video

Cell Count Prep with Trypan Blue Video
W: 10/23

EXAM #2

Vero Cell Culture:
Part 2: Cell Passage, Confluency, and Counting - Introduction
Primary Literature - Introduction

 

W: 10/30

Vero Cell Culture:
Part 2 cont.: Cell Passage, Confluency, and Counting - Practice

Draft Protocol Due

MODULE: CITATION CHASING and ASSESSMENT (Part B)

(open from Friday October 25 - Monday October 28)

W: 11/6

Vero Cell Culture Research:
Part 3: Experimental Set-up, Day 0 Cell Counts

Approved Protocol Due

Open Lab

W: 11/13

EXAM #3

Vero Cell Culture Research:
Part 3 cont.: Day 7 Cell Counts, Data Compilation

Open Lab

W: 11/20

Draft  Lab Reports Due

Open Lab

W: 11/27

Thanksgiving Break

No Class
W: 12/4

EXAM #4

W: 12/11

Human Karyotyping

*Post-lab assessment

Final Draft  Lab Reports Due

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