Biology 22 Spring 2010
Lecture: TTh 9:30-10:50 am, SCI 151
Section 1238 Laboratory:► Fri 9 am-12:05 pm, SCI 225
Section 1239 Laboratory:► Fri 1 pm- 4:05 pm, SCI 225
Dr. M. A. Bober / Dr. Mary ColavitoScience 281 / Science 276
(310) 434-3140 / (310) 434-4710
Office Hours: See listing on homepage / Office Hours: See listing on homepage
/
http://homepage.smc.edu/bober_mary / http://homepage.smc.edu/colavito_mary
Texts and Lab Manual
Ø Genetics: A Conceptual Approach, Second Edition. B. Pierce, W.H. Freeman and Company, New York, 2005.
Ø Biology 22: Genetics and Molecular Biology Lab Manual, M. Colavito,
M. Bober and R. Logan. Santa Monica College, 2006.
Ø Gene Therapy. M. Colavi to, Benjamin Cummings, San Francisco, 2007.
A copy of this booklet will be loaned to you for use during the course.
Grading
2 Lecture Exams @ 100 points each 200
2 Quiz/Essays @ 65 points each 130
2 Lab Reports @ 50 points 100
4 Lab Worksheets @ 10 or 15 points each 45
Class Problems and Problem Sets 60
1 Lab Practical Exam 65
Final Exam 100
Total 700
Percentage of Total Points / Grade Earned90-100% / A
80-89% / B
65-79% / C
50-64% / D
Below 50% / F
Student Learning Outcomes
After completing the course, students should be able to:
1. Apply the scientific method by proposing a hypothesis; researching the topic; determining appropriate tests; performing tests; collecting, analyzing, and presenting data; and finally proposing new questions about the topic.
2. Analyze polymorphisms found in the human genome by Polymerase Chain Reaction, e.g. variable tandem repeats.
3. Analyze and interpret the effect of genotype on phenotype.
4. Evaluate and critique the relationships between data from molecular biology methods and genetic patterns of inheritance.
5. Interpret the effects of DNA mutations on patterns of inheritance.
Institutional Learning Outcome
Students should demonstrate confidence in their understanding of biological concepts and the scientific method to evaluate and critique current media or a scientific report.
Assessment Due
/ Text Chapter / Lab Manual1 / T 2/16 /
Mendelian Genetics
/ 3Th 2/18 /
Chromosomal Basis of HeredityPedigrees
/ 46
F 2/19 /
Corn Genetics
Practicing with Probability
Pedigree Analysis
/ 10 / 3-1—3-31-35--1-39
2 / T 2/23 /
Gene Interaction
/ 5Th 2/25 /
Genetic Mapping
/ 7F 2/26 /
DNA: Chemical Nature of the Gene
Plasmid Transformation / 10 / 2-7--2-183 / T 3/2 /
Specialized Mapping
/ 7Th 3/4 /
Worksheet 1 Due (Corn Genetics)Gene Transfer in Bacteria/Phage
/8
F 3/5 / NO CLASS: Staff Day
/
M 3/8
/Deadline to drop and avoid a “W”
/ /4 /
T 3/9
/DNA Replication and Recombination
/ 12Th 3/11
/Transcription
/ 13F 3/12
/Quiz/Essay 1
Evaluate and record data from your plasmid transformation
5 / T 3/16 /RNA Molecules and RNA Processing
/ 14Th 3/18 /
No Class Campus Flex Day
F 3/19 /Plasmid Isolation, Purification, Identification
(may be necessary to discuss some lecture material during remaining lab time.)
/ 3-51--3-54Handout will also be provided
6 / T 3/23 /
EXAM 1
Th 3/25 /Problem Set 1 Due
Genetic Code and TranslationProtein Structure and Function
/ 15F 3/26 /
Control of Gene Expression Operons
(dry lab: lac operon mutational analysis exercise)
/ 16 / 3-7—3-247 / T 3/30 /
Genetic Fine Structure
/ 8, 15Th 4/1 /
Recombinant DNA Technology and Analysis
/ 18F 4/2
/Ion exchange chromatography: protein purification
/ 3-25—3-338 / T 4/6 /
Recombinant DNA Technology and Analysis
/ 18Th 4/8 /
Genomics (Bioinformatics)BLAST Search Assigned
Worksheet 2 Due (Ion Exchange Chromatography)
/ 19 / 3-101—3-118F 4/9 /
Digest, Data Analysis for Lab Report 1 Restriction Plasmid Mapping
/3-55—3-69
Su 4/11 / Deadline to drop and receive a GUARANTEED “W”. After this point you must use the Late Withdrawal Process. The process requires faculty approval as well as documented and extenuating circumstances. No grade check required. Note Late Withdrawals are not easily obtained; please do not wait until this date to drop the course since it is likely you will not receive the “W”. This is a new SMC policy. /
WK / Date / Lecture Topic/ Lab Exercise/
Assessment Due
/ Text Chapter / Lab ManualSPRING BREAK 2010 NO CLASSES
APRIL 12TH-APRIL 18TH
/ J9 / T 4/20 /
Genomics (Bioinformatics)
/ 19Th 4/22 /
Gene Mutation
/ 17F 4/23 /
Southern Blot (part 1)
/ 3-73—3-9010 / T 4/27 /
Mechanisms and Analysis of DNA Mutations
/ 17Th 4/29 /
Worksheet 3 Due: BLAST Search
DNA Repair Mechanisms
/ 17F 4/30 /
Quiz/Essay 2
Southern Blot (part 2)
/ 3-73—3-9011 / T 5/4 /
Changes in Chromosome Structure
/ 9Th 5/6 /
Lab Report 1 Due
Changes in Chromosome Number
/ 9F 5/7 /
Drosophila GeneticsData Analysis for Lab Report 2
/ 1-11--1-26Su 5/9 /
Last Day to Drop with a “W” BUT ONLY WITH EXTENUATING CIRCUMSTANCES Only students with documented true emergency conditions that also receive faculty approval will be considered for withdrawal at this point. Documentation must be presented to the instructor by 5/4/10 to allow time for verification.
12 / T 5/11 /Problem Set 2 Due
Population Genetics
/ 23Th 5/13 /
EXAM 2
F 5/14 /Mitochondria DNA PCR Analysis
/ Review pp 530-532 / Handout to be provided13 / T 5/18 /
Immunogenetics
/ pp 620-627Th 5/20 / Prions
HIV / pp 226-229
F 5/21 /
ELISA: Simulated Anti-HIV lab
/ Back of lab manual14 / T 5/25 /
HIV and AIDS
(Recent information will be discussed including new molecular targets for treatment; URL addresses will be provided.) / Specific links to be providedTh 5/27 /
Lab Report 2 Due
Cancer as a Genetic Disease
/pp 627-637
F 5/28 /
Cancer Gene Detection
/ 3-119--3-13015 / T 6/1 /
Transposable Elements
/ 11Th 6/3 /
Worksheet 4 Due (Cancer Gene)
Transposable Elements
/pp. 614-621
F 6/4 /
LAB PRACTICAL EXAM
16 / Th 6/10 / FINAL EXAM: 8:00 am - 11:00 am
Biology 22 Class Policies
1. Material covered on the exams and quizzes will come from lecture presentations, lab observations and exercises, and textbook readings. You are responsible for some material not covered in lecture or laboratory, especially ideas that require application of and reasoning about assigned material. You are also responsible for applications of the material that are described in the textbook readings, whether or not these are discussed in class.
2. Exams and quizzes are mandatory and must be taken when scheduled. No scores are dropped. Makeup exams or quizzes will only be given under extraordinary circumstances and only if the instructor has been contacted in advance. No makeups will be given without verifiable documentation for your absence, such as a physician's excuse, court summons, obituary, or police report. The makeup exam or quiz will cover the same material but will have a different format, essay questions as opposed to multiple-choice questions, for example. Makeups will be scheduled for the day of the final exam.
3. You must sign in for each Friday’s lab. The sign-in sheet will be on the front lab bench. You may have occasion to work with different lab partners during the semester but at other times you can choose your lab partners.
4. Your cooperation is required for cleaning up your group’s lab area after experiments are completed.
5. There are no make up exams or quizzes or laboratories and the lowest grade is not dropped.
6. All papers are due at the beginning of class on the date indicated. Papers turned in anytime after the start of class on the due date lose 4 points. If your paper is late and your instructor is unavailable, you may submit it to Mrs. Ingrid Cardwell, Department Secretary, in Science 258, during department business hours between 8:30 am and 4:30 pm. She will verify the date and time, sign the paper and place it in your instructor’s mailbox. Papers turned in after 4:30 pm on the due date will not receive credit.
7. Lab reports, worksheets and solutions to problems cannot be emailed to the instructor. All work must be handed in at the required class time as outlined in the syllabus.
8. In order to receive full credit for lab reports and worksheets, the student must have participated in the lab activity that generated the data. A 15-50% reduction of that lab grade may occur if the student was not present to collect the data or has left the lab prior to the completion of the experiments. The lower percentage relates to reports using data from one lab session while the higher percentage pertains to reports using data from multiple lab sessions. Due to limitations on materials and time, it is not possible to make up missed laboratory experiments.
9. Unless authorized by the instructor, cell phones must be turned off and may not be used for ANY purpose during the lab or lecture; these purposes include(butare not necessarily exclusive to) theuse of a cell phoneas acalculator, dictionary or camera. You may leave the room to take a call, if necessary, but not during any examination unless you have completed and handed in your exam.
10. During exams and quizzes, students are not permitted to leave the room until the exam or quiz has been turned in. Students are not permitted to be listening (ear phones) to any type of electronic device during an exam. Dictionaries or other resources cannot be used during the exam. Calculators can be used but the calculator cannot be associated with a cell phone, blackberry or other similar electronic device. The student may be asked to use a different calculator if the electronic device used by the student is considered inappropriate.
11. Students who are absent for three laboratory sessions will be dropped from the class roster.
12. Students are responsible for maintaining their own enrollment status. Students may drop the course with a W through the eighth week of the semester. In order to drop the course between the eighth and twelfth weeks, instructor’s approval of an extenuating circumstance is required. Verifiable documentation of the emergency is required. (Note that this is a new, stricter policy). It is NOT possible to drop the class after the twelfth week of the semester. SMC policy allows students to request an incomplete for emergency situations arising at the end of the semester. Incompletes are subject to the instructor’s approval. It is the policy of these instructors that students must provide documentation to demonstrate the need for an incomplete. In deciding whether or not to approve the incomplete, the instructors will consider the veracity of the documentation along with the amount of outstanding work that the student needs to complete.
13. Some exam questions will be returned to you when you receive your grade, however, other questions will only be posted so that you can note the correct answer. Do not copy the exam questions that are not permanently returned; if it is observed that students are copying and/or making any electronic version of the exams or quiz-essays these actions will be considered as lacking integrity and academic honesty and will be handled according to the SMC Honor Code (see below AR 4412).
14. If you use email to correspond with the instructor, you can expect a response within approximately 24 hours, Monday through Thursday. Email messages sent on Friday or through the weekend are not necessarily obtainednor responded to by the instructor. Thus for important matters that require immediate attention it is best to communicate this information directly to the instructor.Lab reports, worksheets and solutions to problems cannot be emailed to the instructors. All work must be handed in at the required class time as outlined in the syllabus.
15. We expect our students to show professionalism in their email correspondence. Basic civility and email etiquette are expected; however, if inappropriate (impolite, crude or similar styles) email messages are received, they will not obtain a response from the instructors. Neither anonymous emails nor emails lacking the identity of the actual student who is attending the class will be given credibility or receive any response.
16. Working together is encouraged for studying and completing laboratory experiments. Apply the following guidelines to:
· Problem Solving: To facilitate learning, collaboration on solutions to problems is encouraged. While problem sets from students in the same study group are expected to show certain similarities, no credit will be given for instances where it appears that students have simply copied from one another. You should also keep in mind that you will be required to independently show an understanding of genetics applications on quizzes and exams.
· Worksheets: While members of a group will have recorded identical data, the worksheet must represent independent work.
· Laboratory Reports: The laboratory reports must be written
independently. To receive credit, the wording, organization, data presentation and data interpretation in each report must be distinguishable from any other student’s report, including those of lab partners. While you may discuss the experimental results with your partners and your instructor, the written analysis must be completed on your own and represent your own work.