Download BIOL 221_syllabus_part1_2010

BIOL 221 (Spring 2010) Molecular Biology and Genetics
Lectures: Tuesdays and Thursdays from 9:00-10:30 am
Location: Stiteler Hall B6
Instructors: Dr.Kimberly Gallagher ([email protected])
Office Hours: Tuesdays 12-1 in 121 Lynch
Dr. Nancy Bonini ([email protected])
Office Hours: TBD
Teaching Assistants: Dr. Stewart Gillmor ([email protected])
Problem Sessions: Weds 6-7 pm
Office hours: Weds. 4-5 pm
Dr. Katy Claiborn ([email protected])
Problem Sessions: Tues 5-6 pm in Leidy 10
Office hours: Thurs. 5:30-6:30 pm Goddard 101
Penn Blackboard Gateway:
HYPERLINK "https://courseweb.upenn.edu/"
https://courseweb.upenn.edu/
Description: This course will survey the discipline of Molecular Genetics. This
will include two broad areas in molecular biology and genetics.
Genetics - We will discuss both the application of Mendelian and molecular
genetic techniques and principle to answering question in modern biology . We will learn
how genes are passed from one generation to the next and how genetic analysis
contributes to our understanding of other areas of biology including Biochemistry and
Cell Biology. Lectures include discussion of experiments and techniques used in a variety
of genetic systems including prokaryotes, eukaryotes and viruses.
Molecular Biology - We will discuss, at the molecular level, processes such as
DNA replication, transcription, and translation, and study the regulation of gene
expression in both prokaryotes and eukaryotes. We will also discuss
recombinant DNA technology and learn how powerful this technology has proven
in elucidating the mechanisms of complex genetic control, and insights it has
provided on the molecular basis for many human diseases and genomics.
Textbook
The text that we will be using this spring is Genetics: From Genes to Genomes (3rd
Edition) by Hartwell et al. ISBN# 0077388046. The version of the text from the Penn
bookstore is bundled with complete online/pdf access to the text and to the companion
website. You will require access to the textbook for readings, study materials and
homework.
Occasionally you be required to read articles from the Encyclopedia of Life Sciences
series published by Wiley. These article are in addition to readings from your textbook
and often provide a more complex or in-depth look at particular concepts of processes.
As these are written by experts in their field, they are often excellent. You are strongly
encouraged not to ignore these. The free content articles are available through Wiley
Publishing at http://www.els.net/. You can search by title or by author.
Exams and Grading: This class is graded on a curve based upon the normalized mean
scores for each exam. There are three exams scheduled during the semester and a
cumulative Final Exam. Each exam, including the cumulative final, will be worth 100
points. Only your 3 highest normalized scores from the 4 total exams are included in the
calculation of the final grade (i.e. we drop your lowest grade). This means that you may
choose to not take the cumulative Final Exam, if you think you have done well on the
three other exams. Since only three of the four exams are included in the calculation of
your final grade, NO MAKE-UP EXAMS WILL BE GIVEN. You are strongly
encouraged to take all four exams. Only students who take all four exams are eligible to
receive an A+ in the class.
Students who are enrolled in BIO 527 are required to take all four exams. Your grade
will be based upon a total of 400 points 300 exam points plus 100 points from a term
paper that will be assigned sometime during the middle of the semester. The grade on the
term paper cannot be dropped. In addition throughout the semester there will be
additional readings that you are strongly encouraged to complete.
For all students, the overall class mean will be calculated after the lowest grade for each
student is dropped. This means that the class average displayed in Blackboard is an
underestimate of the actual class mean.
Regrades and questions about grading of your exam will be considered only during a
one-week interval after the day the exam has been returned to you and the exam key
posted. These questions must be submitted in writing (typed- no handwritten requests
will be accepted). It should be noted that when an exam is considered for regrading, all
answers of the exam are subject to reconsideration. Exam submitted in pencil are not
eligible for regrade.
Homework: Throughout the semester you will be assigned homework problems (from
the text, and questions of our own design). All homework assignments are optional,
however you are srongly encouraged to complete all assignments and discuss any
problems with the TAs during recitation sessions. We may occasionally request that you
turn-in some of these homework problems for review. These will not be graded as such,
but will be used as a class participation/extra credit score that we will take into
consideration, if you are on the border between two grades.
221_2010_Syllabus_01_12_10.xls
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BIOLOGY 221 SYLLABUS 2010
Date
Lecture Topics
Required Reading: Reading in italics may not Additional Recommended
be explicitly covered in lecture, but are
Readings (Required for 527
assumed knowledge.
Students):
Additional materials of interest
Transmission Genetics
14-Jan Th
Introduction to Genetic Analysis (KG)
1:1-13, 2:13-21 (Qs. 2: 3,4b,5,6,7,8,9,12)
19-Jan T
Application of Mendel's Principles to Human
Genetics (KG): Chromosomal Basis for Mendelian
Inheritance (Oogenesis and Spermatogenesis);
Introduction to Pedigrees
13:465-472;479-482 4:81-103, 2:30-37
21-Jan Th
Analysis of Probability (KG)
26-Jan T
28-Jan Th
2-Feb T
2:21-30, Conditional Probability and the
Reverend Thomas Bayes B. Everitt, Chance
Rules, DOI: 10.1007/978-0-387-77415-2_9
Application of Mendels Principles to Model System Encyclopedia of Life Sciences Articles by Andrew
Genetics and Disease (KG): The Significance of
Wilkie: Dominance and Recessivity and by
Dominance (Muller's Morphs); Introduction to Forward Burke Judd: Experimental Organisms Used in
and Reverse Genetics.
Genetics
Beyond Mendel- Complex Dominance and
Applications to Model System Genetics (KG):
Incomplete and Co-Dominance; Penetrance and
Expressivity; Complementation; Epistasis
3:47-72
Genetic Analysis in Practice (KG): Dissecting Yeast
Secretion
Peter Novick, Charles Field and Randy Schekman
Identification of 23 Complementation Groups
Required for Post-translational Events in the
Yeast Secretory Pathway. and Lamason, et al.
SLC24A5, a Putative Cation Exchanger,
Affects Pigmentation in Zebrafish and
Humans
Gene Mapping
4-Feb Th
Gene Identification: Linkage Analysis (part I)
(KG)
9-Feb T
Linkage Analysis (part II) (KG)
11-Feb T
16-Feb Th
Experiments in Plant
Hybridization (1865)
by Gregor Mendel available in
English at:
http://www.mendelweb.org/Men
del.html
Encyclopedia of Life Sciences Encyclopedia of Life Sciences Article
Article by Laura L Hall: Turner by Jean-Pierre Fryns: Monosomies
Syndrome
and by Michel Vekemans: Trisomy
HJ Muller (1932) Further studies
on the nature and causes of
gene mutations Of particular
interest are pages 231-252
beginning with "On the character of
mutations."
Huang and Sternberg Genetic
Dissection of Developmental
Pathways
5:123-142
Encyclopedia of Life Sciences Article by Alan F
Wright: Genetic Variation: Polymorphisms and
Mutations
Exam I
The Genetics of Bacteria and Viruses (KG) : Use of 15: 539-573
Microorganisms in Science and Society; Modes of DNA
Encyclopedia of Life Sciences Article by Jill B
transfer and mating.
Keeney: Microorganisms: Applications in
Molecular Biology
Encyclopedia of Life Sciences
Article by Sabine Hofmann and
Matthias F Bauer Mitochondrial
Disorders
Molecular Biology of the Gene
18-Feb Th
Cracking the code of life: DNA structure &
replication (NB)
6:167-191
Watson & Crick (1953) Nature
171: 737-8; Lucia & Cairns
(1969) Nature 224: 1164-6.
221_2010_Syllabus_01_12_10.xls
23-Feb T
25-Feb Th
A messenger between the nucleus and cytoplasm: 8:255-275
RNA transcription & processing (NB)
Translating the genetic code: Proteins & their
8:275-284
synthesis (NB)
Yanofsky (2007) Cell 128: 8158; Crick et al. (1961) Nature
192: 1227-32.
Gene Regulation
2-Mar T
Gene regulation in prokaryotes: the Lac operon
(NB)
8:282-284, 17:609-635
4-Mar Th
Gene regulation in Eukaryotes (NB): Enhancers;
chromatin remodeling; activation & inactivation of
whole chromosomes
18:643-677, 13:465-482
Timko et al. (1985) Nature 318:
579-582; Lomvardas et al.
(2006) Cell 126: 403-13.
SPRING BREAK WEEK
16-Mar T
Maintaining integrity of genome: Mutation &
repair (NB)
7:207-244
18-Mar Th
Variations in chromosome structure & number:
Large scale chromosome changes (NB)
14:489-508, 516-526
23-Mar T
Genomics
25-Mar Th
30-Mar T
1-Apr Th
Zhang et al (2009) Annu Rev
Genomics Hum Genet 10:45181.
Exam II
Techniques of DNA manipulation (NB):
9:310-339
Recombinant DNA; gel electrophoresis; blots; restriction
maps; PCR; sequencing
Aligning Genetic and DNA maps, and Genomics
10:351-383
(NB): Genome assembly; microarrays; bioinformatics
Functional Genomics (NB)
11:391-425
Saiki et al (1988) Science 239:
487-491.
Waterston et al. (2002) PNAS
99: 3712-6.
Gene variation, evolution and complex interactions
6-Apr T
8-Apr
13-Apr
15-Apr
20-Apr
Th
T
Th
T
22-Apr Th
27-Apr
6-May
Jumping genes (NB): Transposable elements in
plants, animals and bacteria
Developmental & behavioral genetics (KG)
Developmental & behavioral genetics (KG)
Population & evolutionary genetics (KG)
Cancer, or the genome gone awry: oncogenes &
tumor suppressors (NB)
The Immune system: the components, antibodies
& genome rearrangements, & HIV (NB)
Exam III
**CUMULATIVE FINAL**
Scheduled for Thursday, May 6th, 12-2 pm
14:508-516, 22:811-813
Jones (2005) Cytogenet
Genome Res 109: 90-103.
19:685-709
Murchison et al (2010) Science
327: 84-87.
8:270-271, 14: 492-494, 22:791-794,813-822
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