Biology 202- Molecular Biology and Genetics
Fall 2013 (Section 006) Dr. Kelly Hogan and Dr. Lillie Searles
Lectures: 201 Coker Hall (MWF 11:00- 11:50 AM)
Recitations: (you must be registered for one of the 8 sections: 601-608); attendance required.
601
602
603
604
605
606
607
608
Monday
Monday
Monday
Monday
Monday
Tuesday
Tuesday
Tuesday
Instructors:
1-1:50 PM; GSB Room 1377
2-2:50 PM; GSB Room 1377
4-4:50 PM; GSB Room 1377
5-5:50 PM; GSB Room 1377
6-6:50 PM; GSB Room 1377
12:30-1:20 PM; GSB Room 1377
5-5:50 PM; GSB Room 1377
6-6:50 PM; GSB Room 1377
Dr. Kelly Hogan
Email: Kelly_Hogan@unc.edu
Office location: Wilson Hall 104B
Office Hours: Mondays 1-3 PM and Wednesdays: 3-5
Dr. Lillie Searles
Email: lsearles@email.unc.edu
Office location: 508 Fordham Hall
Office hours: TBA.
Graduate TAs: Stephen Sojka: sojka@live.unc.edu; sections 601, 602, 603, 606; Office hours: Wed 1:30-2:30, Fordham 212
Felix Peng: fpeng@email.unc.edu; sections 604, 605, 607, 608; Office hours: Thur 12:30-1:30 Fordham 212
Undergraduate S.I. instructors: Christine Ha (hac2105@live.unc.edu), Caroline Porter (clporter@live.unc.edu), Peter Fan
(pjfan@live.unc.edu), Sean Rankin (strankin@live.unc.edu), Paige Tummons (ptummons@live.unc.edu)
(Check Sakai for times/rooms for S.I.)
Undergraduate Tutors: Tutors who were top students last Fall in Hogan/Searles Bol 202 class are available to help you go over homework
problems once you have turned it in. They can give you tips about how to best study too. See: http://bio.unc.edu/undergraduate/courseinfo/tutoring/ for this semester’s information. More info will be posted on Sakai too.
COURSE WEBSITE: www.SAKAI.unc.edu
This site will have postings from our lectures such as outlines, power point slides, supplemental material that we mention in lecture. We will also post
announcements on this site. It is your responsibility to check it regularly.
TEXTBOOK: 1) Genetic Analysis. Sanders and Bowman, Pearson, 1st edition. 2) Mastering Genetics Access is required too.
The ebook with Mastering is likely the cheapest way to go, but if you prefer a physical text that is fine too.
ADDITIONAL REQUIREMENTS: Basic knowledge of biology and chemistry as demonstrated by a C or
above in BIOL 101 and CHEM 101 or 102 or equivalent.; a laptop or phone to answer in-class questions.
COURSE GOALS:
1. To provide you with the core principles of genetics and molecular biology and a set of useful skills. You will use the book and class time to
gain the content knowledge you will need to work with. We will take a historical approach at times to see how famous experiments were
performed. We will also examine the basic “rules” of genetics that may then be altered to account for more complex situations. Skills you will
practice relate to building hypotheses to answer a specific scientific question, designing an experiment using an appropriate technique/assay to
answer the question, and predicting results of their experiment; identifying and explaining the purpose of positive and negative controls in welldesigned experiments; interpreting experimental data and inferring conclusions from the experimental results; calculating probabilities and using
statistics to compare data sets; and giving examples of how advances in genetics and molecular biology, have changed the world. After this class,
you will be prepared to do research in a lab on campus and to build upon this content with Biol 205 and upper level genetics courses.
2. To gain higher level thinking skills that are necessary for scientists.
To the right you can see the “Amended Bloom’s Taxonomy” pyramid. It was
developed as a method of classifying educational goals for student performance
evaluation. You should be well –equipped at remembering facts and content with
good study habits. We are looking for you to apply and analyze. You are UNC
students, we KNOW you can memorize! Move beyond this level of thinking.
How can we achieve this? We will have in-class questions to practice this
immediately and you will have homework problems to practice on your
own. We will also explore classic experiments as a way of thinking
through the logic of experiments and to see where the foundations of this content come from. While
these may be new ways of thinking for you, practice is the most important way to gain these skills. FYI:
UNC’s medical school sees this is an excellent pre-req course for medical school because it teaches
students to think.
3. This course should excite you about basic science and its applications.
A foundation in genetic crosses with model organisms (basic science tool) allows you to understand human genetic diseases. A foundation in
making recombinant DNA constructs (basic science tool) allows you to understand how plants are modified to be herbicide resistant or how
recombinant proteins can be turned into medicines. Genetics and molecular biology provide the “tools” that other disciplines call upon in
biological research. Plant biologists, evolutionary biologists, clinical researchers etc. all use these tools.
COURSE POLICIES
1. Exams:
Three semester exams and one final exam will be given. The final examination is not cumulative. 72% of your grade will be determined by the 4
exams (18% for each exam). All students are expected to take all exams when they are scheduled. Students who are unable to take an exam must
request permission to take a make‐up exam (possibly an oral exam). Students are expected to notify the instructor prior to missing an exam and to
assume responsibility for scheduling a make‐up exam in a timely manner. If, for some reason, you feel an error has been made in determining an
exam score, you may submit the exam for a re‐grade within 3 school days after the exam has been returned to the class. You must submit in
writing your reasons for requesting a re‐grade. Staple the request to your exam, and give it to the appropriate instructor or TA. Legitimate reasons
for a re‐grade request include, for example, incorrect summation of scores and bona fide errors in grading a particular problem; this does not
include student judgments about the amount of partial credit deserved for incorrect answers. Written responses to student requests will be returned
in class.
2. Recitation:
Attendance and participation in one of the recitations sections is required. These recitations are an extension of the class and allow time to go
beyond material in class. They are not “help sessions”, but they will help you learn class material better. Material covered in recitation may be
covered on exams too. For recitation, you will also be given pre-class assignments or in‐class assignments, each worth 5 points, that are designed
to reinforce and deepen your understanding of the material related to the course. Your pre-class recitation assignments must be printed and handed
in at the beginning of recitation. In-class assignments are typically group problems. You must work out this problem in groups and turn in one
answer on behalf of the group during the recitation period. There will be no make-up opportunities for in-class assignments if you do not attend
a recitation in a given week. You may earn up to 5 additional points, during each half of the semester for class participation during the recitation
sessions. If you are unable to attend the recitation for which you are registered one week, you may attend another section with prior permission of
the TAs if there is room in another section. There is a maximum capacity for each section so please do not assume that you can attend another
section if you miss a recitation.
3. Grading:
54% (Three semester exams worth 18% each)
18% (Final examination)
6% (Poll Everywhere)
10% (recitation—includes homework, 4-minute podcast assignment, required attendance/participation and in-class problems)
12% (Mastering Genetics homework)
CLASSROOM PARTICIPATION (POLL EVERYWHERE):
To ensure that you have done the reading assignments BEFORE class and to interact during class, you will have poll questions based on readings,
as well as problems to solve during class. Each student must have either a laptop, smart device, or cell phone for SMS texting. See our Sakai site
for registration details. Registration is free but required so that each answer can be linked to each student. It is the student’s responsibility to bring
the device to each class, there will NOT be an opportunity to regain points if the laptop/phone was forgotten one day. Make-up points for absences
are not possible, but to account for life and its unexpectedness, the average of one day’s worth of points will be excused for all students.
HOMEWORK: Mastering Genetics is where all homework assignments/due dates can be found. Late homeworks will receive a zero. See the
detailed syllabus for all Mastering Genetics assignments that are due. Assignments are due by 2AM on the day they due; they are due BEFORE
class, as a way to prepare for class. (Thus, if they are due at 2AM on a Monday—this is several hours BEFORE class starts.) Many assignments
will have a review component of previous material too. Occasionally, there will not be a homework due before class. See detailed syllabus.
How to register for Mastering Genetics? See Sakai for detailed instructions. Our course ID is: MGENHOGAN60086
SUPPLEMENTAL INSTRUCTION (S.I.): A few open-ended problems will be posted for each week that you can bring to S.I. You are not
required to have done these problems to attend S.I., but these will be discussed during the sessions this week. S.I. is a help session. It is for you!
Please plan to attend if you are struggling with how to approach problems assigned in Mastering or that you practice from the back of the book.
During S.I., instructors will help you learn how to approach and analyze problems—not simply give you the answers.
HONOR CODE: All work done in this class must be carried out within the letter and spirit of the UNC Honor Code. You must sign a pledge on all
graded work certifying that no unauthorized assistance has been given or received. You are expected to maintain the confidentiality of examinations by
divulging no information about any examination to a student who has not yet taken that exam. You are also responsible for consulting with your
professors if you are unclear about the meaning of plagiarism or about whether any particular act on your part constitutes plagiarism. Please talk with
the professor if you have any questions about how the Honor Code pertains to this course.
EXPECTATIONS:
 It is expected that you will spend up to 10 hours reading/working problems associated with each class each week. If you stay on top of your
reading and homework, there will be no need to cram for an exam. This is not a class based on memorization of facts—you must think
critically and solve logic-based problems. There is no cramming for that! Practice, practice, practice. Do problems that are assigned and then
do others that are not assigned! Use the internet or other textbooks in the library to find more problems if you run out from your textbook.
 You are expected to VISIT TUTORS, TAs and S.I. for content questions and weekly review/help with problems. Successful students use these
resources routinely. Successful students don’t cram. They use classmates. Form your own study groups too.
Copyright Information: All materials used in this course including notes, tests and assignments are covered by copyrights which forbid you from sharing class materials with
any group. The University’s Copyright Policy, which can be found at http://www.unc.edu/campus/policies/copyright%20policy%2000008319.pdf indicates
"STUDENT WORKS THAT CONSTITUTE NOTES OF CLASSROOM AND LABORATORY LECTURES AND EXERCISES SHALL NOT BE USED FOR COMMERCIAL
PURPOSES BY THE STUDENT GENERATING SUCH NOTES." What this means is that you are in violation of the law (and the honor code) if you post/text/share any
course materials for use by others.
Lecture Schedule: Part I (Hogan)
Date
Lecture Readings and Mastering Genetics to
be complete BEFORE this lecture
#
Objectives for class (bring blank “Class Outlines” to class each day)
08/21 W
1
- Introduce ourselves
-List the basic components of the course
- Define the terms genes and alleles
-Set up and complete single gene autosomal crosses to determine dominance and genotype.
08/23 F
2
Guided Reading Questions (GRQs)
for 2.1 and 2.2
Mastering Genetics (MG): (complete
before first class)
 Introduction to Mastering
Genetics
 MG Assignment 1
GRQs for 2.3 and p. 79-80 and “The
Growing Menace from Superweeds”
article on Sakai
MG Assignment 2 (complete before
class)
- Demonstrate Mendel’s first and second laws using chromosome models of meiosis.
- Set up two and three gene crosses (independent assortment) and determine the phenotypes and
genotypes of the offspring.
-Predict the genotypes of the parents based on the phenotypes of the offspring of two-gene crosses.
-Explain what genetically modified plants are and how these relate to Mendel’s work.
Upcoming week Recitation: Introduction and group problems
Upcoming week S.I.: Solving problems related to independent assortment with Punnett squares and forked-line method
08/26 M
3
Guided Reading Qs 2.6 and “Couples
Cull Embryos to Halt Heritage of
Cancer” article on Sakai
MG Assignment 3 (complete before
class; includes review Qs for all of
Ch 2)
08/28 W
4
Guided Reading Qs for “SNPs,
Haplotypes and Personalized
Medicine”
MG Assignment SNP1
- Analyze phenotypic data and deduce possible modes of inheritance (e.g. dominant, recessive,
autosomal, X-linked, Y-linked) from family histories.
-Determine the mode of inheritance if given a pedigree and defend your reasoning.
- Draw a pedigree based on information in a story problem.
-Calculate probability that an individual in a pedigree has a particular genotype.
-Argue for the use or non-use of preimplantation genetic diagnosis (PGD).
-Discuss how primary care medicine is being affected by personal genetic testing.
-Define “direct to consumer” (DTC) genetic testing and how it differs from prescribed testing.
-Define a SNP, locate SNPs in DNA sequences when given numerous samples to compare, and make
a link between SNPs and disease associations.
-Explain how haplotypes are inherited and identify individual haplotypes when given parent and
offspring alleles.
-Determine if specific SNPs are associated with disease, as an application of Chi Square analysis.
Guided Reading Qs for Chi Square
No Mastering assignment due before -Calculate Chi Square values and make conclusions based on the calculations.
class. (A graded assignment will be
completed in class.)
*No recitation week of 9/2
Upcoming week for S.I.: Pedigrees and probability and chi square analysis
- Explain the molecular basis at the protein level for allele types with different genetic behaviors such
09/04 W
6
Guided Reading Qs for 4.1
as when wildtype alleles are haplosufficent or haploinsufficient and when mutant alleles represent
MG Assignment 4 (complete before
null, hypomorphic, hypermorphic, and neomorphic mutations.
class)
08/30 F
09/06 F
5
7
Guided Reading Qs for 4.2 and 4.3
MG Assignment 5
-Predict outcomes of crosses involving traits with incompletely dominant, co-dominant, lethal,
multiple, and temperature sensitive alleles.
- Contrast variable expressivity and incomplete penetrance; Calculate penetrance in pedigrees.
- Define and recognize examples of pleiotrophy.
-Interpret phenotypic ratios and assign genotypes when two genes are interacting through epistatic
gene interactions.
Upcoming week Recitation: “Gene Testing Speed Dating” activity – complete and PRINT short assignment before your recitation time!
Upcoming week for S.I.: Gene interactions and more…More with pedigrees, problems related to epistasis, incomplete dominance, and more
09/9 M
8
Guided Reading Qs for 4.4
MG Assignment 6 (includes review
Qs for all of Ch 4)
-Utilize complementation tests for heterogeneous mutations to determine the number of genes
involved.
-Describe what kinds of genetic crosses should be set up to determine if inheritance patterns follow
Mendelian or extensions of Mendelian genetics.
END of material for exam
09/11 W
09/13 F
9
No Guided Reading Qs or MG
assignment due
-Describe how the movements of chromosomes in meiosis link to the inheritance patterns described
by Mendel.
-Describe differences between mitosis and meiosis.
-Calculate the number of chromatids, chromosomes, and centromeres at various stages of the cell
cycle.
-Differentiate between possible and impossible allele combinations in gametes when given parental
genotypes.
Exam 1
Upcoming week for Recitation: Mitosis/Meiosis & review. (Be sure to print and cut out chromosomes; see Sakai assignments)
Upcoming week for S.I.: Problems related to meiosis/mitosis
09/16 M
10
Guided Reading Qs for Chapter 13.1
and MG assignment 7
-Determine if non-disjunction could have occurred maternally or paternally and in which stage of
meiosis when given offspring genotypes.
-Contrast mitotic and meiotic non-disjunction and give examples of both.
09/18 W
11
Guided Reading Qs for 3.6 and “The
Problem With an Almost-Perfect
Genetic World” and “Down
-Compare and contrast different types pre-natal testing for trisomy 21 and discuss the ramifications
for individuals and a society that utilize these tests.
-Determine the gametes that form from monosomic or trisomic organisms.
-Explain the gene dosage dilemma in anueploidy and aberrant euploidy conditions.
- Give two examples of dosage compensation.
- Describe the basic molecular mechanism for dosage compensation in mammals involving Xist.
- Explain how female mammals can be mosaics.
syndrome’s extra chromosome
silenced in lab cells” and MG
Assignment 8
09/20 F
12
Guided Reading Qs for 5.1 and 5.2
and MG Assignment 9
-Compare recombination in genes that independently assort vs. genes that are linked.
-Identify if a dihybrid with linked genes is in the cis or trans configuration based on offspring
genotypes or phenotypes.
-Design an experiment to calculate the map distance between two genes.
-Calculate the genotype/phenotype frequencies when given map distances between two genes.
-Revisit haplotypes as “completely linked genes”
Upcoming week for Recitation: BRCA case study: Complete and print assignment before your recitation time!
Upcoming week for S.I. : Problems related to linked genes
09/23 M
13
Guided Reading Qs for 7.1-7.2 and
“Learn .Genetics” and MG
Assignment 10 (includes review
questions from chapter 5)
-Describe the historical experiments and the methodology used to conclude that DNA was the genetic
material.
-Name the chemical components of DNA.
-Draw the structure of DNA
-Describe how DNA is purified and explain what the reagents do chemically to DNA.
09/25 W
14
Guided Reading Qs for 7.3 and 7.4
and MG Assignment 11
09/27 F
15
Guided Reading Qs for 7.4 (cont.)
and 7.5 and MG Assignment 12
-Describe the differences between conservative, semiconservative and dispersive replication models.
-Explain and draw how the Messelson & Stahl experiments supported only the semiconservative
replication model.
-Draw a replication bubble with bidrectional replication, labeling the leading and lagging strands and
associated proteins.
-Explain why the ends of chromosomes shorten with each round of replication and how telomerase
prevents this.
-Distinguish between cancer cells, germ cells, and somatic cells in their telomerase activity.
- Compare and contrast the polymerase chain reaction in vivo DNA replication.
Upcoming week for Recitation: PCR activity; PODCASTS MUST BE COMPLETED AND SUBMITTED BY 11:55 PM Sunday 9/29
Upcoming week for S.I.: Review of DNA replication; 5’ and 3’ polarity
09/30 M
16
Guided Reading Qs for Epigenetics
and MG Assignment “Epigenetics”
Print your podcast transcript bring it to
class (all group member names on it).
10/02 W
17
Guided Reading Qs for Stem cells
“Diseases in a Dish”, “Your Inner
Healers” and “The iPSC-ESC gap”;
no MG Assignment
-Explain the statement, “epigenetics may fit with a Lamarckian view of evolution” by using
preliminary data presented in the video.
-Explain a variety of ways the epigenome varies within a single individual.
-Compare and contrast DNA methylation and histone acetylation.
-Describe data in humans and mice that demonstrates evidence of epigenetic gene regulation.
-Compare and contrast ESCs, iPSCs, and adult stem cells in potency, sources, safety, and uses.
-Describe processes in which cells can be customized to individuals.
By 11:55 PM on 10/3 each person in
class must listen to and comment on
three other podcasts in their topic
area
10/04 F
18
Guided Reading Qs for Modeling
Genetic Disease in Mice and MG
“Gene targeting”
- Describe how homologous recombination is used to “target” a gene of interest
- Explain why stem cells are needed for gene targeting
- List the steps to go from a “knockout” stem cell line to a colony of mice lacking a gene in
homozygous form
Upcoming week for Recitation: PCR applications
No topics scheduled, S.I. may or may not be cancelled this week. Check Sakai.
No readings or assignments; be prepared Selected class presentations: 4 minute science
10/07 M
19
for class presentations
10/09 W
Exam II
**The schedule for the 2nd half of the semester with Dr. Searles is in a separate document.
TIPS FOR SUCCESS: The textbook is your source of content. Go back to the reading assignment after the lecture and re-read the portions that were
stressed during class. Invest time reviewing what we did in class—what problems did we cover? Did you get Poll questions correct? Recognize that
your attendance at the lectures is the only way to clearly grasp what we stress, because we may also present topics and material that are not necessarily
in the book.
Take notes in class; reinforce what you learned. Don’t feel compelled to take notes on a computer—handwriting and solving problems with a pen is
what most successful students still do. Learning is an active process. If you get confused during a lecture, mark in your notes the point during the
lecture where you became confused. Mark in your notes the point where your understanding returned (i.e. change of topic or new topic). This will
allow you to clearly identify that part of the lecture that you did not understand. Then go back to the assigned reading and seek clarification.
Immediate reinforcement is most effective directly after hearing the lecture. So, instead of leaving the lecture hall and immediately checking your cell
phone for messages, think calmly to yourself as you walk to your next class “What are the main take home messages from today’s lecture?” Cramming
is unlikely to be successful. Trust us.
Ask questions and participate in recitations and supplemental instruction! Raise your hand, be engaged! Ask for clarifications from the lecture
material; come to instructor and TA office hours, study with other students. Discussions help reinforce the material we learn.
Do the homework on your own. A portion of the exam questions will be similar to the homework questions. Thus homework is like a practice exam!
So make sure you understand the answers. Do extra problems. More practice thinking in this way will make a difference. Use the end-of-chapter
questions and the additional S.I. problems as more practice besides assigned Mastering Genetics problems.