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Home , Genetics, Molecular genetics

303 Course Syllabus Molecular and Spring 2017

Instructor: Dr. Joshua Corrette-Bennett Office Phone: 724-946-7208 Office: 370 Hoyt Center e-mail: [email protected]

OFFICE HOURS: M 9:20-10:20am, M 1-2pm, T 11am-12pm, F 1-2pm If I am not in my office during scheduled times I am probably somewhere nearby (another faculty member’s office, a research lab, etc.) and will return momentarily. Please be patient and wait by my office door for 5-10 minutes until I return. If I do not return in a timely manner, please leave a note on my door so I can contact you asap. If I am absent from my office during my office hours, I will leave a note on my door indicating where I have gone. You can always reach me by e-mail (preferable) or leave a message on my answering machine; I do not use text messaging. If it is a medical or family emergency, please leave a message on my office phone and send me an e-mail.

REQUIRED: Text: Robert J. Brooker. Genetics: Analysis & Principles. 5th Edition. McGraw-Hill. New York, NY. 2009 (paper, loose-leaf)

Laboratory Manual - accessed on the R-drive

9 3/4 in X 7 1/2 inch, composition-style, quad-lined laboratory notebook. (This is the only acceptable lab notebook. Use of any other lab notebook will result in subtraction of 20 pts. from the notebook grade.)

COURSE DESCRIPTION: This course serves as a broad introduction to the and of nucleic acids, basic processes that regulate expression of genetic information, biological processes that direct inheritance of genetic information, and the outcome of those processes – inherited traits. Prokaryotic and eukaryotic will serve as model systems for studying topics such as structure, function, replication, damage, repair, and control of expression. Additional topics include Mendelian genetics, and , and if time permits genetics, developmental genetics, and molecular . Weekly laboratory exercises are an essential component of this class and will be used to explore various molecular and biochemical techniques for isolating, replicating and analyzing nucleic acids and studying modes of inheritance. Lab will also be used to enhance skills such as scientific information literacy, scientific writing, and presentation. Prerequisite: C- or better in BIO 201.

COURSE OBJECTIVES: This course is being taught as an intermediate level biology course and is geared towards sophomores, juniors, and seniors majoring in biology, , , and . Comprehension and recall of concepts covered in BIO 201 are essential for this course and will be assessed throughout the semester. Students who successfully complete this course:

1. will demonstrate initiative, self-assessment, and a mind-set for intellectual achievement;

2. will demonstrate comprehension of the structure, organization and function of nucleic acids and ;

3. will demonstrate comprehension of and control of gene expression in prokaryotes and ;

4. will demonstrate knowledge of basic molecular and biochemical skills and techniques used for the study of nucleic acids, proteins, and cells;

5. will demonstrate the ability to utilize qualitative and quantitative reasoning skills required for scientific inquiry, laboratory investigation, and problem solving;

6. will demonstrate proficiency with basic laboratory skills, scientific observation and notation (lab notebooks), scientific writing (formal lab reports), information literacy, and presentation of scientific information.

STRUCTURE: Each week there will be three 1 hour lecture/discussion/group work sections (MWF 10:30am-11:30am; Hoyt 292) and one 3 hour lab/research section (W 2:00 pm-5:00 pm; HSC 343). Unauthorized electronic devices are not allowed to be on during class or lab ( phones, MP3 devices, etc.). If a cell phone rings or buzzes during class or lab, or a student answers their cell phone or engages in text-messaging during class or lab, they disrupt the learning environment. Points will be deducted from their total course grade for any of these distractions (1 point for the first occurrence; 2 points for the second; 4 points for the third; etc.) If I hear a cell phone vibrate and no one accepts responsibility, then I will deduct 0.5 pts from everyone's grade. I will make an exception to these rules if a student tells me that she/he is waiting for a call prior to that class and it pertains to a personal or medical emergency. Students are more than welcome to bring a laptop to lecture, but it should only be used for accessing the Powerpoint presentations and taking notes. If a student has software or files opened other than what is necessary for class, I will tell the student to close them immediately. A second warning will result in a deduction of Discretionary points. products are not permitted in any building.

ACCESSIBILITY STATEMENT: Westminster College actively strives for the full inclusion of all our students. Students with disabilities who require access solutions for environmental or curricular barriers should contact Faith Craig, Director of Disability Support Services, located in 209 Thompson-Clark Hall. phone: 724-946-7192 e-mail: [email protected]" If you have any of learning, or physical disability (documented or un-documented) that might affect your performance, please stop by my office within the first week of classes.

ATTENDENCE POLICY: I consider you all to be adults so there is no numerical penalty for missing class lectures, but I have noticed a strong correlation between missed classes and grades earned on exams. I will be taking note of absences. Students are responsible for any material covered if absent from class, regardless of the reason. Notes must be obtained from classmates, not the instructor. Missed handouts or assignments can be obtained from me during office hours, not at the beginning or end of class. I will be more than happy to help clarify material missed during any absence, but it must be during my office hours or another time outside of class that is convenient for both of us and you must come prepared (having read and thought about the material before our meeting). We will be covering significant amounts of material during the class periods so it is important that you miss as few classes as possible. While I do not penalize for missing lectures, unexcused absences will factor into the amount of discretionary points a student can earn. Attendance for exams and labs is required. You must identify any conflicts between these and college sponsored activities or events and report them to me at least 2 days prior to the absence so that alternative plans can be arranged. The only excused absences for exams or labs are the ones stated in the Westminster catalog. Any exams that conflict with other college sponsored activities must be taken prior to the scheduled exam or lab date. Do to the complex preparation and methods for many of the labs, making up a lab at a later time or date is not always possible. If you miss a lab, your lab group members will be left to fill in for you and will be responsible for getting you “up to speed” on the concepts, procedures and goals of the lab. Any medical or personal conflicts with exams must be brought to my attention immediately and passed onto the Dean of Academic Affairs. Absences due to illness must be reported to the center and require a formal written excuse from the Health Center or your doctor.

EXAMS: There will be four exams evenly spaced throughout the semester. The fourth exam will take place during finals week; a portion of the fourth exam will be comprehensive. Exams will cover material presented in lectures and labs. You will also be quizzed and tested on relevant material covered in BIO 201 and any assigned readings, but not necessarily covered in lecture. I will prepare a study guide for the first exam. You will be required to hand in a study guide prior to the second exam. The study guide for the second exam will be graded and count towards 5% of the exam grade. Study guides handed in for a grade cannot be more than eight pages long. Study guides will not be required or provided for the final two exams.

LABS, LAB NOTEBOOKS & FORMAL LAB REPORTS: We will begin the semester with a re- introduction to basic tools and techniques used for molecular biology. Familiarity with the metric system will be assumed and incorporated into each lab. Labs will reinforce concepts discussed in lecture, although they may not always coincide with that week's lecture material. Due to the of scientific inquiry, many of the labs will require completing steps outside of the designated lab period. You will need to adjust your schedules as needed and according to group member availability. Preparation for labs and maintenance of lab notebooks must follow procedures described in the Lab Notebook Guidelines (on the R-drive). The Introduction section of each lab might contain a few questions that require further research and writing down the answers in your lab notebooks prior to entering the lab. A flow chart/concept map of procedures (methods) must also be prepared prior to the start of each new lab and checked by me prior to the start of the lab. This flowchart should be based on procedures located in the methods section(s) of each lab. If you do not have a flow chart when you come into the lab, you cannot earn points for that section (although you are welcome to write it down after the lab to help organize your thoughts). During the beginning of the lab period I will ask 1-3 questions based on concepts presented in the introduction of the lab exercise and material from lecture. Students will be given a few minutes to write their answer(s) to the question(s). If you miss the beginning of the lab period for reasons other then a college- sponsored activity or medical emergency, you will have to wait in the hall until this part of the lab is completed and you will not receive credit for this part of the lab. All labs will be performed and completed as group work. Individual group members are responsible for any missed instruction or group work. Lab notebooks will be collected for grading at various times in the semester, so it is in your best interest to fill in information for each week's lab before the end of each week. Total possible points earned for the lab notebook is 180 points. Each lab will be worth 19 points (8 labs total) and grading will be based on the following criteria – quality and completeness of flow charts, answers to pre- lab questions, detail of observations and any changes to steps during lab procedures, thoroughness of the Results section, quality of the Discussion and citations. Organization and clarity of information will account for the final 28 points. Selected labs will be converted into one formal lab report. The formal lab report will be written and submitted as a group project (one report will be submitted by each group). Guidelines for writing the formal reports will be handed out prior to completion of the designated labs. Formal reports require significant amounts of background research before writing the report. The final report should be submitted as an electronic copy no later than 10 calendar days after completion of data collection for that lab. I will be happy to review outlines/rough drafts of reports prior to their due dates, but only for academic integrity issues – nothing more – and the draft must be handed to me at least 3 days prior to the due date. Note: a portion of your grade for the formal report will involve self and peer evaluation.

LAB QUIZZES: Three laboratory quizzes spread throughout the semester will be used to assess comprehension of techniques and concepts from labs as well as interpretation of actual and/or hypothetical data. Please note the date of each quiz on the course schedule. Lab quizzes will cover lab material from all labs prior to the lab quiz. Students will be allowed to use their laboratory notebooks and a calculator, but no other supplementary materials.

PRESENTATION: At the end of the semester each student will be required to perform a literature search and give an 8-10 minute presentation on a particular concept or technique presented in a primary source. The literature search will require a minimum of one secondary source and two primary sources, both from journals (Internet/Web sites are not allowed). Each student will provide a brief introduction of the purpose and significance of what they have researched, select 1-2 important data figures and explain them in detail, summarize the final conclusions of the article, then provide a personal evaluation of the article. A copy of each source and an electronic version of the presentation must be submitted at the time of the presentation. Your presentation grades will be based on: (1) identification and use of appropriate resources/references; (2) organization and clarity of information presented (relevant background, methods, results, and evaluation), (3) responses to question during the presentation, and (4) self and peer evaluation.

DISCRETIONARY POINTS: Throughout the semester I will utilize a variety of learning tools to augment student instruction and assessment of course and student goals. These include, but are not limited to, announced or unannounced quizzes at the beginning of lectures or labs, group assignments, and problem sets. Participation and proper attitude are the final components of these points.

COURSE GRADING: Lecture Exams (first three-120 pts.; fourth-170 pts.)…...... 530 points Lab Notebooks...... 180 points Formal Lab……………………………………………….. 100 points Lab Quizzes (3 Quizzes, 20 pts ea.)………………………. 60 points Presentation...... ………………….. 80 points Discretionary……………….…………………………….. 50 points Total = 1,000 points

A...... 93% or greater C+..... 77% - 79.95% D+..... 60% - 62.95% A-...... 90% - 92.95% C...... 73% - 76.95% F...... below 60% B+..... 87% - 89.95% C-...... 70% - 72.95% B...... 83% - 86.95% D-...... 67% - 69.95% B-...... 80% - 82.95% D...... 63% - 66.95%

ACADEMIC INTEGRITY: Academic integrity is one of the cornerstones of any academic and is an essential component of the scientific process. Much of the progress achieved by various scientific disciplines, such as physics, , engineering and biology, over the past two centuries is a direct result of academic rigor and integrity. Scientific theories such as gravity, , atomic theory and evolution are constructed from the observations and experimentation of many individuals, all relying on the accuracy and authenticity of previous work. Research shows that studying in groups is one of the most productive ways of learning. This can mean explaining a difficult concept to a friend or asking for help with explanations. It can also mean asking a friend to edit your completed assignment for mistakes. While faculty and administration strongly encourage student collaboration and the use of all available resources when studying or researching topics, it is important that the student (1) properly acknowledge the origins of their information and (2) process the information in a way that allows them to reach their own conclusions and express concepts in their own words. In order to achieve these goals, the student must learn proper paraphrasing and citation of scientific resources, have a thorough understanding of the material, and be willing to accept and learn from constructive criticism. The mission of Westminster College is clearly stated in the College catalog (pp. 10-11):

The mission of Westminster College is to help men and women develop competencies, commitments, and characteristics which have distinguished beings at their best. [. . .] Develop and demonstrate moral and ethical commitments to neighbor, society, and the natural world consistent with an understanding of self.

The academic integrity policy of this institution can be found in the College catalog (pp. 73-78). Violations of academic integrity are included, but not limited to, those found in the College catalog, along with the process, consequences and stipulations. While the academic community and scientific process is severely undermined by any of these violations, the biology department would like students to pay particular attention to the categories of “plagiarism” and “providing false information”. Failure to acknowledge the ideas of others or document your sources is called plagiarism and will be handled in accordance with Westminster's academic integrity policy. Providing false or fabricated information is another serious violation of scientific integrity (lab notebooks, formal lab reports). Obtaining laboratory results from another source or person and/or fabricating results will result in a minimum penalty of zero for the assignment or a failing grade for the course. All students should realize that papers or lab reports submitted to me may also be submitted to Turnitin.com to confirm originality.

Breach of academic integrity applies to any student participating in activities listed in the College catalog either for their own or for another’s benefit. Other forms of academic dishonesty that are not tolerated for this discipline include, but are not limited to:

A. Lending of one’s work to another so that he/she may turn it in as his/her own. B. Claiming to have attended a seminar or colloquium when one has not actually done so. C. Stealing class materials from students, the professor, or the library and preventing others from using library materials or other resources necessary for the class. D. Any inappropriate, disruptive, and/or aggressive behavior towards other students in the classroom (e.g., threatening, bullying, intimidating) or the instructor.

Tentative schedule:

Date Day Lecture Topic (Chapter) Lab (Wed., 2-5pm) 1/16 M MLK Day - No Class 1/18 W Introduction; Overview Lab 1 - Introduction to lab skills and Structure of DNA and RNA (Chp. 9) agarose gel 1/20 F Structure of DNA and RNA (Chp. 9)

1/23 M Org. and Struct. (Chp 17.1, 10) 1/25 W Chromosome Org. and Struct. (Chp 17.1, 10) Lab 2 - Genomic DNA Isolation 1/27 F and Chromosomal Transmission (Chp 3; sections 1, 2, 3)

1/30 M Reproduction and Chromosomal Transmission (Chp 3; sections 1, 2, 3) 2/1 W Functional (Chp 23.3) Lab 3 - Intro to 2/3 F Cytogenetic and Linkage Mapping (Chp 22, sections 1, 2, 4, 5)

2/6 M The Rise of the Pangenome (Handout) 2/8 W Exam I Lab 4 - PCR 2/10 F DNA Replication (Chp 11)

2/13 M DNA Replication (Chp 11) 2/15 W (Chp 12) Lab Quiz #1 (Labs 1, 2, & 3) Lab 4 – PCR (cont.) 2/17 F Transcription (Chp 12)

2/20 M (Chp 13) 2/22 W Translation (Chp 13) Lab 5 - RNA Isolation 2/24 F Gene Regulation (Chp 17.2, 17.3)

2/27 M Gene Regulation Prokaryotes (Chp 14) 3/1 W Gene Regulation Prokaryotes (Chp 14) Lab 5 - RNA Isolation 3/3 F Exam II

3/6 M Gene Regulation Eukaryotes (Chp 15) 3/8 W Gene Regulation Eukaryotes (Chp 15) Lab 6 - Gene Express. Assay 3/10 F Gene Regulation Eukaryotes (Chp 16)

3/11-3/19 Sat.-Sun. Spring Break - No Class No lab

3/20 M Gene and DNA Repair (Chp 18) 3/22 W Gene Mutations and DNA Repair (Chp 18) Lab 6 - Gene Express. Assay (cont) 3/24 F Gene Mutations and DNA Repair (Chp 18)

3/27 T Recombination and Transposition (Chp 19) 3/29 W Recombination and Transposition (Chp 19) Lab 6 - Gene Express. Assay (cont) 3/31 F Variation in Chrom Struct and Numb. (Chp 8)

4/3 M Variation in Chrom Struct and Numb. (Chp 8) 4/5 W Exam III Lab Quiz #2 (Labs 4, 5, & 6) Lab 7 - Isolation and Quantification 4/7 F Genetic Transfer in (Chp 7.1-6)

4/10 M Genetic Transfer in Bacteria (Chp 7.1-6) 4/12 W CRISPR/Cas Gene regulation in Prokaroytes Lab 7 - Plasmid Isolation and Quantification

4/13-4/17 Thrs.-Mon. Easter Break - No Class

4/19 W (Chp 2) Lab 8 - Mendelian Inheritance 4/21 F Mendelian Inheritance (Chp 2)

4/24 M Extensions of Mendelian Inher. (Chp 4) 4/22 W URAC - Attendance required (no formal class) URAC - Attendance required (no formal lab) 4/28 F Extensions of Mendelian Inher. (Chp 4)

5/1 M Linkage and Genetic Mapping (Chp 6.1-6.3) 5/3 W Non-Mendelian Inheritance (Chp 5) Lab Quiz #3 (Labs 7 & 8) Presentations (everyone must stay until 5:30 pm.) 5/5 F Course Evaluations Non-Mendelian Inheritance (Chp 5)

5/9 T Exam IV/Final; 8-10:30 am