Dr - Association of College and University Biology Educators

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Bl 306 Cell Physiology
Spring 2013
Dr. Debra Meuler
Office Phone:
410-4136
Office Hours:
Monday
10:00-10:50
Thursday
1:00-2:00
Or by appointment
Office RB 204
[email protected]
2:00-3:00
Wednesday
Lecture: 3 hrs/wk – MWF 11:00-11:50 RB 212
Lab: 3 hrs/wk – Thursday 9:30-12:20 RB 212
Catalog Description: This course explores the structural and molecular organization of the cell as the basis of life
processes.
The biology major is organized around six major biological concepts. These concepts are recurring themes that unify
all of biology. The six core themes that serve as the basis of the biology curriculum are (1) The Nature of Science,
(2) Energy Transformation, (3) Information Flow, (4) Structure and Function, (5) Cellular Communication, and (6)
Evolutionary Patterns and Processes.
The Nature of Science theme refers to the discovery process by which information is obtained and evaluated. It also
refers to the changing body of knowledge that characterizes scientific understanding. This theme systematically
exposes you to the processes of science. This includes making observations, making inferences, assembling
evidence, developing hypotheses, designing experiments, collecting data, analyzing and presenting results, and
communicating and evaluating conclusions.
The Energy of Transformation theme refers to the idea that all living organisms consume and transform energy.
The survival of a living organism depends on the continuous input of energy. This theme exposes you to the
chemical reactions that are designed to extract energy from the environment and how organisms use that energy to
sustain existing cells and help form new ones.
The Information Flow theme refers to the idea that all organisms sequentially transfer information. This includes
genetic information that flows from DNA to RNA to protein. This theme exposes you to the core concept that DNA
controls the development and maintenance of organisms and that the gene is the fundamental unit of genetic
information. It includes the processes of replication, transcription, RNA modification, translation and protein
modification and targeting. It also includes the myriad ways that cells regulate the expression of genes including
what, when, where and how much gene expression occurs and how genetic information is transferred from cell to
cell and from one generation to the next.
The Structure and Function theme refers to the idea that in biological systems form and function are related at all
levels of biological organization from molecules to cells to whole organisms. This theme will expose you to the
concept that cells are the basic units of structure and function and that the structure of molecules, cells, organs, and
organ systems relate to their function.
The Cellular Communication theme refers to the idea of how cells and organisms communicate. This theme
exposes you to the different types of communication systems between living cells. This includes how cells
communicate with each other, homeostatic mechanisms, and how organisms perceive and respond to changes in the
environment.
The Evolutionary Patterns and Processes themes refer to the idea that life changes and develops through
evolution, and that all life-forms known have a common origin. This includes the various mechanisms of speciation
including natural selection and how the great diversity of life was created.
Each biology course that forms the core of the biology major will revolve around these themes. In this course we
will focus on five of the themes describe above – namely (1) Nature of Science (2) Energy Transformation (3)
Information flow, (4) Cellular Communication and (5). Structure and Function The Nature of Science theme will be
explored mainly during lab.
Course outcomes:
Theme 1: Nature of Science
We will continue to explore the process of science by investigating questions using the scientific method. We will
continue to learn how to communicate these understandings to others. By the end of the semester you should be
able to
1. Write in a scientific manner using the appropriate format for science articles. (BSLO#8)
Assessment:
Formal lab report
2. Communicate orally the results of scientific research. (BSLO#8)
Assessment:
Disease oral presentation
3. Solve scientific problems using mathematical relationships and measurement systems, analyze and
draw conclusions from data, and interpret graphed and tabulated data. (BSLO#7)
Assessment:
Lab reports, lab practical, formal lab reports
Exams
4. Graph and tabulate data both manually and with a computer. (BSLO#1)
Assessment:
Lab reports and lab practical
5. Demonstrate the ability to use instrumentation appropriate to the discipline (BSLO#7)
Assessment:
Lab practical
Assessment:
Exams
Theme 2: Energy Transformation
We will develop an understanding of how cells obtain the necessary energy required to run the wide variety of
chemical reactions that occur within the cytoplasm. By the end of the semester you should be able to
6. Describe how plant and animal cells obtain energy. (BSLO#2)
Assessment:
Exams
Theme 3: Information Flow
We will improve our understanding of how information flows from DNA to RNA to proteins.
7. Explain how information flows from DNA to proteins (BSLO#3))
8. Identify ways a cell can regulate the expression of its genetic information (BSLO#3))
Theme 4: Cellular Communication
We will explore the complex system of communication that controls basic cellular processes. By the end of the
semester you should be able to
9. Describe how cells communicate over short distances. (BSLO#5)
Assessment:
Exams
10. Describe how cells communicate over long distances. (BSLO#5))
Assessment:
Exams
Case Study
11. Describe how cells communicate via direct contact. (BSLO#5))
Assessment:
Exams
Theme 5. Structure and Function
During the course of the semester we will explore the characteristics and structure of the cell and why the cell is
considered the basic unit of life. By the end of the semester you should be able to
12. Describe the general characteristics of eukaryotic cells. (BSLO#4)
Assessment:
Essay
13. Describe the structure and function of the principle organelles in plant and animal cells. (BSLO#4)
Assessment:
Exams
14. Explain how the structure of a cell determines its function. (BSLO#4)
Assessment:
Essay
15. Describe the currently accepted model for the structure of the plasma membrane, the methods for
moving material across the membrane, and how receptors are used to transfer information across a
membrane. (BSLO#4)
Assessment:
Exams
Essay
16. Describe how proteins are targeted to various organelles. (BSLO#4)
Assessment:
Exams
17. Explain how the structure of a protein relates to its function. (BSLO#4)
Materials needed for course:
Textbook:
The World of the Cell, - Becker et. al.
Lab Notebook –from the bookstore
Course Pack - Meuler
Class requirement:
Your major responsibility is the understanding of the material as presented in lecture. Since lectures will not
entirely reflect the material in your textbook, your notes will have to be detailed. I expect, however, that relevant
chapters from the textbook be read to aid you in understanding lecture contents. A laboratory report will be written
for each lab session.
Bibliography:
No special bibliography will be given. Additional readings may, however, be assigned in order to complete a lab report.
Class Attendance:
Class attendance is strongly recommended. Attendance during laboratory sessions is required. Absence from
two lab periods is considered excessive. If absent from the lab, you will be expected to obtain raw data from your
lab partner and turn in a report. If you miss a laboratory period in which students are working individually, you will
not be expected to turn in a report. Your grade for that session will be the average of your laboratory grades for the
semester. There are NO MAKE-UP EXAMS. There are NO MAKE-UP LABS. If you are absent for an exam,
your grade will be based on 4 instead of 5 exams. Unexcused absences will result in a grade of 0 for missed labs
and examinations.
Evaluations:
Your grade will be based on your performance on five written examinations, chapter questions/quizzes, a final, an
oral presentation of a disease linked to an abnormality in cell structure or function, and laboratory reports/notebook. A
rubric for the assessment of the notebook and formal lab report can be found at the end of the syllabus. For
examinations, you will be responsible for all material covered in lecture and on laboratory exercises. In general,
examinations will consist of multiple choice, true/false, and long and short answer questions. The final examination
will cover material from the entire course. You will be expected to turn in laboratory reports on each experiment
exactly 1 week after the lab session, unless otherwise indicated. Late laboratory reports will be accepted but will be
penalized 10% of the point value of the report for each day that it is late. The day ends at 4:30 p.m.
Oral presentation: Many diseases are related to abnormalities of cell structure and/or function. For example cystic
fibrosis is a disease caused by an abnormal anion channel protein found in the membrane of lung epithelial cells.
For this assignment you will research diseases that are caused by problems with cell structure/function and prepare a
5-10 minute presentation of that disease. Your presentation should include the epidemiology of the disease
(specifically how it is related to cell structure/function), symptoms, treatment options, test/diagnosis and any vital
statistics associated with your disease (cure rates, how many humans contract the disease, etc). A rubric for
assessing your presentation can be found below.
Rubric for disease presentation
A. Explanation of epidemiology/symptoms of disease
3
Provided a complete explanation
2
Provided an adequate explanation
1
Provided a poor explanation
0
Provided no explanation
D. Effort
3
Showed excellent effort
2
Showed adequate effort
1
Little effort was evident
0
No effort was evident
B. Explanation of relationship to cell structure/function
3
Provided a complete description
2
Provided an adequate description
1
Provided a poor description
0
Provided no description
E. Explanation of test/diagnosis, treatment options
3
Provided a complete explanation
2
Provided an adequate explanation
1
Provided a poor explanation
0
Provided no explanation
C. Quality of presentation
0 pts = poor
1 pt = good
2 pts = excellent
Eye contact
Voice variation
Presence
Visual Aids
0 pt
0 pt
0 pt
0 pt
20-17 pts = A
1 pts
1 pts
1 pts
1 pts
2 pts
2 pts
2 pts
2 pts
16-13 pts = B
12-9 pts = C
8-5 pts = D
4-0 pts = F
Midterm and final grades are determined as follows:
Midterm
Hourly exams
60%
Laboratory work
30%
Chapter questions/quizzes 10%
Oral presentation
0%
Final exam
---
Final
45%
20%
10%
10%
15%
Grading Scale for exams, quizzes, lab reports and chapter questions are as follows:
100%-93%
A
77%-79%
C+
60%-62%
D90%-92%
A73%-76%
C
Below 60%
F
87%-89%
B+
70%-72%
C83%-86%
B
67%-69%
D+
80%-82%
B63%-66%
D
Cheating and Plagiarism:
Using the ideas of others, whether quoted word for word or paraphrased requires proper citation when used in a
laboratory report. Failure to do so constitutes plagiarism and is deemed unsatisfactory work and will be graded with
a D. You may use data collected with your partner. Interpretation is, however, to be your own work.
Students with Special Needs:
Cardinal Stritch College and this instructor wish to positively affirm the intent of Federal Law, the Rehabilitation
Act of 1973, Section 504. Any person enrolling in this course who may require alternative instruction and/or
evaluation procedures due to a handicapping condition should feel free to discuss these needs with this instructor so
that appropriate arrangements can be made.
Important Dates:
Last day of drop/add:
Midterm:
Last day to withdraw:
Honors day:
Last day of classes:
January 29
March 15
April 5
April 25 @ 3:00 pm
May 13
Writing and Speaking Across the Curriculum:
Students will be required to provide formal written reports for two lab exercises and present an oral report on a
disease related to abnormal structure or function of cells.
Tentative Laboratory topics:
1/24
Basic lab techniques
1/31
2/7
2/14
2/21
2/28
3/7
3/14
3/21
3/28
4/4
Fragility of the Red Blood Cell Membrane
Partial Purification of Myoglobin Pre-lab I: Determination of Protein Content Using the Bradford Assay
Partial Purification of Myoglobin Pre-lab II: Introduction to Column Chromatography
Make solutions for Part I
Partial Purification of Myoglobin Part I: Isolation of Myoglobin from Ground Beef
Partial Purification of Myoglobin Part II: Size Exclusion Chromatography
Spring Break
Part II Con’t: Protein Assays and Total Myoglobin Determination
Partial Purification of Myoglobin Part III: Determining the Efficacy of the Myoglobin Purification
Technique using SDS PAGE
Easter Break
Growing Human Cells in Culture – Practice aseptic technique
4/11
4/18
4/25
5/2
5/9
Growing Human Cells in Culture
Growing Human Cells in Culture
Evaluation of cultures/ Practice for the practical
Lab Practical
Testing for the Effects of Anti-tumor Drugs on Cytoskeletal Proteins in Human Fibroblast Cells
Formal reports:
1. Fragility of red blood cell membranes
2. Isolation of myoglobin from ground beef
Tentative Lecture Topics:
1/23
1/25
1/28
1/30
2/1
2/4
2/6
2/8
2/11
2/13
2/15
2/18
2/20
2/22
2/25
2/27
3/1
3/4
3/6
3/8
3/11
3/13
3/15
3/18
3/20
3/22
3/25
3/27
3/29
4/1
4/3
Introduction
Introduction to the thematic curriculum
Answer chapter questions: 4.5 a-h and 4.6 Due on January 28
Structure and Function: How do cells maintain a separate internal environment?
Cell membranes Chpt. 7
Structure and Function: How do cells transport molecules across membranes?
Facilitated Diffusion, Chpt. 8
Essay: Why is the plasma membrane considered fluid and mosaic? Due February 1
Answer chapter question: 8.2 Due February 1
Ion channels/active transport
Data Debrief of the RBC lab
Endocytosis pp. 341-352
Con’t
Cellular Communication: How do cells respond to external stimuli?
Hormones and receptors Chpt. 14
EXAM I
Receptors: G protein signal transduction
Receptors: Receptor Tyrosine Kinase case study
Con’t
Quiz on pp. 392-402
Receptors: The JAK/STAT pathway
Energy Transformation: How do cells get energy?
Chloroplasts and Photosynthesis Chpt. 11
Energy Transformation: How do cells get energy?
Energy Conversions in Mitochondria: Chpt. 9 and 10
Con ‘t
Explain the difference between oxidative and substrate level phosphorylation and indicate where in cell
respiration each occurs. Due on March 11
EXAM 2
Spring Break
Spring Break
Spring Break
Con’t
Structure and Function: How do proteins get to their intended destinations?
Protein Targeting to Organelles pp. 696-705
Con’t
Secretory pathway Chpt 12 pp. 324-340
EXAM 3
Con’t
Data Debrief for the Myoglobin Lab
Con’t
Easter Break
Easter Break
Vesicular Trafficking
Quiz on Chpt 12 pp. 324-340
4/5
4/8
4/10
4/12
4/15
4/17
4/19
4/22
4/24
4/26
4/29
5/1
5/3
5/6
5/8
5/10
5/13
Structure and Function: How do cells get rid of wastes?
Lysosomes and peroxisomes pp. 352-360
Structure and Function: The Cytoskeleton Chpt. 14 and 15
Microfilaments
EXAM 4
Intermediate filaments
Microtubules
Structure and Function: The Genetic Blueprint
Chromatin Structure. pp. 512-517 and pp. 524-533
Oral Presentations
Oral Presentations
Chromatin Structure Con’t
Nuclear Structure pp. 536-543
Nucleolus and Ribosomes pp. 543-544
Cellular Communication: The Cell Cycle pp. 580-590
Cells Gone Wild: Cancer Cells, Chpt 24
Cell Motility pp. 453-459, 471-475
EXAM 5
Collecting data from Tumor Drug lab
Discussion of the themes
Final Exam: Friday May 17 10:30-12:30
Lab Practical Study Guide
There will be a lab practical May 2, 2013. The following is a list of information that should help you prepare for the
exam.
For this practical, you should be able to:
1. Make a solution of a specified molarity.
2. Create a table and/or graph based on data provided.
3. Solve dilution problems.
4. Determine the OD of a solution and determine the AMAX of a solution.
5. Create a standard curve and use it to determine the concentration of an unknown solution of protein.
6. Demonstrate proficiency in using a light microscope
7. Properly use aseptic technique to feed cells in culture.
8. Determine the number of cells in a solution using a hemocytometer.
9. Explain how size exclusion chromatography can be used to separate proteins and determine when various
molecules will elute from a SEC column
10. Describe how immunofluoresence works to label molecules and describe the basics of the procedure.
11. Describe the process of SDS PAGE and size exclusion chromatography
12. Identify organelles from an electron micrograph
13. To perform a task using protocols used during the course of the semester using information. For example
you may be asked to determine the AMAX of a solution or determine the protein concentration of a
solution. You will not be given directions on how to do this. You will be allowed to use your notebook
however. The list of possible tasks include determining the AMAX of a solution, determining protein
concentration of a solution, determine myoglobin concentration, using size exclusion chromatography to
separate molecules in a mixture, or splitting and determining the concentration of cells in a culture. The
key to this part of the pratical is to have a good notebook.
Lab Notebook Assessment
You will be required to keep a lab notebook. The notebook is to be used to record your data and prepare for the
day’s activity. Before the lab period you must create an outline of the day’s activities. This should be found in your
notebook. The purpose of this is to help you prepare yourself for the day’s activities and to maximize efficiency in
the lab. The outline should include the following:
a.
b.
c.
d.
Summary of the objectives for the lab. This is to be in your own words.
A general outline or flow chart of what is to be done during the class. You don’t need a step-by-step chart
but generally what you are going do during the lab.
A list of all data to be collected - essentially what data you should have when you are done with the
experiment.
Any questions you might have before the lab begins. This is your time to clarify any part of the process. I
won’t be spending a lot time preparing you for the lab. So be prepared to ask questions. If you don’t have
any questions, I assume you know what you are doing and will let you get started.
The outline will be worth 4 points toward the final point total for the lab notebook grade. At the beginning of the
lab class you will show the instructor your outline to get credit. You must have it completed before you come to
class or you will automatically lose the 4 points. You can miss one without penalty. If you leave it at home, you
will still lose points.
So don’t forget the outline!
Here are the assessment criteria for the outline:
4 pts
Complete and goes beyond what is expected. Includes an accurate, well thought
out and well written statement of the purpose of the lab. Has an outline that
accurately reflects lab activities and includes a complete list of data to be
collected.
3 pts
Diverges from the above standards in one substantial way or a few minor ways
2 pts
Diverges from the above standards in two substantial way or many minor ways
1 pts
Diverges from the above standards in three substantial ways.
0 pts
Not done
What should be found in the notebook?
1. Your outline – Make sure to review the items required in your outline. (4 pts)
2. Procedure (2 pts)
You must write out the procedure in enough detail that you could go back in 6 months and
successfully repeat your experiment. DO NOT paste in a copy.
3. All data and any observations from your work in lab (4 pts).
The notebook doesn’t have to be neat, but it must be complete. I should be able to find in your notebook any and all
data presented in your lab report. For example if you measured the diameter of 5 red blood cells during your lab, all
five measurements should be found in your notebook in a way that is easy to find and interpret. In addition, any
sample calculations should also be included in your notebook. Your notebook is a record of what you did in lab on
any given day. You should be able to go back to your notebook after several months and know exactly what you did
on that day in the lab. If data presented in a lab report cannot be found in your notebook, points will be deducted
from your final score. In your notebook, always include the date on which you collected your data. Here are the
assessment criteria for the data section of your notebook.
4 pts
3 pts
2 pts
1 pts
All data/observations are present
Missing some of the necessary data/observations required of the lab
Missing more than half of the necessary data/observations required of the lab
Missing most of the necessary data/observations required of the lab
What should not be found in your notebook?
1. Your lab report. This is to be handed in separately.
2. Answers to questions. This is to be included in your lab report.
Formal Research Report Rubric
Abstract (5 pts)
5 pts
Includes a statement of the general topic, the question being answered, a short
description of the methodology, a short summary of the results, and the
conclusions written in a format appropriate for an abstract.
4 pts
Diverges from the above standard in a few minor ways
3 pts
Diverges from the above standard in one substantial way or many minor ways
2 pts
Diverges from the above standard in two substantial ways and many minor ways
1 pts
None of the above criteria are met
0 pts
Did not include an abstract
Results (10 pts - Score X 2)
5 pts
Results are clearly stated, narrative is organized so it is easy for the reader
to see trends, the data and observations are analyzed accurately, enough
data was taken to establish conclusion, proper format for a results section is
followed.
4 pts
Diverges from the above standard in a few minor ways
3 pts
Diverges from the above standard in one substantial way or many minor ways
2 pts
Diverges from the above standard in two substantial ways and many minor ways
1 pts
None of the above criteria are met
0 pts
Did not include a results section
Data Presentation (10 pts – Score X 2)
5 pts
Data is clearly presented and appropriately labeled, all figures and tables include
titles and figure legends when appropriate, all the required data is presented that
supports the conclusion,
4 pts
Diverges from the above standard in a few minor ways
3 pts
Diverges from the above standard in one substantial way or many minor ways
2 pts
Diverges from the above standard in two substantial ways and many minor ways
1 pts
None of the above criteria are met
0 pts
Did not include the appropriate data in the report
Format (10 pts – score X 2)
5 pts
Sentences are complete, grammar is excellent, no spelling errors, organization is
clear, science content is correct, etc. is at college level, good word choice.
4 pts
Diverges from the above standard in a few minor ways
3 pts
Diverges from the above standard in one substantial way or many minor ways
2 pts
Diverges from the above standard in two substantial ways and many minor ways
1 pts
None of the above criteria are met
Total (35 pts)
35-32 pts
31-28 pts
27-24 pts
23-19 pts
Below 19
A
B
C
D
F
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