GENETICS & MOLECULAR BIOLOGY (BIOL3010)
FALL 2012
COURSE DESCRIPTION
What makes humans different from fruit flies? Why do you look like your mother? Why
does your brain have neurons and not liver cells? The short answer to each of these
questions is: It's the genes! And, that's what this course is about. Throughout the
semester, we will consider what genes are, both physically and functionally. We will
consider their chemical make-up, how they are passed on from generation to generation,
how they are expressed and how that expression is regulated, how disruptions in the
structure and expression of genes arise and how those disruptions lead to cellular defects
and disease.
WHY STUDY GENETICS?
Ultimately, genetics underlies not only how organisms develop, but also how they respond to
and interact with each other and their environments. But, aside from that and any
particular curiosity you have about our relationship to fruit flies in the grand scheme of life,
why should you care about genetics? Genetics has an enormous impact on modern society.
Our increasing understanding of the molecular genetic basis of heritable traits, including
disease, prompts difficult health and reproduction-related questions for both individuals and
lawmakers. Our growing knowledge of the function and control of our genome is enabling
greater opportunities for developing effective gene therapies to treat/cure genetic diseases.
Rapidly evolving technical advances are making it possible to gather unprecedented
information about our individual genetic profiles (our genetic fates?). This course is
designed to help you develop the analytical skills necessary to enhance not only your
continuing studies in biology, but also your future contributions to the vigorous societal
debates that focus on these genetics issues.
COURSE OBJECTIVES
The overall goals of this course are that you will (1) develop an understanding of how genes
and traits are related, (2) learn how to think like a geneticist for future analyses of complex
biological phenomena and (3) use your acquired genetic literacy to become an informed
member of society.
Specifically, at the end of this course, you will:
• be able to connect all aspects of the function of genes & genomes with their molecular
anatomy.
• understand the mechanisms by which an organism's genome is passed on to the next
generation and be able to assess where during that process structural abnormalities
in the genome arise.
• be able to analyze gene variants, genetic crosses and inheritance patterns to deduce
information about genes, alleles and gene functions.
• be able to analyze and understand how different types of mutations affect genes and
their corresponding RNA/protein products.
• be able to relate genes & gene function to core principles in other major disciplines of
biology, such as cell biology, development, biochemistry, and evolution.
IMPORTANT COURSE DETAILS
Lectures: 1:00-1:50 MWF Chem 402
Semester Tests: 7:00-9:00 PM Mondays (see calendar) Chem 402
Required Discussion Sessions: as scheduled
INSTRUCTOR INFORMATION
Claire Cronmiller, Professor of Biology. Born in Syracuse, New York, but grew up in New
York State, Washington State, Massachusetts and New Jersey. Started out as a German
literature major in college, but eventually had to admit to a less than scholarly talent for
literary criticism. Took Introductory Biology in college to fulfill a science requirement: The
rest, as they say, is history. In the lab, grows fruit flies as an experimental model to study
the genetic regulation of development, but at home cares for 18-year-old Pulcino, a Quaker
parrot.
Office:
Phone:
email:
Office Hours:
Gilmer 260
982-5484 (office), 979-1758 (home)
crc2s@virginia.edu
T 10-11, W 2:15-3:15 [Gilmer 227] & by appointment [Gilmer 260]
(TEACHING ASSISTANTS)
Krista Aschenbach, Erin Kodis, Brittany Sutherland, Rich Smindak
Email addresses, office locations & office hours posted on the course Collab site.
TEXTBOOK & ONLINE LEARNING PROGRAM
The required textbook is: Genetic Analysis: An Integrated Approach by Sanders and
Bowman, 1st ed., Pearson. This book will be used throughout the semester to provide
foundational knowledge, as well as application practice problems; the book is available in
both hardcover and loose leaf editions. There is also an associated Student Study Guide
and Solutions Manual, which is not required but might be useful (if used effectively: see
Cronmiller's Tips for Success in Genetics on Collab). Mastering Genetics is an online
learning program that will be used to give you help with problem solving and to provide you
with feedback on the depth of your understanding of fundamental concepts; access codes
are available either bundled with the textbook or separately. Pre-class quizzes (due by
10:00 AM each class day) and weekly homework assignments (due by 5:00 PM each
Sunday) will also be provided through Mastering Genetics.
PREREQUISITES
BIOL 2010 and at least one semester college chemistry (e.g. CHEM1410/1420/1810/1820).
The premise for this course is that you have completed these prerequisites and are familiar
with their concepts and principles.
IMPORTANT COLLEGE DATES:
Last Day to Add: September 11
Last Day to Drop: September 12
Last Day to Withdraw: October 23
TO DO YOUR BEST, I'D RECOMMEND:
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Complete the pre-class assignments. Class time will be used to consider concepts and
processes at levels that go beyond simply "define and describe." To participate fully
in class time discussions and activities, you will need to come prepared. The reading
for each class is listed in the course schedule. By 10:00AM on each class day,
complete the short Mastering Genetics quiz that is based on the reading material;
this will help you gauge your comprehension of the reading, and it will help me
identify particularly difficult material that needs to be clarified during class.
Come to class. Class presentations and activities will help you understand
extensions, implications and applications of genetic concepts. Case studies and word
problems will give you guided practice analyzing genetic scenarios. We will also use
iClickers to help you assess your own understanding of these concepts and your
ability to apply them to problems and simulations.
Use the available resources. Among the Learning Aids under the Resources menu,
you will find suggestions for reading your textbook, solving problems, integrating
concepts throughout the semester, etc. You will also find Cronmiller's Tips for
Success in Genetics, which includes strategies for developing your problem solving
skills.
Practice, practice, practice! Confucius said: I hear and I forget, I see and I
remember, I do and I understand. If listening and reading are as far as you go with
your course involvement, you will undoubtedly be dissatisfied with your encounter
with genetics this semester. Unfortunately, we cannot offer you the hands-on “doing”
experience that would most effectively lead you to genuine understanding of genetic
principles. Instead, we use problem solving to simulate "doing." Typically, we are
not born with an instinctive ability to dissect and explain genetic scenarios: That
ability needs to be developed. Moreover, cultivating that ability is not a passive
activity: It will require significant time and effort on your part. However, since
solving practice problems, diligently and honestly (see Cronmiller's Tips for Success
in Genetics), is the only reliable way to gauge your understanding of genetics
concepts, that time and effort will be well worthwhile.
If you need it, get help early and often! Each week we offer you 10 hours of walk-in,
open office hours. No standing in line -- just come in and ask questions, get help on
problems, or listen to questions asked by others.
EVALUATION & GRADING
Your learning will be assessed by:
• 3 problem-based semester tests (35%)
• online quizzes related to the pre-class reading (~12%)
• weekly homework problems (15%)
• discussion activities (~17%) [see Discussion Information & Policies on Collab]
• final exam (~18%)
You will also receive 20 points (~3% of the course grade) for taking 2 short online
assessments of your general knowledge of genetics. These multiple choice assessments are
closed book and require no advance preparation. Check the Syllabus (for the Class &
Assignment Schedule) and Tests & Quizzes links on Collab for information regarding the
timed, limited access and deadlines for these assessments (one at the beginning of the
semester and one at the end).
Although iClicker responses will not contribute to your course points, you should take this
class participation seriously and answer all questions thoughtfully: iClicker scores will be
considered for cases of borderline final grades.
The final letter grades for the course will be assigned according to a distribution that uses
the standard deviation to describe the dispersion, variability and spread of scores around
the average score.
TESTS
All tests are comprehensive. Genetics, like science generally, is cumulative. Be careful not
to “pigeonhole” your learning: On every test you will encounter questions/problems that
will require you to combine several concepts to synthesize plausible answers. In these
cases, just memorizing isolated concepts and examples will not work. You will need to
draw on and integrate concepts you saw in Chapter 4, even as you consider problems that
you encounter in Chapter 7. [Concept maps can help you re-examine and relate material
continuously throughout the entire course!] Moreover, what you understand by the end of
the course matters most. Comprehensive tests not only give you multiple chances to show
and get credit for your comprehension, but they also put the emphasis for assigning final
grades on the knowledge and abilities that you’ve developed by the end of the class, rather
than on the average of your accomplishments throughout the semester. If, in spite of
sincere and conscientious efforts for the 3 semester tests, you perform better on the
comprehensive final exam than collectively on the semester tests, your final exam
score (x3) will be used as your total tests + final exam score in the calculation of
your final grade.
All tests are closed book format, and only nonprogrammable calculators may be used
during tests! (Tip: Get the calculator now, and use it for all problem solving, so that you're
comfortable with it during the test.) For suspected test grading errors, please email CC
after the test scores & answer keys have been posted on Collab.
MAKE-UP TESTS
Alternate test times for semester tests may be requested for varsity athletic or legitimate
academic reasons; requests must be made and approved at least 5 days in advance.
Otherwise, students who miss any one of the 3 semester tests and have an excusable
justification (e.g. death in the family or incapacitating illness with hospital/physician
verification), may take a single, comprehensive make-up test (Monday, November 26th,
7-9 PM). Except in case of emergency, approval to take the make-up test must be
requested before the test that will be missed.
ELECTRONIC DEVICES
Cell phones and pagers that ring during class are disruptive; please turn them off and put
them away before class begins. If there is an emergency situation that requires that you be
reached, set your phone/pager to vibrate/mute; if it rings, leave the class to take the call.
Laptops/digital notebooks may be used during class only if they are being used for a class
activity, such as taking notes. "Multitasking is mostly wishful thinking." So, please do not
IM, tweet/facebook, surf the web, play games or prepare/read/send email or text messages
during class. Students who violate these rules will be asked to leave the classroom. [FYI:
Studies show that laptop abuse during class lowers grades (research citation available upon
request). So, it is in your best interest to stay focused during class.]
No electronic devices, except nonprogrammable calculators, may be used at any time during
tests.
ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES
If you have a disability and need accommodations, please provide the Learning Needs and
Evaluation Center (LNEC) with the appropriate paperwork. It is your responsibility to file
this paperwork in a timely fashion and to follow-up with me (Professor Cronmiller) about
any accommodations required. If you would like to discuss your need for accommodations
with me, please contact me to set up an appointment. The LNEC is located in the
Department of Student Health and can be contacted at 434-243-5180/5181.
HELP FOR STUDENTS IN DISTRESS
A recent American College Health Survey found that stress, sleep problems, anxiety,
depression, interpersonal concerns, death of a significant other, and alcohol use rank among
the top ten health impediments to academic performance. Students experiencing personal
problems or situational crises during the semester are encouraged to contact Counseling
and Psychological Services (CAPS) at Student Health (434-243-5150;
www.virginia.edu/studenthealth/caps.html) for assistance, support and advocacy.
RECORDING & COPYRIGHT POLICIES
University Policy prohibits or limits the recording of classroom lectures, as well as the redistribution of course materials. In this course, recording of lectures/presentations is
allowed for personal use only. Students may not post such recording (or any provided
course materials) to any internet site. Furthermore, according to the Technology
Harmonization and Education Act of 2002, I am required to provide this legal notice that
online materials provided for your use in this course could be copyright-protected. Fair Use
laws permit me to provide this material for your personal use, but we are all prohibited
from unlimited copying and distribution of it.
HONOR STATEMENT
We trust that every student will comply fully with all provisions of the UVA honor system.
We also assume that any student, who observes an incidence of cheating, will contact an
Honor Advisor. Any student who is caught (by the instructor/TA) cheating or committing
academic fraud will receive a "0" (zero) on the assignment/test, irrespective of any
subsequent action taken by the Honor Committee. For all assignments, please pay
attention to explicit instructions regarding what resources you may (or may not) use for
their completion and whether you may (or may not) collaborate with classmates.
CLASS/ASSIGNMENT SCHEDULE (under construction)
Class # Date Topics Class Preparation Assignments Assessment Activities Unless otherwise indicated, reading assignments must be completed before the class for which they are listed. (They also need to be completed before the associated Mastering Genetics quiz.) Unless otherwise noted, pre-­‐class quizzes must be completed before 10:00 AM on the day of the class for which they are listed. Weekly homework assignments (HW) must be completed by 5:00 PM on the indicated due date. There are no assignments due before the first class. The following tutorial should be completed before taking Quiz #2. Quiz #1: Beginning Assessment Test (under “Tests & Quizzes” on Collab) (must be completed before 5:00 PM on Sunday, 9/2/12!) #1: Genetics is all around us. W Aug. 29 Welcome! The big picture Course learning goals Course format & tools Introductions Assignment (MG): Introduction to Mastering Genetics #2: Historical & molecular foundations of modern genetics F Aug. 31 The big picture Gene-­‐trait connection Chapter 1 Course Syllabus Graphic Syllabus Quiz #2: Mastering Genetics #3: What genes are. [DNA structure & replication] M Sept.3 DNA chemistry DNA replication D#1 Chapter 7, pp. 222-­‐243 MG: Ch.7 Tutorial #1 Bidirectional Replication (animation) Quiz #3: Mastering Genetics HW #1 available (MG): due 9/9 DNA Replication "Trombone" (animation) #4: What genes are. [DNA replication, telomeres] W Sept. 5 DNA replication cont’d DNA proofreading End-­‐of-­‐replication problem Telomeres Chapter 7, pp. 243-­‐248 MG: Ch.7 Tutorial #2 Quiz #4: Mastering Genetics "A structure for deoxyribose nucleic acid" (Watson & Crick, 1953) Telomere Replication (animation) #5: Molecular analysis of genes. [PCR, Electrophoresis, Sequencing] F Sept. 7 PCR Molecular markers Chapter 7, pp. 248-­‐256 MG: Ch.7 Tutorial #3 Quiz #5: Mastering Genetics PCR amplification (animation) #6: How genes function. [RNAs, Transcription] M Sept. 10 RNA chemistry Transcription D#2 Chapter 8: 8.1-­‐8.3 MG: Ch.8 Tutorial #1 Transcription (animation) Quiz #6: Mastering Genetics HW #2 available (MG): due 9/16 #7: How genes function. [Transcription, RNA processing] W Sept. 12 Transcription, cont'd RNA processing Chapter 8: 8.4 MG: Ch.8 Tutorial #2 RNA Splicing (animation) Quiz #7: Mastering Genetics #8: How genes function. [Protein structure, Translation] F Sept. 14 Proteins The "components" of translation Chapter 9: 9.1-­‐9.4 MG: Ch.9 Tutorial tRNA (animation) Translation I (animation) Translation II (animation) #9: How genes function. [Ribosomes, tRNA, Genetic Code] M Sept. 17 tRNA, genetic code, wobble Nonsense suppression D#3 Chapter 9: 9.5-­‐9.6 Quiz #8: Mastering Genetics Quiz #9: Mastering Genetics HW #3 available (MG): due 9/23 #10: Integrating Gene Structure & Function W Sept. 19 Sickle Cell Disease Chapter 10: complete MG: Ch.10 Tutorial Quiz #10: Mastering Genetics Molecular Visualization: Sickle Cell Hemoglobin Tutorial (molecular models) #11: Integrating Gene Structure & Function F Sept. 21 Application of material Chapter 10: complete Quiz #11: Mastering Genetics #12: Semester Test #1 (7:00-­‐9:00 PM) M Sept. 24 Chapter 1, 7-­‐10 D#4 Quiz #12: Mastering Genetics (random selection from everything so far) HW #4 available (MG): due 9/30 #13: Where “Transmission Genetics” begins: Meiosis! W Sept. 26 Chromosomes Meiosis Nondisjunction Chapter 11: 11.1-­‐11.3 MG: Ch.11 Tutorial Chapter 3: 3.1-­‐3.3 MG: Ch.3 Tutorial #1 Mitosis (animation) Mitosis (animation) Meiosis (animation) Meiosis (animation) Quiz #13: Mastering Genetics #14: How genes behave. [Mendel monohybrid -­‐ segregation, di/trihybrid -­‐ independent assortment] F Sept. 28 Mendelian patterns of inheritance Chapter 2: 2.1-­‐2.3 MG: Ch.2 Tutorial #1 Quiz #14: Mastering Genetics Independent Assortment (animation) #15: How genes behave. [sex linkage, pedigrees] M Oct. 1 Pedigrees X-­‐Y chromosomes D#5 Sex linkage Chapter 2: 2.6 Chapter 3: 3.3-­‐3.5 MG: Ch.3 Tutorial #2 MG: Ch.2 Tutorial #2 Quiz #15: Mastering Genetics HW #5 available (MG): due 10/7 Chapter 2: 2.4-­‐2.5 MG: Ch.2 Tutorial #3 Quiz #16: Mastering Genetics #16: [Probability, Chi square] W Oct. 3 Probability Chi square analysis #17: How genes function. [Gene interactions, morphs] F Oct. 5 Gain/Loss-­‐of-­‐function mutations "Muller's morphs" Chapter 4: 4.1 MG: Ch.4 Tutorial #1 Quiz #17: Mastering Genetics M Oct. 8 Fall Break HW #6 available (MG): due 10/14 #18: How genes function. [Gene interactions, dominance, penetrance, variable expressivity] W Oct. 10 Dominance relationships Variable phenotypes Chapter 4: 4.2 MG: Ch.4 Tutorial #2 (end-­‐
of-­‐chapter problems for whole chapter Quiz #18: Mastering Genetics #19: How genes function. [Gene interactions, epistasis] F Oct. 12 Intergenic interactions Modified Mendelian ratios Chapter 4: 4.3 MG: Ch.4 Tutorial #3 Quiz #19: Mastering Genetics #20: How genes function. [Gene interactions, complementation] M Oct. 15 Complementation D#6 Chapter 4: 4.4 MG: Ch.4 Tutorial #4 Quiz #20: Mastering Genetics HW #7 available (MG): due 10/21 #21: How genes function. W Oct. 17 (Catch-­‐up) Polygenic inheritance Chapter 4 Chapter 21: pp.708-­‐714 #22: How genes behave. [Linkage & recombination] F Oct. 19 Genetic recombination Linkage Genetic maps Chapter 5: 5.1-­‐5.2 MG: Ch.5 Tutorial #1 (activities for the whole chapter) Quiz #21: Mastering Genetics (cumulative review of all reading so far) Quiz #22: Mastering Genetics # 23: Semester Test #2 M Oct. 22 D#7 Chapters 1-­‐4, 7-­‐11.3 & Chapter 21 (pp.708-­‐714) Quiz #23: Mastering Genetics HW #8 available (MG): due 10/28 #24: How genes behave. [Linkage & recombination] W Oct. 24 Mapping Mitotic recombination Chapter 5: 5.2-­‐5.4 Quiz #24: Mastering Genetics #25: How genes behave. [Linkage & recombination] F Oct. 26 Mapping function Mitotic recombination Chapter 5: 5.4-­‐5.5, 5.8 (omit: LOD Score Analysis, 5.6 & 5.7) Quiz #25: Mastering Genetics MG: Ch.5 Tutorial #2 (end-­‐of-­‐chapter problems for the whole chapter) #26: University classes cancelled (Hurricane Sandy) M Oct. 29 D#8 (Chapter 12: 12.1-­‐12.3) Quiz #26: Mastering Genetics HW #9 available (MG): due 11/4 #27: When things go wrong. [Mutations] W Oct. 31 Mutations Chapter 12: 12.1-­‐12.3 MG: Ch.12 Tutorial #1 Quiz #27: Mastering Genetics #28: Why don't things go wrong more often? [Mutagens, carcinogens] F Nov. 2 Chemical mutagens Chapter 12: 12.4 MG: Ch.12 Tutorial #2 Quiz #28: Mastering Genetics #29: Why don't things go wrong more often? [DNA repair] M Nov. 5 DNA repair D#8 Chapter 12: 12.5-­‐12.6 (omit 12.7 & 12.8) MG: Ch.12 Tutorial #3 Quiz #29: Mastering Genetics HW #10 available (MG): due 11/11 MG: Ch.12 Tutorial #4 (end-­‐of-­‐chapter problems for the whole chapter) #30: The whole equals more than the sum. [Genic Balance, number] W Nov. 7 Euploidy/Aneuploidy Chromosome number Chapter 13: 13.1-­‐13.2 Chapter 3: 3.6 MG: Ch.13 Tutorial #1 Quiz #30: Mastering Genetics #31: Chromosomal changes [dosage] F Nov. 9 Dosage compensation Chapter 13: 13.3 MG: Ch.13 Tutorial #2 Quiz #31: Mastering Genetics #32: Semester Test #3 (7:00-­‐9:00 PM) M Nov. 12 Chapters 1-­‐12 D#9 Quiz #32: Mastering Genetics (“problematic” questions from Chapters 5 & 12) HW #11 available (MG): due 11/18 #33: Chromosomal changes [structure] W Nov. 14 Deletions Duplications Chapter 13: 13.3 MG: Ch.13 Tutorial #3 Quiz #33: Mastering Genetics #34: Chromosomal changes [structure] F Nov. 16 Inversions Translocations Chapter 13: 13.4 MG: Ch.13 Tutorial #4 Quiz #34: Mastering Genetics #35: Chromosomal changes [structure, transposable elements] M Nov. 19 Transposition Chapter 13: 13.5-­‐13.6 MG: Ch.13 Tutorial #5 (end-­‐of-­‐chapter problems for the whole chapter) Quiz #35: Mastering Genetics Nov. 21 Thanksgiving Break Nov. 23 Thanksgiving Break #36: Prokaryotic Gene Regulation [operon] Chapter 14: 14.1-­‐14.2 M Nov. 26 Gene regulation defined Lac Operon D#10 The Operon in general (Animation) #37: Prokaryotic Gene Regulation [mutational dissection] W Nov. 28 lac operon mutants Chapter 14: 14.2-­‐14.3 (up to Arabinose operon) Quiz #36: Mastering Genetics HW #12 available (MG): due 12/2 Quiz #37: Mastering Genetics #38: Prokaryotic Gene Regulation [catabolite repression] F Nov. 30 lac operon positive control ara, trp operons Chapter 14: 14.2, 14.3 Quiz #38: Mastering Genetics (plus pp. 473-­‐476: feedback inhibition) Chapter 14: omit rest of 14.4-­‐14.6 MG: Ch.14 Tutorial #1 MG: Ch.14 Tutorial #2 (end-­‐of-­‐chapter problems for whole chapter) #39: Eukaryotic Gene Regulation [cis & trans acting] M Dec. 3 Transcriptional regulation D#11 Chromatin Chapter 15: 15.1-­‐15.2 MG: Ch.15 Tutorial #1 (includes end-­‐of-­‐chapter problems) Quiz #39: Mastering Genetics HW #13 available (MG): due 12/9 #40: Eukaryotic Gene Regulation [DNA modification] W Dec. 5 Genomic imprinting Chapter 15: 15.3 Quiz #40: Mastering Genetics #41: F Dec. 7 Dec. 17 9:00 AM -­‐
12:00 noon Quiz #41: NOTE!! This final quiz is NOT on MG, but is under “Tests & Quizzes” on Collab. Ending Assessment Test (under “Tests & Quizzes” on Collab) (must be completed before 5:00 PM on Sunday, 12/16/12!) Time to tie it all together! Final Exam