Biology 212A: Cell Biology
Spring 2016 Syllabus
Instructor:
Leslie Saucedo
Office:
TH257F
Office Phone: 879-2788
Email:
lsaucedo@pugetsound.edu
Office Hours: Monday and
Thursday 11am-noon
& by appointment
Required Texts: 1. Cell and Molecular Biology, Concepts and Experiments, 7th ed., 2013, Karp
2. Biology 212 Laboratory Manual, Spring 2016, Staff
3. Bound lab notebook with duplicate pages
Recommended Text: A Student Handbook for Writing in Biology 4th ed., 2013, Knisley
OR A Short Guide for Writing about Biology 8th ed., 2012, Pechenik
Course Outline
Biology 212 builds complexity upon the fundamentals of cell structure and function that were
introduced in the prerequisite course, Biology 111. In this course, we will cover, in depth, the
molecular processes that give life to the cell and the mechanisms by which cells receive and
respond to signals from their environment. We will examine how cells work together under normal
circumstances, focusing on nerve transmission, endocrine and immune responses. We will also
explore the consequences of abnormal cell function, including cancer. Finally, this course strongly
emphasizes methodological approaches and data interpretation used to build models of cellular
processes.
Course Objectives
I. To understand and apply five core concepts of biology:
1. Evolution: the diversity of life evolved over time via genetic alterations and
selection of resultant phenotypes (from the protein to organismal level).
2. Structure and function: structure reflects function (from molecules to organisms).
3. Information flow, exchange, and storage: organisms interact with their environment
through the context-dependent expression of the genetic information that they
inherit (from cells to organisms).
4. Pathways and transformations of energy and matter: biological systems grow and
change by processes based upon chemical transformation pathways and are governed
by thermodynamics.
5. Systems: a quantitative understanding of complex biological processes at multiple
functional scales.
II. To introduce you to common methods used to study cell biology
III. To further develop research and analytical reasoning skills
IV. To augment your ability to perform and present scientific research
Class Sessions
Lecture section meets Tuesday and Thursday from 9:30-10:50pm in TH395. Lecture topics and
readings that complement each lecture are provided in the attached schedule. Completing the
readings prior to the corresponding lecture is HIGHLY recommended. Pay particular attention to
the figures as they often present a concise, visual summary. This will greatly aid in comprehension
and effective note taking during lecture. Following lecture, I suggest revisiting the assigned reading
and directing your focus to the specific material that was addressed in class. Lectures will include
student participation in the form of questions posed to the students, class activities and discussions.
Additionally, students are wholly encouraged to ask the instructor to clarify points that are unclear
during the lecture.
There will be a short break during each class session to get your blood recirculating.
Exams will be held during the normally scheduled class period.
Laboratory Exercises and Notebooks
The weekly laboratory component of Biology 212 (TH313) is designed to accompany and extend
subjects introduced in the lecture. It is essential to come to lab prepared. Carefully read the
appropriate section of your lab manual BEFORE coming to lab. Most of the lab exercises contain
PRE-LAB PREPARATIONS AND QUESTIONS THAT MUST BE SUBMITTED AT THE
BEGINNING OF THE LAB SESSION. Preparing for labs in this manner is essential for
establishing confidence and competence while performing lab activities.
All pre-lab assignments and laboratory data must be recorded using ink in a bound notebook with
duplicate pages. Reserve the initial pages for identification (your name, course number and
semester) and a table of contents. In your lab notebook, you should keep an orderly account of
procedures actually used and data collected. Without such a record, it is unlikely that you’ll
remember accurately what you did and found, making it difficult to use results as a guide to further
experiments. ALL DATA SHOULD BE RECORDED DIRECTLY INTO YOUR LAB
NOTEBOOK WHILE YOU ARE PERFORMING AN EXPERIMENT. Your notebook doesn’t
need to be a work of art—just legible. Record your data in tables and use titles, headings and
labels. THE GOAL OF KEEPING A LABORATORY NOTEBOOK IS TO ALLOW ANYONE
TO REPLICATE YOUR EXPERIMENT WORKING ONLY FROM YOUR NOTEBOOK. If you
make a mistake, cross it out with a single line (you may find out later that the data is useful) and
although it is tempting to recopy your notes, it is highly unrecommended because it easily
introduces errors.
Whatever format your pre-lab takes, for each lab you should record the following in your
notebook:
1) The purpose of or the question to be answered by the lab exercise.
2) List of reagents (when applicable), including any hazardous properties.
3) Outline of the procedure in a stepwise manner.
Duplicate pages will be turned in at the end of each lab period.
In EXTENUATING CIRCUMSTANCES ONLY, you may be able to attend a different lab section
than for which you are registered, provided that you first seek approval of the instructor(s). Labs
cannot be made up after the last lab section of the week has met.
Quizzes and Exams
There will be six short quizzes given over the course of the semester (see schedule). QUIZZES
WILL BE GIVEN DURING THE FIRST 15-20 MINUTES OF LECTURE and will cover the
indicated previous lectures. These short quizzes are designed to help you identify any areas of
weak comprehension before taking exams.
Three “mid-term” exams (see schedule) will each be designed to be 60 minutes in length. Exams
will consist of short answer-based questions (including explanations, inference and application).
The topics covered by each exam are indicated in the schedule and will include material from
lectures, laboratory and readings. A take-home Data Set will be provided before each exam for
your contemplation. You are free to discuss data sets with any currently enrolled cell student, but
not with anyone outside of this class. Several questions to assess comprehension of the Data Set
will appear on the exam.
THERE WILL BE NO MAKE-UP OF EXAMS OR QUIZZES. Absence for a bona fide medical
reason will require written evidence and MAY (OR MAY NOT) be considered in assigning the
final grade.
The final exam is scheduled for Tuesday, May 10th from 8:00-10:00am. This exam will include a
section on material following the third “mid-term,” material from topics covered earlier in the
course, and will require you to integrate the important concepts covered throughout the semester.
THE FINAL EXAM MUST BE TAKEN AT THE SCHEDULED TIME.
Additional Reading:
A Student Handbook for Writing in Biology 4th ed., (Knisley 2013) OR A Short Guide for Writing
about Biology 8th ed. (Pechenik 2012) are useful guides for writing in biology courses. Either book
provides guidance for scientific writing and presentation (including construction of figures, tables,
graphs and posters).
Moodle:
Course material including the syllabus, data sets and keys to quizzes/exams will be posted in a
timely manner. In addition, links to external sites (animations, movies etc…) that are shown in
class will also be available.
Academic honesty
All assignments must be written individually (including lab assignments that are performed
with partners). PLAGIARISM, CHEATING AND OTHER FORMS OF ACADEMIC
DISHONESTY WILL NOT BE TOLERATED. You are responsible for understanding what
constitutes academic honesty. Refer to The Logger (the University’s academic handbook) for
definitions and examples of academic dishonesty and the resultant penalties.
Grading
Final letter grades will be based on your total accumulated points at the end of the semester and
are partitioned as follows:
5 quizzes:
10%
3 “mid-term” exams:
36%
final exam:
24%
laboratory :
30%
TOTAL:
100%
Biology 212A: Cell Biology
Spring 2016 Lecture Schedule
Required Texts:
Instructor: Leslie Saucedo
Office: TH257F
Phone: 879-2788
Email: lsaucedo@pugetsound.edu
Cell and Molecular Biology, Concepts and Experiments, 7th ed., 2013, Karp
Biology 212 Laboratory Manual, Spring 2015, Staff
Bound lab notebook with duplicate pages
Recommended Text: A Student Handbook for Writing in Biology 4th ed., (Knisley 2013) OR
A Short Guide for Writing about Biology 8th ed., 2012, Pechenik
Schedule:
Date
Lecture Topic
Text (Karp)
Lab Exercise
Tue. 1-19 Course introduction/general overview
pp 1-23
No labs
Thu. 1-21 Macromolecules I: polysaccharides, lipids & nucleic acids
pp 40-49, 77-79
___________________________________________________________________________________________________________
Tue. 1-26 Macromolecules II: proteins
pp 50-70, 76-77. 541-542
Light Microscopy
Thu. 1-28 Membranes: composition and function Quiz I (1/19-1/26)
pp 120-144
___________________________________________________________________________________________________________
Tue. 2-2
The endomembrane system: targeting and trafficking
pp 270-289
Protein Analysis I
Thu. 2-4
The endomembrane system: trafficking continued and
pp 290-307
lysosomal function
___________________________________________________________________________________________________________
Tue. 2-9
Nuclear structure and import/export Quiz II (1/28-2/4)
pp 488-493, 510-512
Protein Analysis II
Thu. 2-11 Enzymes and general overview of metabolism
pp 94-117
___________________________________________________________________________________________________________
Tue. 2-16 Cellular respiration I: moving energy from chemical
pp 178-197
Bioinformatics
bonds to a chemical gradient
Thu. 2-18 Exam I (1/19-2/11)
___________________________________________________________________________________________________________
Tue. 2-23 Cellular respiration II: all about ATP Synthase
pp 198-209
Centrifugation
Thu. 2-25 Photosynthesis
pp 211-232
___________________________________________________________________________________________________________
Tue. 3-1
Membrane transport Quiz III (2/16-2/25)
pp 147-163
Enzymes I
Thu. 3-3
Nerve function
pp 164-174
Date
Tue.
Thu.
Lecture Topic
3-8
3-10
Text (Karp)
Lab Exercise
Cytoskeleton I : Microtubules
pp 324-345
Literature Workshop I
Cytoskeleton II: intermediate filaments and
pp 354-364
microfilaments Quiz IV (3/1-3/8)
___________________________________________________________________________________________________________
Tue. 3-15 Spring Break
No Labs
Thu. 3-17
___________________________________________________________________________________________________________
Tue. 3-22 Cell motility and movement
pp 345-353, 364-382
Enzymes II
Thu. 3-24 Extracellular matrix
pp 236-250
___________________________________________________________________________________________________________
Tue. 3-29 Exam II (2/16-3/22)
Advanced Microscopy
Thu. 3-31 Cellular interactions
pp 250-266
___________________________________________________________________________________________________________
Tue. 4-5
Signal transduction I: G protein-coupled receptor p.w.
pp 617-636
Cell Culture I
Thu. 4-7
Signal transduction II: tyrosine kinase p.w.
pp 636-648
Lab Report
Quiz V (3/24-4/5)
Consultations
___________________________________________________________________________________________________________
Mon. 4-12 Signal transduction III: crosstalk and apoptosis
pp 653-655, 656-660
Cell Culture II
Thu. 4-14 Immunology I: B cells and T cells
pp 699-710
Lab Report Due
___________________________________________________________________________________________________________
Tue. 4-19 Immunology II: recognizing self from non-self
pp 716-726
Literature Workshop II
Quiz VI (4/7-4/14)
Thu. 4-21 Mechanics and regulation of the mitotic cell cycle
pp 572-600
___________________________________________________________________________________________________________
Tue. 4-26 Exam III (3/24 to 4/19)
Bioethics & Lab
Thu. 4-28 Biology of cancer
pp 664-681
Practical
___________________________________________________________________________________________________________
Tue. 5-3
Strategies to combat cancer and course summary
pp 687-693
No Labs
Thursday, May 10th FINAL EXAM (comprehensive)
8 to 10am