KINGSBOROUGH
COMMUNITY COLLEGE
The
City University of New York
Department
of Biological Sciences
Anthea M.
Stavroulakis, Ph.D.
Office: Room S-109
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 are listed below; they are intended to give you a perspective (direction)
to your Genetics studies. Throughout
the semester, specific (topical) objectives will be given. 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,
especially in the field of molecular genetics, that demonstrates applicability
to our daily lives.
3. Provide students with current genetic
laboratory experiences using 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 genetical experimentation will be applied to
laboratory and independent research assignments. 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
Required Lecture Textbooks:
Genetics. Analysis of Genes and Genomes. Fifth Edition. (2000)
D. L. Hartl and E. W. Jones.
Jones and Bartlett Publishers, Boston.
Required Laboratory Manual:
Genetics: Laboratory Investigations. Twelfth Edition. (2001)
Thomas R. Mertens and Robert L. Hammersmith.
Prentice Hall, Englewood Cliffs, NJ.
GRADE CALCULATION
Lecture: Examinations (2) 16%
Opinion / Reaction Paper 5%
Term Project - Debate 9%
Final 20%
Laboratory: Homework’s (6) 12%
Reports (5) 20%
Unknowns (8) 16%
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.
Homework’s / Reports / Unknowns:
Laboratory, activities will require either: answering questions upon completion of the exercise, written laboratory reports, or determination of the identity an unknown. Assignment details specific to each exercise will follow.
Term Project:
On Wednesday, June 2nd, our class will engage in an
end-of-term debate concerning whether “The Problem of Identity Theft Can be Solved By Mandatory DNA
Databasing”. Recently, we hear and read
a lot about people’s “identity” being stolen, such as by social security
number, credit card information, etc.
If all persons were required to have their DNA entered into a database
as their unique identification, would that solve the problem of confirming an
individual’s identity? Is this a
possible solution to the problems we are seeing? Whether it should be done, arguments for and against it will be discussed.
Will legislation need to be written?
What are arguments for and against doing this? 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?
Safety:
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.
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.
Additional Laboratory
Hours:
Our class
is scheduled to meet Monday’s, 1:50-5:10pm in room S201, and Wednesday’s,
1:50-5:10pm in Room M389. S201 is the
laboratory room.
Certain
exercises and assignments will require you to come in and work additional
hours, many in the laboratory, similar to the Drosophila melanogaster
experiment in Biology 14. You are
expected to devote your time to complete the projects. In many cases, you will be part of a
group. Each individual is expected to
make an equitable contribution to on-going group projects.
Deadline Dates:
Deadline
dates and format for opinion/reaction papers, homeworks, reports, unknowns,
term project papers and presentations will be provided separately. Lecture examinations and final examination
dates will be announced in class.
College Calendar
Considerations relevant to our class:
There are
no classes after 4:00pm on Monday April 5th.
Spring recess is April 6th to April 13th. We resume classes on Wednesday, April 14th. Classes follow a Monday schedule on Wednesday
April 21st. There are no classes on
Monday, May 31st (Memorial Day), and the last day of class is Wednesday, June
2nd. The finals exam period is June 4th
to 13th; the date, time and room of your final will be announced in class. Commencement is Friday, June 11th.
LECTURE
TOPICS AND SEQUENCE*
(*
Additional textbook readings appear under certain laboratory topics)
1 Introduction –
Molecular Genetics and Genomics 1
[DNA as genetic material; history, Experimental
organisms:
Arabidopsis thaliana, Caenorhabditis
elegans, Drosophila spp.]
Genes and Chromosomes 4
[Mitotic cell division]
Molecular Genetics of the Cell Cycle and Cancer 15
[Cell cycle; Genetic Analysis of the cell cycle;
Checkpoints;
Cancer cells; Oncogenes; Hereditary cancer
syndromes]
2
Genes and Chromosomes (cont’d.) 4
[Chromosome complements;
Meiosis; Sex-linked inheritance;
Probability and Chi square]
3
Transmission Genetics: The Principles of Segregation 3
[Gene segregation; Pedigree Analysis; Multiple
Alleles and
Gene
Interaction; Allelic variation; Quantitative Traits and
Polygenetic
Inheritance (qualitative vs. quantitative traits);
Complementation
Analysis]
4
DNA Structure and DNA Manipulation 2
[Genomes and genetic differences among people;
Molecular structure
of DNA; Separation and Identification of DNA
fragments; Types of
DNA markers (SNP, RFLP); Applications of DNA
markers]
5
Molecular Biology of DNA Replication and Recombination 6
[Origins; Semi-conservative
Replication; DNA polymerases;
Rolling Circle Replication;
Topoisomerases; Recombination]
6
Molecular Biology of Gene Expression 11
[Amino acids, polypeptides
and proteins; Colinearity; Transcription
and RNA Processing;
Translation and the Genetic Code]
7 Human Karyotypes and Chromosome Behavior 9
[Chromosome abnormalities in spontaneous abortion;
Cytogenetics:
Variation in Chromosome Number and Structure;
Position effect;
Polyploidy and Evolution]
8 Molecular Mechanisms
of Mutation and DNA Repair 7
[Types of mutations; Molecular basis of mutation;
Transposable
Genetic Elements; Spontaneous vs. Induced
mutations; Mutagens;
DNA repair mechanisms]
Molecular Organization of Chromosomes 8
[Genome size and complexity; C-value paradox;
Supercoiling;
Chromosome structure
in prokaryotes and eukaryotes;
Repetitive sequences; Renaturation kinetics;
Unique and repeated
DNA sequences; specialized sequences (centromere,
telomere)]
9 Genetic Engineering
and Genomics 13
[Restriction enzymes and vectors; Cloning
strategies; Applications of
Genetic Engineering (Gene therapy; Transgenics;
Site-directed
mutagenesis; Knockout mutations); Functional
genomics (DNA Chips)]
10 The Genetic Basis of
Complex Inheritance 18
[Complex traits; Genotypic variation; Genetic
analysis of complex
traits; Artificial selection; Correlation between
relatives;
Heritabilities of threshold traits; Identification
of genes affecting
complex traits]
Population Genetics and Evolution 17
[Allele and genotype frequencies; Mating;
Inbreeding; Genetics and
Evolution; Mutation, Migration and Natural
Selection]
11 Extranuclear Inheritance: 16
[Patterns of extranuclear inheritance; Organelle
heredity (snail shell
coiling, leaf variegation, CMS); Cytoplasmic
transmission of symbionts;
Imprinting); Mitochondrial inheritance and human
disease;
Mitochondrial Eve]
12 Genetic Manipulations
and the Biological Future discussion
/
of the Human Species debate
Course Evaluation
Lecture: Tentative Assignment and Examination
Dates
OPINION / REACTION PAPER = 5%
(Due: Wednesday March 10,
2003)
LECTURE EXAMINATIONS: - 2 (x 8pts.):3 = 16%
Lecture Examination 1
(Wednesday, March 31, 2004):
History, Cell Division,
Molecular Genetics of the Cell Cycle and Cancer
Transmission Genetics
Lecture Examination 2
(Wednesday, May 5, 2004):
DNA Structure and
Manipulation, Replication, Recombination, Transcription and Translation
Lecture Examination 3
(Wednesday, May 26, 2004):
Cytogenetics, Mutation,
Molecular Organization of Chromosomes, Genetic Engineering and Genomics,
New Material on Final = 20%
Population Genetics and
Evolution, Genetic Basis of Complex Inheritance, Extranuclear Inheritance,
Genetic Manipulations and the Biological Future of the Human Species
TERM PROJECT - OPEN CLASS
DISCUSSION / DEBATE - 9%
Class discussion / debate
will be Wednesday June 2, 2004):
The class will participate in a term project concerning
the topic testing for a gene for violence.
Each student will submit a paper on their aspect of this discussion, and
participate in an open discussion / debate.
Opinion Paper 5 %
Lecture Examinations 16
%
Debate
9 %
__________________________________________________________________
LABORATORY EXERCISES AND
SEQUENCE
Week # Activities Laboratory Manual
1 Introduction: Discussion of Individual and Group
[3/8] Term
Projects, Activities and Assignments
Arabidopsis thaliana
project set-up and discussion supplement
Inheritance of Albinism in Nicotiana
spp. supplement
2 Cell
Reproduction: Mitosis #
5
[3/15] Preparation
of HeLa Cell Chromosomal Spreads supplement
Human
Chromosomes; G-banding # 11
3 Meiotic
Chromosomes – Lilium spp. prophase I
slides # 6
[3/22] Linkage and
Mapping in Drosophila melanogaster: #
12
Three Point Test Crosses
Read:
Genetic Mapping in a Three Point Test Cross
(Chapter 5, pp. 192-197)
4 Protein
Microarrays supplement
[3/29] AIDS
Kit I: Simulation of HIV-I Detection supplement
DNA Gel Electrophoresis: supplement
Introduction and Gel Loading
practice
5 DNA Gel
Electrophoresis: supplement
[4/5] Analysis
of Restriction Enzyme Cleavage Patterns of DNA
Multimedia presentation: "Human Genome Project”
Impact of Automated DNA Sequencing on
Bioethics supplement
SPRING
RECESS [ 4/6/04 – 4/13/04 ]
6
Quantification of DNA #15
[4/19] Read: DNA Absorption Kinetics (p. 55; p. 325)
Video presentations: "Footpath Murders: DNA Profiling's supplement
Landmark Case" and "Planted
Evidence: Plant DNA Forensics"
7
DNA Gel Electrophoresis: supplement
[4/21] Genetically
Inherited Disease Detection – Sickle Cell
Principles
of DNA Sequencing supplement
8 Gene
Mutations: #21
[4/26] Irradiated
Seeds – Chromosomal, Developmental
Morphological
consequences
Chromosomal Mutations (demonstration
slides) #
11
[5/3] the
lac operon in Escherichia coli
Read:
Transcriptional Regulation in Prokaryotes
(Chapter 12, pp. 490-505)
Gene Amplification:
Drosophila
spp. salivary gland chromosomes #
8
Read:
Polytene Chromosomes (Chapter 8, pp. 323-324)
Dosage Compensation: Barr bodies #
10
10
Gel Electrophoresis:
[5/10] In Search of the
Cholesterol Gene supplement
Recombinant DNA Technology: Replica
plating to
identify antibiotic resistance
genes supplement
11
Transformation of E. coli with Plasmids
Containing
[5/17] the green (gfp)
and blue (bfp) fluorescent proteins supplement
Gel Electrophoresis:
In Search of the Cholesterol
Gene (results)
Recombinant DNA Technology: Replica
plating to
identify
antibiotic resistance genes (results)
12 Student
Presentations of Term Assignments and Reports
[5/24] (Continuation
from lecture.)
Summary and Evaluation of semester's
work
Additional (some optional)
Activities:
Web-based projects:
DNA Bioinformatics [database
extrapolation]
TBA [e.g.: Isolation of DNA in
your home]
Field Trips:
DNA Learning Center (Cold Spring Harbor)
Institute for Basic Research (Staten
Island, NY)
Dates and further information will be provided during the
semester.