Faculty of Science Course Syllabus Department of Biology BIOL Genetics and Molecular Biology WINTER 2017

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1 Faculty of Science Course Syllabus Department of Biology BIOL Genetics and Molecular Biology WINTER 2017 Instructor(s): Christophe Herbinger (Professor - Unit I) cherbing@dal.ca LSC Sophia Stone (Professor Unit II) S.Stone@Dal.Ca LSC Jonathan Wright (Professor- Unit III) jmwright@dal.ca LSC Debra Grantham (Instructor) grantham@dal.ca LSC Lectures: MWF 12:35 1:25 pm McCain Auditorium 1 (Scotiabank) Laboratories: 5 lab sessions, 2 hours per lab LSC 6009 and 6012 Tutorials: 10 tutorials, 50 minutes per tutorial Various; check location via Dal Online Course Description The power and prominence of modern genetics have grown from a blend of classical and molecular approaches; both approaches are emphasized. Topics include: Mendelian, population and quantitative genetics; chromosome structure and variation; structure and function of nucleic acids; DNA replication, transcription and translation; gene expression; gene mutations; and genetic engineering. Course Prerequisites -Courses: C+ or better in BIOL 1010/1020/1030/1031or equivalent; 1 st year chemistry recommended. -Knowledge/skills: Before enrolling in this course, students should be able to: Recall the fundamental characteristics of eukaryotic, prokaryotic, diploid and haploid organisms Recall the mitosis and meiosis processes of the cell cycle. Understand the basic concept of heredity, and that genetic information is encoded in DNA. Define genotype, phenotype, chromosome, gene, allele, recessive and dominant. Recall the basic differences between DNA and RNA and how information flows from DNA to RNA to protein. Identify the minimal regulatory elements and how they function in the control of gene expression of inducible and repressible operons in prokaryotes.

2 Define the principal classes of physical and chemical mutagens, the changes mutation introduces to the amino acid sequence of a polypeptide, and the resulting effect on phenotype. Recall the basic methodology of gene cloning and DNA technology/biotechnology, its applications, and the ethical and societal implications. Express the concepts of evolution as changes in allele frequencies and the Hardy-Weinberg principle. Use Hardy-Weinberg equation to calculate expected genotype and allele frequencies in simple cases. Be familiar with using library resources to find scientific literature. Describe the components of a formal lab report. Understand how to properly cite sources in scientific writing. Explain the importance of academic integrity. Course Objectives/Learning Outcomes On completion of this course, students shall be able to: Understand the importance of genetics to society and the study of biology, and be able to effectively explain this to non-specialists. Understand and apply the Mendelian principles of heredity for both autosomal and sex-linked inheritance. Interpret rules of heredity in terms of the eukaryotic cell cycle. Understand the relationship between meiotic crossing over and the phenomenon of genetic linkage. Understand how complex genetic systems lead to modifications of the basic principles of Mendelian inheritance. Apply knowledge of genetics to the analysis of human pedigrees. Comprehend the basic principles of population and quantitative genetics, and give examples of their application to real biological systems. Describe and diagram the structure of DNA. Explain and illustrate how DNA replication and recombination occur. Understand and describe how DNA is transcribed to RNA and how RNA is translated into proteins. Describe the structure of RNA and understand how post-transcriptional processing modifies it prior to translation. Interpret genetic and protein variability using detailed knowledge of the genetic code and the processes of transcription and translation. Understand chromosome structure, the types of rearrangements that occur, and the consequences of variations in chromosomal number. Describe in detail restriction endonucleases, their recognition sequences in DNA, and their application in the Southern blot and hybridization technique for diagnosis of human genetic disease. Explain and illustrate the fundamental biochemistry required in the application of modern techniques of molecular biology: (i) screen complementary (cdna) and genomic libraries to identify and clone specific DNA (gene) sequences; (ii) DNA sequencing by the dideoxy chain termination method; and (iii) the amplification of minute amounts of DNA by the polymerase chain reaction-what biochemical features do these techniques have in common. Compare and contrast the fundamental mechanisms that regulate gene expression in prokaryotic and eukaryotic cells.

3 Define in detail the classes of physical and chemical mutagens, how a chemical mutagen can be identified by the Ames test, and the effect of different types of mutation on phenotype. Apply the theories and topics covered in lecture and readings by solving problems in lecture, tutorials and labs. Develop a basic understanding and appreciation of techniques used in genetic and molecular biology laboratories. Generate and interpret data collected from experiments in the laboratory and communicate results by a variety of written forms. Course Materials - Required: o BIOL 2030 Study Guide/Lab Manual, 2017 Winter term o Pierce, Benjamin A. Genetics, A Conceptual Approach (5 th ed.) NY: W.H. Freeman (Hardcover). + Solutions Manual $~189 + tax o Or Pierce, Benjamin A. Genetics, A Conceptual Approach (5 th ed.) NY: W.H. Freeman (Looseleaf). + Solutions Manual $~151 + tax o Used copies of 4 th or 5 th editions o Reserve copies of 4 th and 5 th editions at Killam Library o Older versions (2 nd or 3 rd editions) of Pierce may be used; page numbers of readings and assigned questions will be different: you will have to compare to the copies on reserve in library and photocopy them yourself - Recommended: o Knisely, Karin A Student Handbook for Writing in Biology. 4 th ed. VA: W.H. Freeman - Course website: Connect through my.dal.ca (Brightspace) Course Assessment Component Weight (% of final grade) Date Tutorial quizzes (best 9 out of 10) 9 Various Midterm I 24 Thurs. Feb. 9, 19:00-21:00 Midterm II 24 Thurs. Mar. 16, 19:00-21:00 Final exam 24 (Scheduled by Registrar) Laboratory Assignments 19 Various Other course requirements None Conversion of numerical grades to Final Letter Grades follows the Dalhousie Common Grade Scale A+ (90-100) B+ (77-79) C+ (65-69) D (50-54) A (85-89) B (73-76) C (60-64) F (<50) A- (80-84) B- (70-72) C- (55-59)

4 Course Policies LABORATORY FORMAT: The green page of the Study Guide/Lab Manual contain more details of the lab content and weekly schedule. Note that labs are held every second week so you should go to DAL ONLINE to check your registration section, CRN and lab location. Labs are due at the beginning of your registered lab period. Online pre-lab quizzes for labs 2, 3 and 4 must be completed before lab begins. Late labs will receive a 10% deduction for each day late. Note: You must attend the lab for which you are registered. TUTORIAL FORMAT: The yellow pages of the Study Guide/Lab Manual contain more details on the content and weekly schedule. Please go to DAL ONLINE to check your registration section, CRN and location. Room locations may be changed by the registrar so check at Note: You must attend the tutorial section for which you are registered. MIDTERM/EXAM FORMAT: The two midterms and final exam have equal weight. There will be an exam at the end of each lecturer s section. These tests are designed to test you on the material presented in lectures, the text and tutorials. The test papers consist entirely of questions requiring multiple choice answers. More details on format and content will be given in lecture before each exam. Both midterms are two hours in length and are held in the evening. The exam on the third lecturer s material will also be two hours in length and will be held during the final examination period scheduled by the registrar s office. The specific date and time for the BIOL 2030 final exam will be announced early in October or February and posted at We do not give early midterms or exams so check the schedule before making travel arrangements. Alternate writing times for midterms/exam will ONLY be given to students who have another Dalhousie exam or class at the same time or who are ill. Students who have a timing conflict with a midterm or exam should contact the Instructor at least two weeks prior to the exam date to arrange another time. Students who are ill should see the ILL policy below. EXAM VIEWING: You will not receive your midterm exams back. the professor for that unit to arrange to view your exam. Contact the exam professor if you have any questions about his/her exam. REGULATIONS REGARDING MISSED MIDTERMS/EXAMINATIONS/ASSIGNMENTS: Requests for an alternative midterm/exam time due to extenuating circumstances: A student requesting an alternative time for a midterm or final examination will be granted that request only in exceptional circumstances. Such circumstances include having another Dalhousie class or exam scheduled at the same time or other mitigating circumstances outside the control of the student. Elective arrangements (such as travel plans) are not considered acceptable grounds for granting an alternative examination time. Students should contact the Instructor at least two weeks prior to the exam date to arrange another time.

5 Special arrangements for missed exams, midterms, tutorials, labs and lab reports due to illness or other exceptional circumstances: Alternate arrangements will be considered provided that: - A student who misses class work (assignment, lab, tutorial, midterm or exam) because of illness: 1. notifies the Instructor on the day in question, 2. notifies his/her physician at the time of illness (or within a few days) and obtains a valid* medical excuse, 3. provides a medical certificate (signed by a physician) to the Instructor within one week. - A student who, for medical reasons (e.g. scheduled day-surgery, etc), anticipates missing class work: 1. notifies the Instructor at least one week in advance, 2. provides the Instructor with appropriate documentation. - A student who is absent due to other exceptional circumstances (e.g. death in immediate family, etc): 1. notifies the Instructor on or before the day in question, 2. is able to produce appropriate documentation upon request (e.g. death certificate, etc). N.B. - A student who fails to comply with any or all of these rules may not be able to make up at for lost work. The decision on when and if special arrangements can be made will be at the discretion of the Instructor. * This certificate should indicate the dates and duration of the illness, when possible should describe the impact it had on the student s ability to fulfill academic requirements, and should include any other information the physician considers relevant and appropriate. (Dalhousie UG Calendar) There will be times during your term when you will have deadlines in several different courses at the same time. PLAN AHEAD. WORK CONSISTENTLY. Your time at University should, among other things, teach you to develop effective time management skills and study habits. On the other hand, unforeseen events such as personal/family crises or illness CAN OCCUR during the term. These occurrences are unavoidable and the teaching staff of 2030 will be most understanding and willing to make alternate arrangements. Please speak to one of the teaching staff.

6 Course Content BIOL TENTATIVE Lecture Outline Unit I (WINTER 2017) (Changes to these readings may occur and will be announced in lecture.) WK LEC TUT DATE PROF TOPIC Jan. 9 Herbinger1 Introduction to Genetics; Pierce (5 th edition) Chapter 1 (5, 11-12) Chapter 2 (17-21) 1 2 Jan. 11 Herbinger2 Cell Reproduction; Mitosis & Meiosis Chapter 2 (20-25) 1 3 Jan. 13 Herbinger3 Basic Principles of Heredity Jan. 16 Herbinger4 5 Jan. 18 Herbinger5 2 6 Jan. 20 Herbinger Extensions and Modifications of Basic Principles; Complementation Probability and Chi-square revisited Strategies to deal with ratios in crosses Sex determination and Sex-linked Characteristics Chapter 3 (46-66) Study Guide: Appendix F&G Chapter 5 ( ) Chapter 3 (54-64) Study Guide: Appendix H Chapter 5 (117) Chapter 4 (78-94) Jan. 23 Herbinger7 Pedigree Analysis & Applications Chapter 6 ( ) 3 8 Jan. 25 Herbinger8 Linkage and Mapping in Eukaryotes 3 9 Jan. 27 Herbinger9 Linkage & Mapping in Eukaryotes (cont d) 4 10 Jan. 30 Herbinger10 Intro to Quantitative Genetics Feb. 1 Herbinger11 Quantitative Genetics Chapter 7 ( , ) Chapter 7 ( , ) Chapter 24 ( , ) [self review ] Chapter 24 ( ) [self review ] 4 Feb. 3 HOLIDAY- Munro Day University closed 5 12 Feb. 6 Herbinger12 Population Genetics Chapter 25 ( ) Feb. 9 Herbinger Midterm 1 ( ) POTTER AUDITORIUM, ROWE 1028 (A THURSDAY night)

7 Unit II (WINTER 2017) WK LEC TUT DATE PROF TOPIC 5 13 Feb. 8 Stone1 The Molecular Basis of Heredity and DNA Structure Feb. 9 Herbinger Midterm 1 ( ) (A THURSDAY night) POTTER AUDITORIUM, ROWE Feb. 10 Stone2 DNA Replication and Recombination Feb. 13 Stone3 DNA Replication and Recombination cont. Pierce (5 th edition) Chapter 10 ( ) Chapter 12 ( ) Review Chapter 2(23-34) Chapter 12 ( ) Review Chapter 2(23-34) 6 16 Feb. 15 Stone4 Transcription. Chapter 13 ( ) 6 17 Feb. 17 Stone5 RNA Interference and Gene Editing Chapter 14 ( ) Chapter 17 ( ) FEB WINTER STUDY WEEK NO CLASSES, Feb 20 University closed, open Feb. 27 Stone6 Post-transcriptional Processing and Editing Part 1 Chapter 14 ( ) Chapter 17 ( ) 7 19 Mar. 1 Stone7 Post-transcriptional Processing and Editing Part Mar. 3 Stone8 The Genetic Code Chapter 14 ( ) Chapter 17 ( ) Chapter 15 ( ) Chapter 18 ( ) 8 21 Mar. 6 Stone9 Translation Chapter 15 ( ) Mar. 8 Stone10 Chromosomal Rearrangements Chapter 8 ( ) 8 23 Mar. 10 Stone11 Variations in Chromosomal Number Chapter 8 ( ) 9 24 Mar. 13 Stone12 REVIEW 9 Mar. 16 Stone Midterm 2 ( ) POTTER AUDITORIUM, ROWE 1028 (A THURSDAY night)

8 Unit III (WINTER 2017) WK LEC TUT 9 24 Mar. 15 Wright1 9 Mar. 16 Stone 9 25 Mar. 17 Wright DATE PROF TOPIC Mar. 20 Wright 3 Gel-electrophoresis and restriction endonuclease mapping. Midterm 2 ( ) (A THURSDAY night) POTTER AUDITORIUM, ROWE 1028 Southern blot & hybridization. Applications: diagnosis of genetic disease & RFLP. Recombinant DNA technology. Pierce (5 th edition) Ch. 19 ( ) Ch. 11 ( ) Ch. 11 ( ) Ch. 19 ( ) Ch. 19 ( ) Ch. 19 ( ) Ch. 19 ( ) Mar. 22 Wright 4 Cloning genes and their transcripts. Ch. 19 ( ) Mar. 24 Wright 5 DNA sequencing and the polymerase chain reaction Mar. 27 Wright Mar. 29 Wright Mar. 31 Wright Apr. 3 Wright 9 Prokaryotic gene regulation the lac operon Four genetic systems for the control of prokaryotic operons. Catabolite repression and control of transcriptional termination. Eukaryotic gene regulation: sites of regulation from DNA to protein Apr. 5 Wright 10 Chromatin conformation & eukaryotic gene regulation Apr. 7 Wright 11 Mutation & its effect on phenotype. Ch. 19 ( ) Ch. 19 ( ) Ch. 13 ( ) Ch. 16 ( ) Ch. 16 ( ) Ch. 16 ( ) Ch. 16 ( ) Ch. 13 ( ) Ch. 13 ( ) Ch. 16 ( ) Ch. 14 ( ) Ch. 11 ( ) Ch. 17 ( ) Ch. 21 ( ) Ch. 18 ( ) Ch. 8 ( ) Apr. 10 Wright 12 Mutagens and the Ames test. Ch. 18 ( ) TBA Wright REVIEW FINAL EXAM SCHEDULED BY REGISTRAR DURING EXAM PERIOD

9 ACCOMMODATION POLICY FOR STUDENTS Students may request accommodation as a result of barriers related to disability, religious obligation, or any characteristic protected under Canadian Human Rights legislation. The full text of Dalhousie s Student Accommodation Policy can be accessed here: Students who require accommodation for classroom participation or the writing of tests and exams should make their request to the Advising and Access Services Centre (AASC) prior to or at the outset of the regular academic year. More information and the Request for Accommodation form are available at ACADEMIC INTEGRITY Academic integrity, with its embodied values, is seen as a foundation of Dalhousie University. It is the responsibility of all students to be familiar with behaviours and practices associated with academic integrity. Instructors are required to forward any suspected cases of plagiarism or other forms of academic cheating to the Academic Integrity Officer for their Faculty. The Academic Integrity website ( provides students and faculty with information on plagiarism and other forms of academic dishonesty, and has resources to help students succeed honestly. The full text of Dalhousie s Policy on Intellectual Honesty and Faculty Discipline Procedures is available here: All students registered in first year science courses are required to complete an Academic Integrity module available through OWL. STUDENT CODE OF CONDUCT Dalhousie University has a student code of conduct, and it is expected that students will adhere to the code during their participation in lectures and other activities associated with this course. In general: The University treats students as adults free to organize their own personal lives, behaviour and associations subject only to the law, and to University regulations that are necessary to protect the integrity and proper functioning of the academic and non academic programs and activities of the University or its faculties, schools or departments; the peaceful and safe enjoyment of University facilities by other members of the University and the public; the freedom of members of the University to participate reasonably in the programs of the University and in activities on the University's premises; the property of the University or its members. The full text of the code can be found here:

10 SERVICES AVAILABLE TO STUDENTS The following campus services are available to help students develop skills in library research, scientific writing, and effective study habits. The services are available to all Dalhousie students and, unless noted otherwise, are free. Service Support Provided Location Contact General Academic Advising In person: Killam Library Rm G28 Dalhousie Libraries Studying for Success (SFS) Writing Centre Help with - understanding degree requirements and academic regulations - choosing your major - achieving your educational or career goals - dealing with academic or other difficulties Help to find books and articles for assignments Help with citing sources in the text of your paper and preparation of bibliography Help to develop essential study skills through small group workshops or oneon-one coaching sessions Match to a tutor for help in course-specific content (for a reasonable fee) Meet with coach/tutor to discuss writing assignments (e.g., lab report, research paper, thesis, poster) - Learn to integrate source material into your own work appropriately - Learn about disciplinary writing from a peer or staff member in your field Killam Library Ground floor Rm G28 Bissett Centre for Academic Success Killam Library Ground floor Librarian offices Killam Library 3 rd floor Coordinator Rm 3104 Study Coaches Rm 3103 Killam Library Ground floor Learning Commons & Rm G25 By appointment: - advising@dal.ca - Phone: (902) Book online through MyDal In person: Service Point (Ground floor) By appointment: Identify your subject librarian (URL below) and contact by or phone to arrange a time: To make an appointment: - Visit main office (Killam Library main floor, Rm G28) - Call (902) Coordinator at: sfs@dal.ca or - Simply drop in to see us during posted office hours All information can be found on our website: To make an appointment: - Visit the Centre (Rm G25) and book an appointment - Call (902) writingcentre@dal.ca - Book online through MyDal We are open six days a week See our website: writingcentre.dal.ca