KINGSBOROUGH COMMUNITY COLLEGE
The City University of New York
Department of Biological Sciences
GENETICS
BIOLOGY 59
(section E01R code 2390)
COURSE
OUTLINE
Spring 2008
Office: Room S-109
Anthea M. Stavroulakis, Ph.D. Telephone: (718) 368-5095
E-mail: AStavroulakis@kbcc.cuny.edu
Biology 59 is a 4 credit course, with a laboratory component, open to students who have completed Biology 14, and have passed the CUNY Math and English exams. Chemistry 11 is a pre-requisite. It fulfills one of the two (Group V) laboratory course requirements for Biology majors.
COURSE GOALS
Broad course goals listed below are intended to give you a perspective (direction) to your Genetics studies. Throughout the semester, specific (topical) objectives will be given for each assignment. Use them to assist in your studies.
1. Provide historical and theoretical foundations on Genetics for students interested in further studies in the biological sciences.
2. To offer advanced study of inheritance, relating advances in molecular genetics to foundation experimentation, and to demonstrate its applicability to our daily lives.
3. Provide students with classical and current genetic laboratory experiences including the use of genetic technologies available in modern research laboratories.
4. Provide a technical research foundation for students interested in furthering their studies in the molecular biological sciences.
5. Learn concepts, techniques and methodologies utilized in genetic experimentation. Data collection, analysis and classroom presentation of results will be required.
6. To demonstrate how modern biology is helping to resolve genetic diseases, reveal the
human genetic composition, and aid in forensic medicine.
Weekly course meetings consist of: 2 hours lecture / 1 hour recitation
3 hours laboratory
Our class meets on Tuesday’s 6:00-9:00pm in Room M-130 and on Thursday’s from 6:00-9:00pm in Room S-226; [Laboratory meets on Thursday in room S226].
COURSE REQUIREMENTS
Required Lecture Textbook*:
i Genetics A Mendelian Approach. (2006)
Peter J. Russell.
Pearson Education – Benjamin Cummings, San Francisco, CA. [ISBN# 0-8053-4666-X]
Required Special Topics Booklets*:
Special Topics in Biology Series Booklets (Michael A. Palladino, Series Editor):
Biology of Cancer by Randall W. Phillis and Steve Goodwin (ISBN# 0-8053-4867-0)
Stem Cells and Cloning by David A. Prentice (ISBN# 0-8053-4864-6)
Biological Terrorism by Steve Goodwin and Randall W. Phillis (ISBN# 0-8053-4868-9)
[* The lecture text packaged with the three Special Topics booklets and lab manual is
ISBN# 0-3215-5609-7]
Required Laboratory Manual:
Genetics: Laboratory Investigations. Thirteenth Edition. (2007)
Thomas R. Mertens and Robert L. Hammersmith.
Prentice Hall, Englewood Cliffs, NJ. [ISBN# 0-13-174252-3]
Required Laboratory Coat / Eye Protection:
A laboratory coat is required. Students without a laboratory coat will not be allowed to conduct experimentation, and may be asked to leave the laboratory room. Safety goggles and/or non-latex gloves are recommended during microbial culturing and preserved specimen dissections.
GRADE CALCULATION
Lecture: Laboratory:
Examinations (2) 18% Laboratory Reports (9) 18%
Opinion / Reaction Paper 4% Reports / Homework’s (5) 21%
Term Project - Debate 8% Unknowns (6) 8%
Final 20% Attend. / Techn. / Partic. 3%
50% 50%
TOTAL = 100%
ASSIGNMENT DETAILS (additional information will provided in class)
Opinion / Reaction paper:
You will read and/or view assigned materials, and be asked to write a brief paper (not to exceed 1 1/2 pages) stating your opinion about it / reaction to it.
Attendance / Participation / Technique:
It is the student’s responsibility to attend all classes as per the college’s attendance / absence policy. Classroom participation is welcome and encouraged, both during the lecture and laboratory periods. This course will require specimen dissections, which should be done meticulously. Your results depend on the quality of your techniques.
{In-class} Laboratory Reports / Reports and Homework’s / Unknowns:
Laboratory, activities will require either: answering questions upon completion of the exercise, written reports, or determination of the identity an unknown. Assignment details specific to each exercise will follow. Assignment details (additional information / due dates) will be provided in class.
Term Project:
On Tuesday, May 27th, our class will engage in an end-of-term debate discussing and deciding whether Embryonic Stem Cells Should be Used. Stem cells have received much attention and controversy in the past decade. We have heard and read about several of them relating to disease treatments and potential cures. Methodologies employed to extract embryonic vs. adult stem cells are controversial. Should there be laws banning their use? Should it be legal and funded? Who will pay? How, when, why should they be used? Will there be a positive benefit in using these cells? Would this create problems? What possible ethical dilemmas may exist in doing so? Whether they should be used at all, arguments for and against it, will be discussed. Will legislation need to be written? It should be assumed that the term required would entail some type of funding, private, local or federal. What are arguments for and against doing this? Arguing in support or in opposition to this statement in our classroom should be done from a scientific perspective, supported by scientific data and articles. Opinions without this basis should not be used to support the person presented, nor should religious arguments. Each student will do one of the following: present pertinent background information; support/rebut either viewpoint of the controversy; be a respondent (their role is that of a lawyer - asking questions, etc.); or be a "jury member" who renders the final decision. And, we will all part as friends, perhaps agreeing to disagree? Maybe we can arrive at an opinion that we can share, in print?
Deadline Dates and Formats:
Detailed deadline dates / format for opinion/reaction papers, homework’s, reports, unknowns, term project papers and presentations will be provided separately. The grade for any assignment that is one week late will be reduced by 10%, and assignments more than one week late will not be accepted (that grade = 0). Tentative lecture examination dates follow; the best two of the three grades will be used for the final course evaluation calculation. There are no make-up examinations given; a missed lecture exam will be assigned a grade of zero, which would count as the lowest grade to be dropped for your course grade calculation. The final examination date will be announced in class when available.
A FEW MORE NOTES TO THE STUDENT
Safety:
A laboratory coat is required. Students without a laboratory coat will not be allowed to conduct experimentation, and may be asked to leave the laboratory room. Safety goggles and/or non-latex gloves are recommended during microbial culturing and preserved specimen dissections.
Observe all safety precautions, as instructed in the laboratory. They are for your protection. Each student is responsible for the proper and safe maintenance of their work area; bench tops and microscopes must be properly cleaned before and after use.
Weekly student clean up groups will oversee that the laboratory room has been left clean, with bench tops cleared of used materials. The clean up groups will rotate – everyone will have a chance to remind their peers to clear up!
Additional Laboratory Hours:
Our class meets for Lecture on Tuesday’s 6:00-9:00pm in Room M-130 and on Thursday’s from 6:00-9:00pm in Room S-226 for Laboratory.
Certain exercises and assignments will require you to come in and work additional hours, many in the laboratory. Care and culture of the Drosophila melanogaster we will use and visualization of electrophoretic gels will be performed during the designated open laboratory hours. You are expected to devote your time to complete the projects. In many cases, you will be a member of a group. Each individual is expected to make an equitable contribution to on-going group projects. Laboratory project reports are to be submitted with all participating group member’s names.
Deadline Dates and Formats:
Detailed deadline dates / format for opinion/reaction papers, homework’s, reports, unknowns, term project papers and presentations will be provided separately. The grade for any assignment that is one week late will be reduced by 10%, and assignments more than one week late will not be accepted (that grade = 0). Tentative lecture examination dates follow; the best two of the three grades will be used for the final course evaluation calculation. There are no make-up examinations given; a missed lecture exam will be assigned a grade of zero, which would count as the lowest grade to be dropped for your course grade calculation. The final examination date will be announced in class when available.
College Calendar Considerations relevant to our class:
Easter recess is March 20th to March 23rd. Spring recess is April 20th to April 27th. On Monday, May 26th (Memorial Day) the college is closed. The last day our class meets is Tuesday, May 27th (which follows a Thursday schedule). The final examination period is June 2nd to June 6th; the date, time and room of your final will be announced in class once it is available. Commencement is Friday, June 13th.
LECTURE TOPICS AND SEQUENCE
Week # Lecture / Recitation Topic Chapter(s) in Textbook
1 Introduction – History and Scope of Genetics and Genomics 1
[2/26] Genetics: An Introduction
Classical and Modern Genetics
Basic Concepts of Genetics, Geneticists and Genetic Research
Including experimental organisms: Arabidopsis thaliana,
Caenorhabditis elegans, Drosophila spp.
2 Mendelian Genetics 2
[3/4] Mendel’s Experimental Design / Mendel’s Principles
Mendel’s Genetics in Humans
3 Chromosomal Basis of Inheritance 3
[3/11] Chromosomes and Cellular Reproduction:
mitosis, meiosis, the cell cycle,
sexual reproduction in diploid organisms
Sex Chromosomes and Sex Determination:
non-disjunction, sex chromosome abnormalities,
dosage compensation
Analysis of Sex-linked traits in Humans:
sex-linked inheritance
4 DNA: The Genetic Material 10
[3/18] The Search for the Genetic Material:
evidences of DNA as the genetic material
The Composition and Structure of DNA and RNA:
molecular structure, alternative forms of DNA
The Organization of DNA in Chromosomes:
viral, prokaryotic, eukaryotic chromosomes,
centromeric and telomeric chromatin,
unique sequence and repetitive sequence DNA
EASTER RECESS 3/20/08 – 3/23/08
5 DNA Replication 11
[3/25] Semiconservative DNA Replication:
Meselson-Stahl experimental evidence
DNA Enzymes
Molecular Model of DNA Replication
DNA Replication in Eukaryotes:
Origins, Replicons, Topoisomerases, Telomerases
DNA Recombination
6 Gene Function 12
[4/1] Gene Control of Enzyme Structure
Genetically Based Enzyme Deficiencies in Humans
Gene Control of Protein Structure
Genetic Counseling
7 Gene Expression: Transcription 13
[4/8] The Central Dogma:
RNA types, structure
Transcription Process:
promoters, steps in process: prokaryotic vs. eukaryotic,
hnRNA processing, split genes
8 Gene Expression: Translation 14
[4/15] Proteins:
amino acid structure, protein folding
The Nature of the Genetic Code:
colinearity, universality, redundancy, tRNA structure
Translation Process
Protein Sorting in the Cell
SPRING RECESS 4/20/08 – 4/27/08
9 Genetics of Cancer 22
[4/29] Relationship of the Cell Cycle to Cancer
Cancers are Genetic Diseases
Genes and Cancer
Telomere Shortening, Telomerase, and Human Cancer
The Multistep Nature of Cancer
Chemicals and Radiation as Carcinogens
10 Variations in Chromosome Structure and Number 8
[5/6] Types of Chromosomal Mutations:
deletion, duplication inversion, translocation
Variations in Chromosome Structure
Variations in Chromosome Number
aneuploidy, polyploidy
11 Applications of Recombinant DNA Technology 17
[5/13] Site-Specific Mutagenesis of DNA
Analysis of DNA Polymorphisms in Genomes
DNA Molecular Testing for Human Genetic Disease Mutations
Isolation of Human Genes
DNA Typing:
DNA fingerprinting/profiling
Analysis of Expression of Individual Genes
Analysis of Protein-Protein Interactions
Gene Therapy:
transgenics
Biotechnology: Commercial Products
Genetic Engineering of Plants
ELSI: Ethics of Biotechnology (ELSI) 18
(pp. 488, 508-9)
- Regulation of Gene Expression:
[5/20] Regulation of Gene Expression in Bacteria and Bacteriophages 19
The lac operon of E. coli
The trp operon of E. coli
Regulation of gene expression in phage lambda
Regulation of Gene Expression in Eukaryotes 20
Operons in Eukaryotes
Levels of Control of Gene Expression in Eukaryotes
Control of Transcription Initiation
Gene Silencing and Genomic Imprinting
Posttranscriptional Control
RNA Interference: A Mechanism for Silencing Gene Expression
Our Biological Future and other pertinent issues Discussion /
Debate
Course Evaluation
Lecture: Tentative Assignment and Examination Dates
OPINION / REACTION PAPER = 4%
(Due: Tuesday March 4, 2008)
LECTURE EXAMINATIONS: - 2 (x 9pts.): 3 = 18%
Lecture Examination 1 (Tuesday, March 18, 2008):
History and Scope of Genetics and Genomics, Mendelian Genetics, Chromosomal Basis of Inheritance
Lecture Examination 2 (Tuesday, April 29, 2008):
DNA: The Genetic Material, DNA Replication, Gene Function, Gene Expression: Transcription and Translation
Lecture Examination 3 (Thursday, May 22, 2008):
Genetics of Cancer, Variations in Chromosome Structure and Number , Applications of Recombinant DNA Technology, ELSI: Ethics of Biotechnology (ELSI), Regulation of Gene Expression: Prokaryotes, Viruses and Eukaryotes
FINAL EXAMINATION (in addition to the term’s work) = 20%
Our Biological Future, Current Issues
TERM PROJECT - OPEN CLASS DISCUSSION / DEBATE - 8%
Class discussion / debate will be Tuesday May 27th, 2008):
The class will participate in a term project concerning the topic of Embryonic Stem Cells. Each student will submit a paper on their aspect of this discussion, and participate in an open discussion / debate.
Opinion Paper 4 %
Lecture Examinations 18 %
Debate 8 %
Final 20 %
__________________________________________________________________
TOTAL LECTURE GRADE = 50 %
LABORATORY EXERCISES AND SEQUENCE
Week # Exercise # in
[date] Laboratory Manual
1 Introduction: Discussion of Individual and Group
[2/28] Term Projects, Activities and Assignments
Drosophila and Maize Experiments in Genetics:
Monohybrid Crosses (Zea mays analyses) 1 (pp.9-15)
2 F1 Generation Drosophila monohybrid crosses
[3/6] Determination of white eye inheritance mechanism 1 (pp.1-8)
Monohybrid Cross in Yeast supplement
3 Meiosis in Angiosperms: Microsporogenesis
[3/13] Preparation of slides from flower buds 6
EASTER RECESS 3/20/08 – 3/23/08
.4 Restriction Endonuclease Digestion and Gel Electrophoresis
[3/27] of DNA [* see textbook pp. 458-462] 15
Introduction and Gel Loading practice supplement
5 DNA Gel Electrophoresis: Bioterrorism and Disease
[4/3] DNA-Based Screening for Smallpox supplement
In Search of the Kissing Gene supplement
6 Forensic Science: Fingerprint Analyses
[4/10] Polygenic Inheritance: Fingerprint Ridge Count 22
Fingerprint patterns (microscope slides)
Latent Fingerprint Kit supplement
Video presentation: "Planted Evidence: Plant DNA Forensics"
7 Gel Electrophoresis: Murder Mystery supplement
[4/17] Murder Mystery - DNA Detectives Lab Activity
Video presentation: "Footpath Murders: DNA Profiling's
Landmark Case"
SPRING RECESS 4/20/08 – 4/27/08
8 Gene Expression
[5/1] DNA/RNA Microarrays [* see textbook p. 460] supplement
Differentiation of Human Cells by Retinoic Acid supplement
Chromosomal Mutations (demonstration slides)
9 Gel Electrophoresis: Cancer Detection
[5/8] Detection of Colorectal Cancer: supplement
In Search of the Cancer Gene
Cancer Cell Morphology supplement
Cytogenetics:
[5/15] Chromosomal Spreads supplement
Preparation of HeLa Cell Chromosomal Spreads
Human Genetics:
Human Chromosomes – karyotypes and banding 10
X-Linkage in Humans 8 (Ex III) Dosage Compensation: Barr Bodies 9
11 Applied Human Genetics: 25
[5/22] Test Papers supplement 3
Testing Familial Relationships using simulated blood supplement
12 Gene Amplification
[5/27] Drosophila spp. salivary gland chromosomes 7
Term Project (Debate)
Summary and Evaluation of semester's work
Additional (optional) Activities for Extra Credit (5 points towards lab portion of grade); the student should make an appointment with the instructor during week 6-7 of the semester. Assignments will be due the first week of May. Late assignments will not be accepted.
One of the following will be agreed upon with the student and assignment details provided:
Examples of Web-based projects:
a- DNA Bioinformatics [database extrapolation]
b- TBA [e.g.: Isolation of DNA in your home]
c- Genetic Counseling [pre-natal cytogenetical analyses]
Also there will be a Field Trip sign up:
DNA Learning Center (Cold Spring Harbor)
Dates and further information will be provided during the semester.
Tentative Due Dates for Laboratory Assignments
{In-class} Lab Reports: 9 x 2pts. = 18%
Drosophila and Maize Experiments in Genetics: [2/28] - Individual
Monohybrid Crosses (Zea mays analyses)
Meiotic Chromosomes – Meiosis in Angiosperms [3/13] - Individual
Gene Expression: DNA/RNA Microarrays [5/1] - Group
Differentiation of human cells by retinoic acid [5/1] - Group
Cancer Cell Morphology [5/8] - Individual Preparation of HeLa cell chromosomal spreads [5/15] - Individual
Human Chromosomes: karyotypes, banding and Mutations [5/15] - Individual
Applied Human Genetics: Genetic Test Papers [5/22] – Group
Gene Amplification: Drosophila salivary gland chromosomes [5/27] - Individual
Reports and Homework’s: 7 x 3pts. = 21%
F1 Generation Drosophila monohybrid cross and
Monohybrid Cross in Yeast data report [3/13] - Group
In Search of the Kissing Gene [4/3] - Group
Polygenic Inheritance: Fingerprint Ridge Count (Ex#22) [4/10] – Individual
Latent Fingerprint / Hair Analysis [4/10] - Group
X-linkage in humans [5/15] - Group
Dosage Compensation: Barr bodies [5/15] - Individual
Testing Familial Relationships Using Simulated Blood [5/22] - Group
Unknowns: 4 x 2pts. = 8%
Restriction Endonuclease Digestion and
Gel Electrophoresis of DNA (Ex#15) [4/1] – Individual
Gel Electrophoresis: Bioterrorism and Disease
DNA-based Screening for Smallpox [5/6] – Group
Forensic Science: Gel Electrophoresis: Murder Mystery –
DNA Detectives Lab Activity [4/29] - Group
Gel Electrophoresis: Detection of Colorectal Cancer [5/13] - Group
Laboratory Assignments - 47 %
Attendance / Technique / Participation 3 %
__________________________________________________________________
TOTAL LABORATORY GRADE = 50 %
KINGSBOROUGH COMMUNITY COLLEGE
The City University of New York
Department of Biological Sciences
GENETICS
BIOLOGY 59
STUDENT QUESTIONNAIRE
SPRING 2008
Anthea M. Stavroulakis, Ph.D.
Welcome to Genetics! What do you want to learn about this semester? I want to find out what your expectations in this course are. Is there a particular topic or question you would like addressed or answered? In the space below, write what you would like to learn. These sheets will be reviewed, and I will make every effort to address your input. Thank you.
Topic:
Question:
Laboratory #
Tuesday Thursday
2/26 2/28 1
3 /4 3/6 2
3/11 3/13 3
3/18 3/20
no class (Easter Recess)
3/25 3/27 4
4/1 4/3 5
4/8 4/10 6
4/15 4/17 7
4/22 4/24
no class (Spring Recess) no class (Spring Recess)
4/29 5/1 8
5/6 5/8 9
5/13 5/15 10
5/20 5/22 11
5/27 12 5/29
Classes follow Thursday Compass testing - Reading Day
Schedule
Final Examinations 6/2 – 6/6
Commencement 6/13 |