Winter 2012
BIOL-6B: Cell & Molecular
Biology
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BIOLOGY-006B:
Lecture |
Tue & Thu 12:30–2:20 |
SC
1102 |
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BIOLOGY–006B–
Lab section 03
–CRN: 00224 |
Mon/Wed 9:30–12:20 |
SC
2118 |
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BIOLOGY–006B–
Lab section 04 –CRN:
00225 |
Mon/Wed 1:30–4:20 |
SC
2118 |
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BIOLOGY–006B–
Lab section 05 –CRN:
00226 |
Tue/Thu 4:30–7:20 |
SC
2118 |
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o Required
Text: Biology,
9th ed., Campbell, N.A. & J.B. Reese;
Pearson Education, 2011. o Required Lab Manual: Biology 6B Laboratory
Manual, Winter 2012, Heyer, B., DeAnza
College á
download and print from the class website. |
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o Required Aplia tutorial-homework-quiz
website: http://www.aplia.com/ o Textbook supplemental Mastering Biology website: http://www.masteringbio.com/ |
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Instructor: |
Email: heyerbruce @ fhda.edu |
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Office:
SC 1212 Office Hours: Mon/Wed
12:30–1:20 Tue/Thu 11:30–12:20 |
Phone: (408) 864-8933 |
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Section 5 Lab Instructor: |
Email: vidyodhaya @
hotmail.com |
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COURSE
DESCRIPTION
This course is designed to introduce you, the student, to the study and understanding of the structure, genetics, biochemistry, and physiology of cells. The cell is the basic fundamental unit of life. All the processes of life, including harnessing energy, reproduction, inheritance of characteristics, and responding to the environment, can only be fully appreciated with an understanding of their cellular bases. Biol-6B will emphasize processes and structures common to most cells, and prepare you for more extensive, specialized upper-division work. The development of the field of cell biology and the focus of current innovative research in molecular biology will also be discussed. You will become more independent by learning to read, interpret, and evaluate original scientific papers.
The laboratory portion of the course provides hands-on experience using the modern instruments and methods of molecular biology. These elegant techniques provide practical experience for those pursuing careers in biological research.
COURSE
OBJECTIVES
By successfully completing and passing Biol-6B, the student
will demonstrate by means of objective exams, essays, oral presentations,
laboratory proficiency, and written research reports, a practical competency
and fluent exposition of the following topics:
o Biological chemistry - Explain the application of
basic chemical principles to the complex chemistry of living systems.
Understand the unique properties of water and carbon as they apply to organic
chemistry. Know the classes of macromolecules and their biological
significance.
o Protein function - Describe the special
significance of proteins in maintaining and regulating the complexity necessary
for all living systems. Define the specific actions of different functional
groups of proteins. Explain how the cellular environment modifies protein
activity.
o Molecular genetics - Explain how the structure of
DNA relates to its function of storing and conveying information. Define a gene
and describe the mechanisms for gene expression and how such expressions are
regulated. Demonstrate how these genetic processes can be manipulated for the
techniques of molecular biotechnology.
o Cell structure - Contrast the structure of
prokaryotic and eukaryotic cells. Elaborate how the cytoskeleton sustains and
transforms cellular organization and provides motility. Identify the eukaryotic
organelles and their functions. Illustrate the dynamic structure of cellular
membranes and their vital roles in selective permeability and
compartmentalization.
o Inter-cellular communication - Describe the chemical and
electrochemical mechanisms of cell-cell interaction. Compare the processes of paracrine and endocrine communication. Contrast the actions
of membrane and nuclear receptors on cellular activities.
o Cell cycle - Describe the processes of
mitosis and cytokinesis in cell division. Explain the
role of stem cells and regulation of the cell cycle in relation to
proliferation, differentiation, apoptosis, and senescence. Postulate how
aberrations of this regulation may lead to cancer.
o Meiosis and sexual reproduction - Explain the modification of
cell division for meiosis and gametogenesis. Explain
how recombination affects the genome. Contrast the advantages of haploid versus
diploid cells, and asexual versus sexual reproduction.
o Bioenergetics - Describe how photosynthetic
cells harness light energy to synthesize organic molecules, and how all cells
use the chemical energy in these organic molecules to power biological processes.
Elucidate the chemistry of proton gradients, redox
reactions, and phosphorylations as they relate to
extracting and distributing energy within the cell. Explain how chloroplast
structure controls the chemistry of photosynthesis, and mitochondria structure
determines cellular respiration.
o Laboratory research - Perform routine procedures
used in biological research laboratories, especially as related to the
techniques of molecular biology. Demonstrate proficiency with standard
protocols of lab etiquette, safety, hazardous materials handling, and
documentation. Interpret published research articles to replicate their
methodology and critique their interpretation of results.
STUDENT
LEARNING OUTCOME
Demonstrate the ability to use appropriate molecular
biology techniques to answer research questions and to interpret and explain
the results.
PREREQUISITES
AND ADVISORIES
Biology-6B is the second part of
the three-quarter introduction to biology series for college students majoring
in biology or a related science. Completion of Biol-6A (organismal
biology) with a grade of C or better is a prerequisite for Biol-6B. This series
is acceptable for transfer to the University of California and California State
University systems and most other colleges. This course is equivalent or
exceeds the rigor and depth of the corresponding introductory biology courses
at these universities. Since the precise sequence of presented topics differs
among institutions, it is strongly recommended that you complete the whole
series at one college.
The study of cell and molecular
biology requires a comfortable familiarity with chemistry. To enroll in
Biol-6B, you need to have passed Chem-1A or Chem-50 with a grade of C or
better, or passed the Chemistry Placement Test administered by the Testing
Center. You needed to meet this chemistry prerequisite before enrolling in
Biol-6A, but Biol-6B is where you'll find that you really use it.
Using equations to calculate
solution concentrations, conversions, and product yields
in lab exercises requires above average math skills. Intermediate algebra
equivalent to Math-105 or Math-114 is recommended.
Students will
be writing essays and lab reports with an expected eloquence appropriate for
scientific professionals. Coherent composition, accurate vocabulary, proper
grammar, and correct spelling DO count! English skills equivalent to EWRT-1A or
ESL-5 are highly recommended.
TIPS
TO HELP YOU DO WELL IN THIS COURSE
There is no
question that this class can seem intimidating with novel concepts, new
vocabularies, and applied chemistry and physics. You must be prepared to invest
a substantial allotment of time and effort to this endeavor. Some keys to
success and satisfaction are:
o Attend every lecture
and lab.
o Be prepared! Do the text
reading before you come to class. If my lecture is the first you hear of a
topic, you'll likely get lost. Especially with the pace we fly through topics:
unprepared = frustrated. Prepare questions for unclear material - questioning
is a form of active
learning.
o Download and
print out the lecture
slides, when available, and bring them to class. But don't expect them to
replace taking notes. Taking notes is another form of active learning.
o Develop good study
habits. Spend time studying outside of class every day. Do not let yourself fall
behind! Review lecture notes after each lecture. Be able to explain the
concepts for each diagram presented in your own words.
o Construct study tools.
Learning content-intensive material such as Biology often requires many steps:
seeing, hearing, thinking, and doing. Create a list of terms in bold print
presented in lecture. Write out flashcards and reorganize your lectures notes
after each lecture as physical activities to help you process the material.
I do not provide study guides for exams - that's your job! I will critique them though if
you wish.
o Form a study group!
Repeated experience has shown that those who study collectively do better. A
study group will help you get to know your fellow classmates and provide
intellectual reinforcement as well as moral support. Come prepared to a group
study session by reviewing lecture material on your own first. Compare notes
and test each other. Learn by teaching: an excellent way to learn how well you
understand a matter is by explaining it to someone else.
o Review! The textbook
supplemental CD-ROM and the publisher's MASTERING BIOLOGY website have flashcards,
quizzes, games, and other tools to enhance your comprehension. They even have
an online tutor to answer questions! Play the games with your study group. For
access, follow the instructions on the first page of the textbook. You can go
to the College Library or the Open Media Lab downstairs in Learning Center West
for help with internet access.
Participation
in this class is expected to proceed with professionalism and mutual respect.
Questions and experiences you have to clarify or enlarge on the topics being
discussed are welcome. Please do not be distracting to your colleagues
(including me) in class. Students are expected to be familiar with the Student
Conduct Code and College Policies on academic integrity and academic freedom
stated in the De
Anza College Catalogue. Individuals found engaging in cheating, plagiarism,
or disruptive behavior will be expelled from the class, awarding a failing
grade, and reported to the administration for further disciplinary sanctions.
Science majors
are also expected to have read the BHES Division Student Handbook for additional advice and
standards. The Handbook
may be downloaded from http://bhs.deanza.edu/StudentHandbook.pdf .
SUPPORT
SERVICES
The
college has a wide range of support services to provide students with
assistance. These services range from tutoring and special short courses
in reading and writing skills to financial aid and special programs for educational
transition, reentry, and disabled students. If you would like to see if
any of these programs would be of help to you, please check with the counseling
office in the Student
and Community Services Center. Consult your class schedule for a list of
telephone numbers, or go to the Student Services website at http://www.deanza.edu/studentservices .
If
you need a special accommodation for a physical or learning disability, please
talk to me after the first class session so that I can make appropriate
adjustments in the class to meet your needs. Visit Disability
Support Services (DSS) in the Student Services Center and the Educational Diagnostic
Center (EDC) in Learning Center West, room 110 for testing, advice,
assistance, and special programs. Consult the Disability Information Student Handbook
(DISH) at http://www.deanza.edu/specialed/dish .
SAFETY
The
laboratory portion of Biol-6B is much more technology-oriented than was
Biol-6A, requiring the use of high-voltage instruments and potentially toxic or
infectious materials. All students will be required to read and sign to affirm
their understanding and acceptance of the "Standard Operating
Procedures" form prepared by the Biology Department. Any student who
knowingly or recklessly endangers anyone's safety, or who repeatedly violates
laboratory safety rules will be expelled from the class and possibly face
further disciplinary actions at the instructor's discretion. If you observe any
activity or situation that you think might be unsafe, please let talk to the
instructor about it. Beyond this course, developing excellent lab safety habits
is essential to your academic progress and scientific career.
Since
De Anza College is located in a seismically active area, students should give
forethought to catastrophic emergency actions. If a significant earthquake
occurs during class, move away from the windows and stay indoors. If you are in
lab, disconnect any gas lines or electrical devices, secure glassware, and take
shelter under the lab bench.
In
the event of an emergency that requires the evacuation of the room, we will
exit the building and regroup outside for roll call and further instructions.
Be careful to avoid traffic lanes. Do not leave campus until you have been instructed
to do so by your instructor or by emergency personnel!
LABS
Biol-6B strongly emphasizes
laboratory-science skill development necessary for biology major degree
programs.
Therefore:
á Participation
in all
labs is expected and you must pass the laboratory portion to receive credit for the course.
á Any
missed lab will result in a proportional loss of points on the lab report for
that day's project or projects.
á If
you miss any three labs you may be dropped from the class or awarded a failing
grade.
á Non-participation
is considered equivalent to non-attendance.
Read the lab experiments before you come to class and come
prepared to begin work. It is next to impossible complete a lab exercise and
learn anything from the process if you are reading the instructions for the
first time. The safety of you and your classmates may depend on your
preparedness when we are using hazardous materials.
The activities explored in lab build
upon concepts presented in lecture, but they do not correlate with the sequence
of topics as they are featured in lecture. The laboratory procedures used will
emphasize the modern tools and techniques of molecular biology that are used to
study cell biology, as well as many other aspects of life sciences.
The course lab exercises are organized
around five
lab project reports. Each report will be a group project and cover
experiments conducted over several lab periods. The students at your lab table
are your lab partners, and your group will turn in one report for each project.
Each project may include different
kinds of experiments over several lab periods, and more than one project may
overlap on the same lab period. So you will need to have very good
organizational and note-keeping practices to keep track of which experiment
relates to which project. The projects will become increasingly complex as the
quarter progresses, and techniques that are used repeatedly will need to be
accomplished with greater efficiency. At first, the instructor will give more
detailed instructions on what to do and how to organize your time. But by the
latter portion of the course, you will be expected to interpret the
instructions and budget your time effectively within your group. It is
important to finish each experiment to complete each project. The better you get at planning and time
management, the more opportunities you will have to repeat experiments if
needed.
The topics for the five lab project
reports are:
1.
DNA restriction
digest, ligation, & electrophoresis. Use enzymes to cleave DNA at specific sites
and electrophoresis to analyze the cleavage products. This project will take 2
lab periods.
2.
Bacterial
conjugation.
Use direct and indirect methods to assess the transfer of genes from one kind
of bacteria to another by culturing them under different conditions and
observing the acquisition of heritable survival characteristics. The project
will take all or part of 2-3 lab periods.
3.
pGLO. Insert a foreign gene into bacteria, isolate the new
protein gene product from the bacteria, and identify the DNA of the transferred
gene in the bacterial DNA. This project will take all or part of about 7 lab
periods.
4.
PV92 polymerase
chain reaction (PCR). Rapidly copy a part of your own DNA. Compare your DNA with
the corresponding part of the DNA of others in the class. This project will
take 2 lab periods.
5.
Bacteriophage. Infect
bacterial cells with bacteriophage virus. Collect the
virus from infected cells and use it to infect more cells. Use molecular
techniques to identify the viral DNA from the dead bacterial cells. This
project will take all or part of about 4 lab periods.
The project instructions in the Lab Manual
include directions for how each report should be composed.
Each report shall be graded on a scale
worth 20 points. Each student's score shall be a portion of those points based
upon attendance, participation, and contribution to the group effort for that
project.
LAB EXAM
The final lab class will consist of a
comprehensive
lab exam derived from all of the lab projects and methodologies. Bring a GB-8 (large) Green
Book for the lab exam essays and illustrations.
QUIZZES
Each lecture topic coincides with a
pair of problem sets presented on the Aplia website. One of these
problem sets is designated as a timed/graded quiz, the other as supplemental
in-depth study material. The required quiz is due before noon of the next
lecture day. Although different quizzes have different numbers of questions,
each counts the same percentage of the overall quiz score.
LECTURE EXAMS
There are three exams based upon material
covered in lecture. (The final exam is Exam 3.) These exams are non-cumulative
and will be composed of multiple choice and matching questions and diagram
interpretations. A new (clean and unwrinkled) Scantron Form # 882-E
(green) answer sheet and a #2 pencil will be needed for each lecture exam.
Please note the
dates of all exams. If you are sick or have an emergency, contact me BEFORE the
exam and special arrangements might be made in extenuating circumstances. Vacation plans are not extenuating
circumstances! If a last-minute crisis occurred on the way to the exam, contact
me before the end of the day.
GRADING
o Lab Project
Reports:
Five reports; each report counts 20 points. (5 x 20 = 100 points)
o Quizzes: ~20 quizzes;
average score of all quizzes counts 100 points.
o Lab Exam: One exam;
counts 100 points.
o Lecture Exams: Three exams.
Each exam counts 100 points. (3 x 100 = 300 points)
The final class
grade will be determined as a percentage of the maximum total 600 points:
92-100% = A
89-91% = A-
86-88% = B+
80-85% = B
77-79% = B-
74-76% = C+
65-73% = C
53-64% = D
<53% = F
á Go
To Bruce Heyer's Homepage.