Syllabus for Fall 2015
Molecular Genetics: Biology 700.4/700.5
Class: Tuesday and Thursday 6:30-8:20 PM (5 credit h)
Science Building D346
Contact information:
AM: Dr. Alicia Meléndez (course head)
alicia.melendez@qc.cuny.edu
NSB D-338, phone 718 997-4580
CSD: Cathy Savage-Dunn
mailto:Cathy.SavageDunn@qc.cuny.edu
NSB D-330, phone 718 997-3440
Required Texts:
1. Walker, M. and Hawley, S. (2003) Advanced Genetics Analysis, Blackwell Publishing.
2. WORMBOOK, (http://www.wormbook.org/toc_complete.html) a comprehensive collection of
original peered reviewed chapters covering topics related to C. elegans biology.
3. Papers from the primary literature: There will also be a series of scientific papers to read, some are
announced on the syllabus and others will be announced as needed throughout the semester on
Blackboard.
Recommended Texts:
1. Hartwell, L. et al (2008) Genetics: From Genes to Genomes, 5th edition, McGraw This edition no
longer includes sections on model organisms for genetic research, but these are available online at
the McGraw-Hill web site. Registration is simple. Complete Information: "Genetics: From Gene
to Genomes"
Leland Hartwell, Leroy Hood, Michael Goldberg, Ann Reynolds, Lee Silver, and
Ruth Veres.
ISBN: 0072848464 © 2008
McGraw-Hill, the publisher's web site. Amazon.
Objectives:
After taking this course, you should
-Understand the basic mechanisms of transmission of genetic traits, as first described by Mendel.
-Understand how genetic research is carried out, how we use genetic techniques to answer biological
questions.
-Understand how epistasis analysis is carried on, and how modifying genes may work: suppressors and
enhancers.
-Understand and recognize the differences involved using different genetic model organisms.
-Understand how to problem solve and how to analyze data from genetic analyses.
-Be able to read an article from the primary literature and understand the genetics described, and be able
to evaluate its conclusions.
Coverage: This course is intended as an advanced course in genetic analysis. The focus is on the basic
principles that underlie genetic analysis: the nature of mutations, complementation, suppression,
enhancement, recombination, segregation, and gene regulation. Our goal is to provide insights into the
process of genetic analysis and how this functions in the study of a biological process. We discuss the
basic tools, current techniques of genetic analyses, and the different genetic model organisms: the yeast
Saccharomyces cerevisiae, the worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and
mouse Mus musculus. For each of these species we will consider methods for the identification of
informative mutations revealing new genes or new gene functions, and methods for testing the expression
of modified genes. Genomics, including applicable genomics resources and practical bioinformatics tools,
will also be covered. Articles from the primary literature to better understand new techniques, and
possible misunderstandings in genetic analysis are also discussed. The course assumes familiarity with the
genetics of eukaryotes, and working knowledge of molecular biology, as for example transcription,
splicing, translation, and replication.
Grading for Bio 700 Students
The final grade for will be calculated as follows:
Quizzes
50% (Students have the option of dropping 2 quizzes from the 12 total quizzes)
Presentation 20%
Final Exam 30%
Makeup Policy
There will be no makeup exams given under any circumstances.
Student Disability Services
To receive disability-related academic accommodations students must first be registered with the Center
for Student Disability Services. Students who have a documented disability or suspect they may have a
disability are invited to set up an appointment with the Director of the Center for Student Disability
Services, Ms. Mirian-Detres Hickey at 718-997-5870, or they can walk-in and make an appointment at
Frese Hall, room 111. If you have already registered with the Center for Student Disability Services
please provide your instructor with the course accommodation form and discuss your specific
accommodation with him/her.
University's Policy on Academic Integrity
The faculty and administration of Queens College support an environment free from cheating and
plagiarism. Each student is responsible for being aware of what constitutes cheating and plagiarism and
for avoiding both. An example would be to use exact words or figures from a source without attributing
those words to the author or the source. The complete text of the CUNY Academic Integrity Policy and
the Queens College procedure for implementing that policy can be found at this site:
http://www.qc.cuny.edu/about/administration/Provost/Policies/Documents/Academic Integrity Memo
Fall 2014.pdf
If a faculty member suspects a violation of academic integrity and upon investigation, confirms that
violation, or if the student admits the violation, the faculty member MUST report the violation. The
penalty for violation will be failure in the course and a report to the Office of Student affairs.
Calendar:
Date
Lec
Topic
tu
rer
Th
AM 1. Intro: Genes to Genomes
8/27
Tue
CS 2. DNA manipulation Techniques
9/1
Th
CS 3. Using Genetics- Mutations
9/3
Quiz 1: Intro and DNA techniques
Tue
9/8
Th
9/10
Tue
9/14
Th
9/17
Tue
9/22
Th
9/24
Fri
9/25
Tue
9/29
Th
10/1
Tue
10/6
Th
10/8
Tue
10/13
Th
10/15
CS
Hartwell
Hawley
Articles/Other
Ch. 4
Problem Set 1 due (Intro Genetics)
Ch. 9
On line
Ch.
C.
elegans
Ch. 7, 8
Ch. 1,
p.1-14,
and p.
31-50
4. Genetics- Mutations
Discussion
Problem Set 2 due (Mutations)
Article 1 for discussion
NO CLASS Mon Schedule
NO CLASS College Closed
AM 5. Complementation
Ch. 8
Ch. 3
WB: Complementation
AM 6. DNA mutation and Repair
Quiz 2: Mutations
Ch. 7
Ch 2
WB: DNA repair
WB: Replication and Repair
Problem Set 3 due (Complementation)
CS
Ch. 5,6
Ch. 8
NO CLASS College Closed
CS
7. Chromosome
Quiz 3: Complementation
8. Genome Rearrangements
CS
9. Recombination
Quiz 4: Chromosome and
Genome Rearrangements
AM 10. Mapping and CloningDiscussion
CS
11. Transposons-Discussion
AM 12. Suppressors
Quiz 5: Mapping and Cloning
AM 13. Enhancers and Redundancy-
Tue
10/20
AM 14. Suppressors and Enhancers
Discussion
Th
10/22
AM 15. Epistasis
Quiz 6: Suppressors and
Enhancers
Tue
10/27
Th
10/29
AM 16. Epistasis- Discussion
CS
17. Gene Regulation
Quiz 7: Epistasis
Tue
11/3
CS
18. Gene Regulation
Discussion
Th
11/5
Tue
11/10
AM 19. RNAi and CRISPR/Cas
Quiz 8: Gene Regulation
AM 20. RNAi and CRISPR/CasDiscussion
Ch. 12
Article 2 for discussion
Ch. 6
Ch. 7
Article 4 for discussion
WB: Transposons in C. elegans
Ch. 10
Ch. 6,7
WB : Mapping
Article 3 for discussion
Problem Set 4 due (Mapping
Ch. 4
WB: Genetic Suppression
Problem Set 5 due (Transposons)
WB: Genetic Enhancers
WB: Gene duplications and Redundancy
WB: LIN-12/Notch signaling
Redundancy article
Problem Set 6 due (Suppressors &
Enhancers)
Article 5 for discussion
WB: Epistasis
Ch. 12
Ch. 12
Ch. 5,
p. 107118
Problem Set 7 due (Epistasis)
Article 6 for discussion
Ch. 15,
16
Problem Set 8 due (Gene Regulation)
Article 7 for discussion
Ch. 16
RNAi articles and CRISPR/Cas articles
Problem Set 9 due (RNAi)
Article 8 and 9 for discussion
Th
11/12
Tue
11/17
CS
CS
21. Epigenetics
Quiz 9: RNAi
22. Genetic Model systems-Yeast
Th
11/19
Tue
11/24
CS
23. Yeast- Discussion
AM 24. Genetic Model systemsDrosophila
Quiz 10: Yeast Genetics
Ch. 16
On line
Ch. Yeast
Ch. 5
On line
Ch.
Drosophi
la
Ch. 7,
p. 168178
Problem Set 10 due (Yeast genetics)
Article 10 for discussion
Ch.5, p. Article 11 for discussion
118126
Th
11/26
Tue
12/1
NO CLASS THANKSGIVING
AM 25. Genetic Model SystemsDrosophila Discussion
Problem Set 11 due (Drosophila
genetics)
Article 12 for discussion
Th
12/3
Tue
12/8
AM 26. Genetic Mosaics
Quiz 11: Drosophila Genetics
CS 27. Genetic Model SystemsMouse
WB: Mosaics
Article 13 for discussion
Problem Set 12 due (Mosaics)
Th
12/10
CS
28. Genetic Model systemsMouse Discussion
Quiz 12: Mosaics
Final exam
On line
Ch.
Mouse
Problem Set 13 due (Mouse genetics)
Article 14 for discussion
TBA
Dec
16-23
Lecture days have a QUIZ on the material from the week before and the reading of this day.
Articles 1-14 in bold are to be discussed by the students.