<p> Biology 202- Molecular Biology and Genetics Spring (Section 007) Dr. Kelly Hogan and Dr. Joe Kieber</p><p>Lectures: GSB 200 (Tues/Th 9:30-10:45 AM)</p><p>Recitations: (you must be registered for one of the 8 sections: 701-708); attendance required. Check Connect Carolina for room location.</p><p>Instructors: Dr. Kelly Hogan Email: [email protected] Office location: Wilson Hall 104B Office Hours: Tuesdays 1:30-3:00 (see “sign up” on Sakai) or informally after class on Thursdays. If you can’t make these hours, I might be able to schedule another time or you might want to see one of our four TAs during their office hours. Content Qs? S.I. and Peer tutoring are helpful!</p><p>Dr. Joe Kieber Email: [email protected] Office location: 4163 GSB Office hours: TBA.</p><p>Graduate TAs: Claire Trincot ([email protected]) (leading recitations) Amelia Clayschulte ([email protected]) Alisha Coffey ([email protected]) Katie Bolling ([email protected])</p><p>Undergraduate S.I. instructors: Blake Hauser ([email protected]) and Noopur Doshi ([email protected]) (Check Sakai under “syllabus” for times/rooms for S.I. We’ll post these after the first week of classes.)</p><p>Undergraduate Tutors: Tutors who were top students in our previous Biol 202 class are available to help you with concepts and problems. See: http://bio.unc.edu/undergraduate/course-info/tutoring/ for this semester’s information. More info will be posted on Sakai too. </p><p>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 and receive email announcements. </p><p>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 smart phone (wi-fi enabled device) to answer in-class questions. You must connect to UNC Secure. http://help.unc.edu/help/connecting-to-the-unc-network-getting-started/  4 X 6 notecards (any style)</p><p>COURSE GOALS:</p><p>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 well- designed 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.</p><p>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 experiments as a way of practicing how scientists think. 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.</p><p>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</p><p>1. Exams: Four semester exams and one final exam will be given. The final examination is cumulative. 72% of your grade will be determined by the 5 exams. All students are expected to take all exams when they are scheduled. Students who are unable to take an exam must request permission to use their final exam to replace one of their missed exams. Students are expected to notify the instructor prior to missing an exam. 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 some class material deeper. Material covered in recitation may be covered on exams and will be covered on recitation quizzes. 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. </p><p>3. Grading: 56% (Four semester exams worth 14% each) 16% (Cumulative Final examination) 6% (Poll Everywhere—participation is required for each question; some questions are graded for correctness too) 10% (recitation—includes recitation pre-assignments, quizzes, required attendance/participation and in-class problems, participation with surveys, etc.) 12% (Mastering Genetics: homework and quizzes)</p><p>HOMEWORK: Mastering Genetics is where all homework assignments/due dates can be found. Late homeworks will receive a zero. This is a tool for you to gauge what you are learning from the reading and what you do and don’t know. Dishonesty on this work only hurts you later on exams. It’s okay if you find these questions challenging at times, the idea is to figure out what you need more practice with. 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: MGENHOGAN52780CLASSROOM 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 or smart device. *** If you use your phone, you must connect to wi-fi (UNC Secure) or your answers will NOT be recorded consistently. The classroom gets spotty cellular reception and even though it works sometimes, your participation grade will likely suffer from technology issues. See our Sakai site for registration details. Registration is required and free 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. Your grade for this component will be participation and correctness of your answers. All questions can be found at pollev.com/khogan during class time. Make sure you are logged in every day when class starts (the system may occasionally sign you out on your device or you may bring a different device one day.) **Poll Everywhere is to be done with students who are in the classroom participating. If you are found polling in answers and you are not in the classroom, you may receive a zero for your poll everywhere grade for the semester. </p><p>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 they will be available for discussion during the appropriate week. Please note that unlike recitation, S.I. is a help session. It is for you! Please plan to attend if you are struggling with how to approach problems or simply want a review. 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 study groups too. </p><p>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): Subject to change if classes cancelled due to snow/ice etc.</p><p>Below is a schematic giving you an overview of the broad topics we will cover in the first half of the course. The detailed scheduled and objectives follow on the next page. Date Lectur Readings and Mastering Genetics to Objectives for class (print “Class Outlines” and bring blank to class each day) e # be complete BEFORE this lecture Please bring 4 x 6 notecards to each class too.</p><p>1/08 Th 1 Guided Reading Questions (GRQs) - Introduce ourselves for 2.1 and 2.2 -List the basic components of the course Mastering Genetics (MG): (complete - Define the terms genes and alleles before first class) -Set up and complete single gene autosomal crosses to determine dominance and genotype.  MG Assignment 1 Recitation: (Th and Fri) Introductions and pre-test </p><p>01/13 Tu 2 GRQs for 2.3 and p. 79-80 and “The - Demonstrate Mendel’s first and second laws using chromosome models of meiosis. Growing Menace from Superweeds” - Set up two and three gene crosses (independent assortment) and determine the phenotypes and article on Sakai genotypes of the offspring. -Predict the genotypes of the parents based on the phenotypes of the offspring of two-gene crosses.  MG Assignment 2 (complete -Explain what genetically modified plants are and how these relate to Mendel’s work. before class)</p><p>01/15 Th 3 Guided Reading Qs 2.6, 3.5 and - Analyze phenotypic data and deduce possible modes of inheritance (e.g. dominant, recessive, “Couples Cull Embryos to Halt autosomal, X-linked, Y-linked) from family histories. Heritage of Cancer” article on Sakai -Determine the mode of inheritance if given a pedigree and defend your reasoning. - Draw a pedigree based on information in a story problem.  MG Assignment 3 (complete -Calculate probability that an individual in a pedigree has a particular genotype. before class; includes review -Argue for the use or non-use of preimplantation genetic diagnosis (PGD). Qs for all of Ch 2) Recitation: (Th and Fri): Introduction to scientific thinking/scientific papers: Superweed resistance to glyphosate part I</p><p>01/20 Tu 4 Guided Reading Qs for “SNPs, -Discuss how primary care medicine is being affected by personal genetic testing. Haplotypes and Personalized -Define “direct to consumer” (DTC) genetic testing and how it differs from prescribed testing. Medicine” and “Chi Square” -Define a SNP, locate SNPs in DNA sequences when given numerous samples to compare, and make MG Assignments: a link between SNPs and disease associations. -Explain how haplotypes are inherited and identify individual haplotypes when given parent and  SNPs offspring alleles.  Chi Square 01/22 Th 5 Guided Reading Qs for “Whole -Explain what exome sequencing is. Exome Sequencing” -Compare and contrast exome sequencing to whole genome and SNP sequencing, including their limitations  MG Assignment “Whole -Justify when whole exome sequencing is warranted Exome Sequencing” Recitation: (Th and Fri) Chi Square SNPs activity 01/27 Tu 6 Guided Reading Qs for 4.1 and 4.2 - Explain the molecular basis at the protein level for allele types with different genetic  MG Assignment 4 behaviors such as when wildtype alleles (complete before class) are haplosufficent or haploinsufficient and when mutant alleles represent null, hypomorphic, hypermorphic, and neomorphic mutations. -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. 01/29 Th 7 Guided Reading Qs for 4.3 and 4.4 -Interpret phenotypic ratios and assign MG Assignments: genotypes when two genes are interacting through epistatic gene interactions.  MG Assignment 5 -Utilize complementation tests for heterogeneous mutations to determine the number of genes involved.  MG Assignment 6 -Describe what kinds of genetic crosses (includes review Qs for all should be set up to determine if of Ch 4) inheritance patterns follow Mendelian or extensions of Mendelian genetics. Recitation (Th and Fri) : Reading a scientific paper 02/03 Exam 1 (tested on all material including class on 1/29)</p><p>02/05 Th 8 Guided Reading Qs for -Describe how the movements of Mitosis/Meiosis (see Sakai for chromosomes in meiosis link to the reading) and Chapter 13.1 inheritance patterns described by Mendel. -Describe differences between mitosis and  MG assignment 7 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. -Determine if non-disjunction could have occurred maternally or paternally and in which stage of meiosis when given offspring genotypes. Recitation: (Th and Fri) Mitosis/Meiosis & review. (Be sure to print and cut out chromosomes; see Sakai assignments) 02/10 Tu 9 Guided Reading Qs for 3.6 and -Contrast mitotic and meiotic non- “The Problem With an Almost- disjunction and give examples of both. Perfect Genetic World” and -Compare and contrast different types pre- “Down syndrome’s extra natal testing for trisomy 21 and discuss the ramifications for individuals and a society chromosome silenced in lab that utilize these tests. cells” -Determine the gametes that form from  MG Assignment 8 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. 02/12 Th 10 Guided Reading Qs for 5.1 and 5.2 -Compare recombination in genes that independently assort vs. genes that are  MG Assignment 9 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” Recitation: (Th and Fri) Reading a scientific paper: Trisomy</p><p>02/17 Tu 11 Guided Reading Qs for 7.1-7.3 -Describe the historical experiments and and “Learn.Genetics” the methodology used to conclude that DNA was the genetic material.  MG Assignment 10 -Name the chemical components of DNA. -Draw the structure of DNA (includes review questions -Describe how DNA is purified and from chapter 5) explain what the reagents do chemically to DNA. -Describe the differences between conservative, semiconservative and dispersive replication models. -Explain and draw how the Messelson & Stahl experiments supported only the semiconservative replication model. 02/19 Th 12 Guided Reading Qs for 7.4 and 7.5 -Draw a replication bubble with bidrectional replication, labeling the MG Assignments: leading and lagging strands and associated proteins.  MG Assignment 11 -Explain why the ends of chromosomes shorten with each round of replication and how telomerase prevents this.  MG Assignment 12 -Distinguish between cancer cells, germ cells, and somatic cells in their telomerase activity. - Compare and contrast the polymerase chain reaction in vivo DNA replication. Recitation: (Th and Fri) PCR activity and PCR applications</p><p>02/24 Tu 13 Guided Reading Qs for -Explain the statement, “epigenetics may Epigenetics fit with a Lamarckian view of evolution” by using preliminary data presented in the  MG Assignment video. -Explain a variety of ways the epigenome “Epigenetics” 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. 02/26 Th EXAM 2 All material since last exam and including material from 2/24 Recitation: (Th and Fri) Recitation Quiz **The schedule for the 2nd half of the semester with Dr. Kieber is in a separate document. We will follow UNC guidelines for snow/ice. If classes are cancelled, we will be. If UNC is open and classes are on, we will have class. 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 Everywhere questions correct? (Check your Poll Everywhere account regularly to review and check that you technology is working.) 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 and your peers from previous semesters! 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.</p>