KINGSBOROUGH COMMUNITY COLLEGE

The City University of New York

Department of Biological Sciences

GENETICS

BIOLOGY 59

COURSE OUTLINE

SPRING 2002

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 placement at Math 03 and English 93 levels or better. It fulfills one of the two (Group V) laboratory course requirements for Biology majors.

COURSE GOALS

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 experiments 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. 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. 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 (8) 16%

Reports (4) 16%

Unknowns (7) 14%

Attendance / Participation 4%

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:

In laboratory, activities will require either: answering questions upon completion of the exercise, a written laboratory report of your experimentation and conclusion(s), or determination of the identity an unknown specimen. Assignment details specific to each exercise will follow.

Term Project:

On Wednesday, May 29th, our class will engage in an end of term debate concerning genetic screening for disease genes titled, “Should Everyone be Screened for Disease Genes?”. Completion of the Human Genome Project impacts many aspects of our lives. How will "life, in general” be affected? Will legislation need to be written?; How are health and life insurance coverage affected? What are arguments for and against screening? 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?…

NOTES TO THE STUDENT

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, 6-9:00pm in room S201, and Wednesday’s, 6-9:00pm in Room S113. 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 ongoing 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:

On Wednesday, March 27, there are no classes after 4:00pm. Spring recess is March 28th to April 3rd. We resume classes on Monday, April 8th. On Thursday, May 25th, classes will follow a Monday schedule. There are no classes on Monday, May 27th (Memorial Day), and the last day of classes is Thursday, May 30th. Finals are after that, the date, time and room of your final will be announced in class.

LECTURE TOPICS AND SEQUENCE*

(* Additional textbook readings appear under certain laboratory topics)

Week # Lecture / Recitation Topic Chapter(s) in Text

1 Introduction – Molecular Genetics and Genomics 1

[DNA as genetic material; history, Experimental organisms:

Arabidopsis thaliana, Caenorhabditis elegans, Drosophila spp.]

2 Genes and Chromosomes 4

[Chromosome complements; Mitosis; Meiosis; Sex-linked inheritance;

Probability and Chi square]

Human Karyotypes and Chromosome Behavior 9

[Chromosome abnormalities in spontaneous abortion; Cytogenetics:

Variation in Chromosome Number and Structure; Position effect;

Polyploidy and Evolution]

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 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]

8 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 Molecular Genetics of the Cell Cycle and Cancer 15

[Cell cycle; Genetic Analysis of the cell cycle; Checkpoints;

Cancer cells; Oncogenes; Hereditary cancer syndromes]

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]

Population Genetics and Evolution 17

[Allele and genotype frequencies; Mating; Inbreeding; Genetics and

Evolution; Mutation, Migration and Natural Selection]

12 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]

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: Monday March 11, 2002)

LECTURE EXAMINATIONS: - 2 (x 8pts.):3 = 16%

Lecture Examination 1 (Wednesday, April 10, 2002):

History, Cell Division, Cytogenetics, Transmission Genetics

Lecture Examination 2 (Wednesday, May 1, 2002):

DNA Structure and Manipulation, Replication, Recombination, Transcription, Translation and Mutation

Lecture Examination 3 (Wednesday, May 22, 2002):

Molecular Organization of Chromosomes, Genetic Engineering and Genomics, Molecular Genetics of the Cell Cycle and Cancer

New Material on Final = 20%

Extranuclear Inheritance, Population Genetics and Evolution, Genetic Basis of Complex Inheritance, Genetic Manipulations and the Biological Future of the Human Species

TERM PROJECT - OPEN CLASS DISCUSSION / DEBATE - 9%

Class discussion / debate will be Wednesday, May 29, 2002):

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 %

Final 20 %

__________________________________________________________________

TOTAL LECTURE GRADE = 50 %

LABORATORY EXERCISES AND SEQUENCE

Exercise #/pages in

Week # Activities Laboratory Manual

1 Introduction: Discussion of Individual and Group

[3/4] Term Projects, Activities and Assignments

Cell Reproduction: Mitosis # 5

Plant and Animal Karyotype Analysis: supplement

Allium sativa and Vicia faba root tip squashes

Arabidopsis thaliana project set-up and discussion supplement

2 Plant and Animal Karyotype Analysis (cont'd.):

[3/11] Human Chromosome Unknowns; G-banding # 11

Preparation and fusion of protoplasts supplement

3 Meiotic Chromosomes - Spermatogenesis: # 6

[3/18] Cricket meiosis supplement

Inheritance of Albinism in Nicotiana spp. supplement

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 Viral Genetics: supplement

[3/25] Tobacco Mosaic Virus Infection

Read: Mobile DNA (Chapter 10, pp. 394-402)

Polyacrylamide Gel Electrophoresis (PAGE): supplement

Introduction

5 Polyacrylamide Gel Electrophoresis (PAGE): supplement

[4/8] Electrophoretic properties of native proteins

6 Quantification of DNA #15

[4/15] Read: DNA Absorption Kinetics (p. 55; p. 325)

DNA GEL Electrophoresis: Introduction and #16

Gel Loading Practice

Video presentations: "Footpath Murders: DNA Profiling's

Landmark Case" and "Planted Evidence: Plant DNA Forensics"

7 DNA Gel Electrophoresis: Fingerprinting supplement

[4/22] Identification of DNA by RFLP analysis

Principles of DNA Sequencing supplement

8 Gene Mutations: # 21

[4/25] Ultraviolet mutagenesis of Serratia marcesans

and Escherichia coli

Chromosomal Mutations (demonstration slides) # 11

9 Gene Regulation: Repression and induction of the lac operon in Escherichia Coli supplement

[4/29]

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 Transformation of E. coli with a Plasmid Containing supplement

[5/6] the gfp gene

Gel Electrophoresis: Cancer Gene Detection supplement

Read: Hereditary Cancer Syndromes (Chapter 15, pp. 661-663)

Recombinant DNA Technology: Replica plating to supplement

identify antibiotic resistance genes

11 Transformation of E. coli with a Plasmid Containing (results)

[5/13] the gfp gene

Gel Electrophoresis: Cancer Gene Detection (results)

Recombinant DNA Technology: Replica plating to (results)

identify antibiotic resistance genes

12 Student Presentations of Term Assignments and Reports

[5/20] (Continuation from lecture.)

Summary and Evaluation of semester's work

Additional (Optional) Activities:

Web-based projects:

TBA [e.g.: Isolation of DNA in your home]

Field Trips:

DNA Learning Center (Cold Spring Harbor)

DNA Crime Analysis Laboratory (Dr. L. Kobilinsky)

Institute for Basic Research (Staten Island, NY)

Dates and further information will be provided during the semester.

Tentative Due Dates for Laboratory Assignments

Homework’s: 8 x 2pts. = 16%

Plant karyotype analysis [3/13] - Individual

Preparation and fusion of protoplasts [3/18] - Individual

Cricket spermatogenesis [3/25] - Group

TMV infection [4/22] - Group

Quantification of DNA [4/24] - Group

Ultraviolet mutagenesis of Serratia marcesans and E. coli [5/1] - Group

Repression and induction of the lac operon in E. coli [5/1] - Group

Salivary gland chromosomes, Barr bodies [5/6] - Individual

Lab reports: 4 x 4pts. = 16%

Albinism inheritance in Nicotiana tobacum [4/10] - Individual

Drosophila melanogaster three point test cross [4/15] - Group

Transformation of E. coli with plasmid containing gfp gene [5/13] - Group

Arabidopsis thaliana growth and development [4/25] - Group

Unknowns: 7 x 2pts. = 14%

Root tip squash preparation and identification [3/13] - Individual

Human chromosomes [3/18, or in class 3/18] - Individual

Protein electrophoresis [4/17] - Group

DNA fingerprinting [4/29] - Group

DNA sequencing - autoradiographs [4/29] - Group

Cancer gene detection [5/15] - Group

Replica plating to identify antibiotic resistance genes [5/22] - Group

Lab Assignments - 46 %:

Attendance / Participation 4 %