San José State University
College of Science, Department of Biological Sciences
BIOL1B, Foundations of Cell Biology and Physiology,
Section 1, Spring 2013
Instructor:
Julio Soto
Office Location:
DH541
Telephone:
(408) 924-4925
Email:
julio.soto@sjsu.edu
Office Hours:
Wednesday 1:00-3:00pm
Class Days/Time:
Tuesday, Thursday noon-1:20pm
Classroom:
SCI 142
Prerequisites:
Bio 1A and Chem 1A (with a C or better), Eng 1A
Co-requisites:
Chem 1B, Eng 1B
Course Description
The objective of Bio 1B is to explore cellular and physiological mechanisms from which
biological diversity has arisen. Concepts will include: organic molecules, cellular
structures/functions, cell-cell communication, cellular energetics, molecular evolution, gene
expression, enzymes, digestion, endocrine systems in animals and plants, nervous system, the
cell cycle, and cancer. The course will culminate in a five-week research project.
Course Goals and Student Learning Objectives
Upon successful completion of this course, students will be able to:
LO1: construct testable hypotheses
LO2: design, carry, and complete a research project
LO3: construct and interpret simple DNA phylogenetic trees
LO4: describe how cellular structures influence function
LO5: understand enzyme regulation by constructing a graphical representation of how
factors influence enzyme activity
LO6: understand cellular energetics by constructing a graphical representation of energy
transfer between the structures involved in ATP production, and by performing ATP
calculations of metabolic reactions occurring aerobically and anaerobically
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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LO7: understand gene expression mechanisms by constructing and performing a
kinesthetic representation of transcription and translation
LO8: Compare and contrast hormonal action in plants and animals
LO9: understand what cell cycle problems can result in cancer development
Required Texts/Readings
Textbook
1) Russell et al., (2011) Biology: The Dynamic Science. 2nd Edition. Brooks Cole Cengage
Learning.
Other Readings
2)
BIOL1B Fall 2012 Lab Manual
3)
BIOL1B Fall 2012 Activity Manual
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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Course Format
Bio 1B consists of two lectures (3 hrs), one workshop activities (2 hrs) and one laboratory (3 hrs)
meeting per week. During the lectures, you will be introduced to major concepts, focused around
a series of sub-themes. During workshops, you will work on skill building and problem-solving.
Workshop activities will reinforce lecture concepts, and will also lead to the development of
skills that are needed for the lab. In the labs, you will be given the opportunity to explore these
topics in more depth through a variety of integrated instructor-guided and self-led research
activities.
Classroom Protocol / Tips for Success
1.
Attend all class periods. Lecture exams will be based entirely (unless indicated) on the
material covered in class.
2.
Turn-off your cell phone. We will ask you to leave the classroom if your phone rings.
3.
Do not to arrive late to class. We will start class on time. If you arrive late, it may take you
a long time to figure out what we are talking about or doing in class.
4.
Feel free to interrupt us during class if you don’t understand something. I will be happy to
write anything on the board if necessary.
5.
Do not talk during the lecture component of the class. If you have a concern please ask me
directly.
6.
Do the assigned reading before hand. It will help you understand the material.
7.
Try to review your notes after each lecture (try rewriting them). Reviewing material within
24 hours can increase retention time and memory longer than you would believe.
8.
Think about the material. Do not rely strictly on memorization because the exams will
require more of an understanding of the material.
9.
Form a study group. You may want to study with one or more of your friends so you can
share ideas. Try giving each other practice exams. Divide tricky concepts up among your
group and write short presentations to explain them to each other.
10.
Feel free to attend our office hours to discuss the lectures and class information. Come with
specific questions. You can make an appointment with me if you cannot make my regular
office hours. I will do our best to accommodate your schedule. You can also communicate
with me via e-mail.
Dropping and Adding
Students are responsible for understanding the policies and procedures about add/drop, grade
forgiveness, etc. Refer to the current semester’s Catalog Policies section at
http://info.sjsu.edu/static/catalog/policies.html. Add/drop deadlines can be found on the current
academic calendar web page located at
http://www.sjsu.edu/academic_programs/calendars/academic_calendar/. The Late Drop Policy
is available at http://www.sjsu.edu/aars/policies/latedrops/policy/. Students should be aware of
the current deadlines and penalties for dropping classes.
Information about the latest changes and news is available at the Advising Hub at
http://www.sjsu.edu/advising/.
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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Assignments and Grading Policy
Specific activity and lab assignments will be discussed during those section meetings. A
grade of C or better is required for entrance to courses listing Biology 1B as a
pre-requisite. Make-up exams will not be provided. If a student misses a midterm, a
comprehensive final will be used to replace the missing exam.
Lecture. The lecture grade will be based on four exams (3 midterm and 1 comprehensive final).
The exams will include a mix of short essay, long answer, and word problems.
Answers that are illegible or ambiguous will be given a zero.
Activity.
Laboratory. The lab grade will be based on three components: two lab exams, a group
presentation, and a report.
Homework. Weekly homework problems will be assigned through APLIA. Homework
problems must be completed before the due date/time.
Class activities
Total possible points
% of the total grade
Lecture
Lecture exam I
Lecture exam II
Lecture exam III
Final exam
50
100
100
200
5%
10%
10%
20%
Activity
Activity Worksheets
200
20%
Lab
Lab exam I
Lab exam II
Group presentation
Lab Report
100
100
50
50
10%
10%
5%
5%
Homework
APLIA Homework
50
5%
1000pts
100%
Final letter grades will be calculated from the points earned:
A+ = 970 or more
A = 930-969 pts
A- = 900-929 pts
B+ = 870-890 pts
B = 830-869 pts
B- = 800-829 pts
C+ = 770-799 pts
C = 730-769 pts
C- = 700-729 pts
D+ = 670-699 pts
D = 630-669 pts
D- = 600-629 pts
F = 590 pts or less
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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University Policies
Academic integrity
Your commitment as a student to learning is evidenced by your enrollment at San Jose State
University. The University’s Academic Integrity policy, located at
http://www.sjsu.edu/senate/S07-2.htm, requires you to be honest in all your academic course
work. Faculty members are required to report all infractions to the office of Student Conduct and
Ethical Development. The Student Conduct and Ethical Development website is available at
http://www.sjsu.edu/studentconduct/.
Instances of academic dishonesty will not be tolerated. Cheating on exams or plagiarism
(presenting the work of another as your own, or the use of another person’s ideas without giving
proper credit) will result in a failing grade and sanctions by the University. For this class, all
assignments are to be completed by the individual student unless otherwise specified. If you
would like to include your assignment or any material you have submitted, or plan to submit for
another class, please note that SJSU’s Academic Policy S07-2 requires approval of instructors.
Campus Policy in Compliance with the American Disabilities Act
If you need course adaptations or accommodations because of a disability, or if you need to
make special arrangements in case the building must be evacuated, please make an appointment
with me as soon as possible, or see me during office hours. Presidential Directive 97-03 requires
that students with disabilities requesting accommodations must register with the Disability
Resource Center (DRC) at http://www.drc.sjsu.edu/ to establish a record of their disability.
Student Technology Resources (Optional)
Computer labs for student use are available in the Academic Success Center located on the 1st
floor of Clark Hall and on the 2nd floor of the Student Union. Additional computer labs may be
available in your department/college. Computers are also available in the Martin Luther King
Library.
A wide variety of audio-visual equipment is available for student checkout from Media Services
located in IRC 112. These items include digital and VHS camcorders, VHS and Beta video
players, 16 mm, slide, overhead, DVD, CD, and audiotape players, sound systems, wireless
microphones, projection screens and monitors.
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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Learning Assistance Resource Center (Optional)
The Learning Assistance Resource Center (LARC) is located in Room 600 in the Student
Services Center. It is designed to assist students in the development of their full academic
potential and to inspire them to become independent learners. The Center's tutors are trained and
nationally certified by the College Reading and Learning Association (CRLA). They provide
content-based tutoring in many lower division courses (some upper division) as well as writing
and study skills assistance. Small group, individual, and drop-in tutoring are available. Please
visit the LARC website for more information at http://www.sjsu.edu/larc/.
SJSU Writing Center (Optional)
The SJSU Writing Center is located in Room 126 in Clark Hall. It is staffed by professional
instructors and upper-division or graduate-level writing specialists from each of the seven SJSU
colleges. Our writing specialists have met a rigorous GPA requirement, and they are well trained
to assist all students at all levels within all disciplines to become better writers. The Writing
Center website is located at http://www.sjsu.edu/writingcenter/about/staff/.
Peer Mentor Center (Optional)
The Peer Mentor Center is located on the 1st floor of Clark Hall in the Academic Success Center.
The Peer Mentor Center is staffed with Peer Mentors who excel in helping students manage
university life, tackling problems that range from academic challenges to interpersonal struggles.
On the road to graduation, Peer Mentors are navigators, offering “roadside assistance” to peers
who feel a bit lost or simply need help mapping out the locations of campus resources. Peer
Mentor services are free and available on a drop –in basis, no reservation required. The Peer
Mentor Center website is located at http://www.sjsu.edu/muse/peermentor/
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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BIOL1B / Foundations of Cell Biology and Physiology, Spring
2013, Course Schedule
Table 1 Course Schedule
Lecture
Date
Topics, Readings, Assignments, Deadlines
Sub-theme: Cellular structure and function
1
Jan 24
2
Jan 29
Overview of Class
Molecules of life; carbohydrates, lipids, amino acids, nucleic acids
3
Jan 31
Membrane structure
4
Feb 5
Membrane Transport
5
Feb 7
Cellular structures 1
6
Feb 9
Cellular structures 2
7
Feb 12
LECTURE EXAM I
8
Feb 14
Sub-theme: Energy
Enzymes
9
Feb 19
Enzyme regulation
10
Feb 21
Digestion System/Digestive enzymes
11
Feb 26
Anaerobic respiration
12
March 5
Aerobic respiration
21
March 7
Electron Transport System
22-23
March
12-14
Photosynthesis
24
March
19
LECTURE EXAM II
Sub-theme: Genetic information transfer
March
21
DNA replication I
March
25-29
SPRING BREAK
26
April 2
DNA replication II
27
April 4
Transcription
28
April 9
Translation
29
April 11
Exam III
25
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Lecture
Date
Topics, Readings, Assignments, Deadlines
Sub-theme: Systems and interactions
30
April 16
Action Potential
31
April 18
Nervous system
32
April 23
Endocrine system
33
April 25
Signal transduction, hormones, and receptors
34
April 30
Plant hormones
36
May 2
Cell cycle
37
May 7
Cell cycle regulation
38
May 9
Cancer
39
May 13
Cancer
Final
Exam
May 20
12:15-2:30pm
SCI 142
Table 2. Lab Schedule
Week of
Lab Activity
Jan 28
Feb 4
Feb 11
Feb 18
Feb 25
March 4
Basic skills
Partial purification of proteins I
Thin layer Chromatography
Osmosis Lab
Lab Exam I
Invertase enzyme lab
March 11
Photosynthesis
March 18
PCR of genetically-modified foods
April 1
DNA separation on agarose gels
April 8
LAB EXAM II
Projects
April 1529
May 6
Research Project Presentations
Table 3. Workshop/Activity Schedule
Foundations of Cell Biology and Physiology, BIOL1B, Spring 2013
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Week of
Activity
Jan 28
Feb 4
Feb 11
Feb 18
Feb 25
Protein Structure
Cell structures
No activity
Enzyme regulation
Digestion
March 4
Cellular Energetics
March 11
Photosynthesis
March 18
No Activity
April 1
April 8
DNA replication and Translation Models
No Activity
April 15
Molecular Phylogenetics
April 22
April 29
May 6
Nervous System
Plant Hormones
Cell Cycle
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