BIO202 Fundamentals of Biology: Molecular and Cellular Biology. Prof. Vitaly Citovsky

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1 BIO202 Fundamentals of Biology: Molecular and Cellular Biology Profs. Vitaly Citovsky/J. Souza Summer 2012 Extended Session Stony Brook University Course Contact Information Also see our Biology online website at Online resource management Content Lecturer: (Including blackboard and any discussion (Including exam content) board related questions: Prof. Vitaly Citovsky Prof. Joanne Souza LSB Rm 414, Phone: LSB Room Office Hours: For Phone or Adobe Connect access: by appointment Administrative Staff (Adding/dropping course, etc) Ms. Lynette Giordano, G05 CMM/BLL, , Ms. Diane Pauciullo, G05 CMM/Biology Learning Labs, GENERAL INFORMATION: BIO202 together with BIO201 and BIO203, make up a three-semester set of courses on Principles of Biology. These courses may be taken in any order. In BIO202, living systems are treated from a molecular, cellular, and genetic point of view, with a focus on the relationship between structure and function. These fundamental insights are vital to the understanding of all of biology. Prerequisites: Level 3 or higher on the mathematics placement examination or BME 100 (for Stony Brook Students): Pre- or Co-requisites: Basic chemistry (CHE 129 or 131 or 141); basic calculus (MAT 125 or higher or AMS 151 for Stony Brook Students). COURSE DESCRIPTION: Welcome to the fundamentals of cell biology, biochemistry and genetics! This course covers the biochemical and molecular bases of cell structure, energy metabolism, gene regulation, heredity, and development in living organisms from bacteria to humans. Our goal is to give you a strong foundation in the principles you need to understand and solve problems in the areas of molecular and cellular biology. Whether your career goal is medicine, basic research, clinical research, or teaching, a sound, rigorous understanding of these basic principles is crucial. This online course is structured to support your efficient mastery of the extensive course material, including content exploration in small asynchronous discussion groups. You will find the problem solving skills you learn here to be crucial throughout the rest of your career, including in the laboratory segments of your academic degree program.

2 COURSE OBJECTIVES: This course is organized in thirds with a live, in-person evening exam given at the end of each third to assess your mastery of the content presented. The cumulative final exam is given concurrently with the exam for the last third of the course (for a total of three live exam sessions). These exams may be taken at either the Stony Brook or Manhattan campuses. All other features of the course are online and delivered through Blackboard. The content of the course is accessible to you via video lectures, lecture Power Points for note taking, and through readings in the 9 th Edition of the Campbell Biology textbook. Multiple choice sample questions covering challenging content will be the basis of your discussions with peers in the asynchronous discussion groups. Three posts per week discussing these questions with your colleagues are required. This portion of your work will also serve as a powerful study aid for mastery of key concepts and performing well on the exams as well as to increase your critical thinking and communication skills. Grading for this portion of the course will consist of the assessment of your critical thinking and application skills as guided by the discussion board rubric (below). COURSE ORGANIZATION: In the first third of the course, we will begin our journey by exploring how the properties of biological organisms emerge with surprising orderliness from the fundamentals of elementary chemistry and physics. These insights, in turn, will allow us explore how the several different classes of biological macromolecules collaborate to build the various levels of structures making up biological organisms, including molecular machines, subcellular organelles, cells, tissues and organisms. Moreover, we will study features of the fundamental chemical process of catalysis, allowing us to begin to understand how biological macromolecules create and control the fundamental chemistry of life. In the second third of the course, we will continue to build our understanding of the molecular and biochemical nature of all living organisms, from viruses and bacteria to human beings. This portion of our exploration will include investigation of how the massive amounts of energy biological organisms require is ultimately captured from solar radiation by photosynthesis. We will go on to explore the biochemical processes that allow organisms to use this energy to function and to incorporate matter during growth and reproduction, the fundamental processes characteristic of all organisms. Finally, we will examine how cells control their growth and division, followed by an investigation of how the macromolecules encoding genetic information (DNA) are distributed when cells divide during growth or are redistributed when organisms reproduce sexually, producing offspring with genetic information from each of two parents. This last topic will lead us to an initial understanding of the pivotal science of genetics. In the final third of the course, we will extend our investigation of the central process of all biological organisms, the functioning of their genetic information. We will explore how genetic information stored in DNA expresses itself to create and control the structure and behavior of viruses, cells and multicellular organisms. These molecular processes, through which DNA sequences are transcribed into RNA sequences, which are then translated into protein sequences, are remarkably elegant in their power and simplicity. Next will explore how these processes of expressing genetic information are controlled so that the same set of genes can build all the different cell types in a complex organism like a woman or a man. Further, we will investigate how chemical accidents and other processes randomly change DNA sequence, creating the variation in design information filtered by natural selection to produce evolutionary change. Finally, we will capitalize on all we have learned to better understand disease processes, such as cancer, and the spectacular new capabilities for biotechnology allowed by the dramatic scientific progress of the last 40 years.

3 Required Textbook: (Available in the University Bookstore) Textbook: Biology by Campbell, Reece. The 9th edition is the most recent, but earlier editions are also acceptable. You may purchase either the entire textbook or a custom edition, which contains only the chapters that are required for BIO 202. New textbooks also contain an access code, which is required to access online resources of the textbook. This is not mandatory for the course. EXAMINATIONS AND GRADES Grades are a combination of three in-person midterm exams, an in-person cumulative final (given concurrently with the third midterm) and three weekly discussion posts. Your lowest midterm exam grade (of the three) will be dropped; therefore, NO MAKEUPS of midterms are permitted. EXAMS: All exams will be given in the evening. See schedule below for dates, times and places or see the Biology ONLINE website at for details. The third midterm will be given along with the cumulative final. Be sure NOT TO register for any other courses that conflict with the exam schedule. Please let Prof. Souza know by if you will be taking the exam in other than the campus in which you have registered. Do not bring pagers, beepers, or receivers to the exam. Cell phones must be TURNED OFF before entering the room and stowed with your bags/book. Based on university policy, a ringing cell phone during an exam represents academic dishonesty. If you are caught cheating, you will receive an F for the course and be reported to the academic judiciary committee. DISCUSSION BOARD POSTS: THERE ARE 22 DISCUSSION POSTS DUE on Blackboard throughout the course. (See the Assignments tab on Blackboard each week for details). Requirements are a minimum of three substantial and documented posts per week. Grading is on a scale of 0 to 5 and post will be graded according to the critical thinking rubric provided. We drop the 2 lowest scoring posts for a total of 20 posts worth a potential 100 points for this section of the course. The first post is due by Thursday each week, and the second and third by Sunday at midnight EST. The discussion portion of your grading cannot be dropped. Student discussion and engagement in the course material is a valuable tool both for you (in studying for exams and achieving long-term retention and mastery) and for us as instructors to assist you in areas of confusion. OBJECTIVES of the group discussions are as follows: You will be given questions and correct answers from prior exams and/or concept questions that have been identified as challenging areas of important content. You will be asked to discuss the following: 1. Why the correct answer is the most correct answer 2. If someone has already posted a comment respond to them and tell us why you either agree or disagree with their explanation. ALSO INCLUDE IN YOUR POST: 3. Note the place in the textbook, Power point slide, lecture, or other outside sources (reference source) where you found your information. If responding to previous post, give us a different reference source. 4. Tell us why knowing the answer to this question is useful to either researchers or medical practitioners. If responding to a previous post, give us a different application for this information. This critical exploration and debate is the essence of the scientific method and of achieving mastery and personal ownership of a body of knowledge. You will have the opportunity herein to sharpen your

4 scientific and intellectual-critical skills as well as providing context and engagement in the fundamentals you are learning. Posts are graded on a scale of 0 to 5 points according to the discussion rubric at the end of this syllabus and posted on Blackboard. ALL DISCUSSION POSTS will be monitored by plagiarism check software. RULES OF THE GAME FOR DISCUSSIONS Please be aware that the information provided by other students in your group is not necessarily correct information. The purpose of discussion groups is to give you the chance to clarify your understanding and sharpen your intellectual skills. Authoritative factual information for EXAM purposes comes from lecture, the textbook, lecture Power Points, and faculty responses to discussions, which will be provided the week after your discussion with your colleagues is over. This is important to remember when studying for exams. The following behaviors during Group Discussion are unacceptable and will result in your being excluded from Discussion Group and forfeiting that portion of your grade that week. - Using abusive, disrespectful or foul language. - Using sexually suggestive language (either explicit or implicit) that could be perceived as offensive or harassing. - Threatening others. - Insulting others or denigrating the opinions of others. Of course, you may respectfully, even strongly, disagree or challenge the opinions of others, but we attack positions, NEVER individuals in scientific debate. - If any inappropriate behavior of the sort listed above should occur, the offender will be issued one and only one warning. A second offense will be grounds for excluding the offender from Discussion Group and forfeiting all his/her credit for this course requirement. - Plagiarism of any sort either copied work from other sources or from other student s posts will not be tolerated. There is zero tolerance for plagiarism of any sort. All quoted material must reference the source. Discussion posts should be in your own words. If any quotes are used they must be in quotes and referenced appropriately. Also see our Academic Honesty statement at the end of this syllabus. Any academic dishonesty will be reported to the Academic Judiciary and can result in an F in the course. COURSE GRADE AND FINAL LETTER GRADE CALCULATION: The lowest of the three midterm grades will be dropped. If you miss one of the midterm exams, the missed exam will count as your dropped grade. NO MAKEUP EXAMS WILL BE GIVEN. The two lowest scoring of the 22 discussion posts will be dropped resulting in 20 graded posts for a total of 100 potential points. Discussion board grading in Toto cannot be dropped. The final exam grade cannot be dropped. Since both the discussions and the final exam cannot be dropped, rigorous engagement in all three thirds of the course is required for a passing grade. Your course grade will be determined as follows: Average of 2 highest midterm exams plus the discussion grading: 65 % Cumulative final: 35 % Final course grades will be assigned on a curve. HOW TO SUCCEED IN BIO202: WATCH THE ORIENTATION VIDEO: The orientation video will take you through how the course is managed and set up on Blackboard so you can spend your time learning content during the term.

5 WATCH ALL ECHO CONTENT LECTURES: The lectures show you which topics to emphasize, how much detail you need to know, and how the topics fit together. Chapters from the book listed in the Course Schedule will help you to find the relevant material for each lecture. Use the textbook to supplement material presented in the lectures. The exams are based on the lectures, which may contain some material that is not found in the textbook; so do not miss any lectures. COMPLETE ALL ASSIGNMENTS ON TIME! Weekly assignments with due dates are posted under assignments on the Blackboard site with the assignment at the top being the one due for the week. You may wish to print out lecture PowerPoints given in the assignments prior to watching lectures for note taking. Put your best foot forward during the discussion board portion of the course and do not miss any due dates. TAKE ALL EXAMS OFFERED: Though one mid-term is dropped, try not to miss any so that you maintain the option of the dropping your lowest score. BIO ONLINE BLACKBOARD SITE: The course is managed completely through the Blackboard site at All syllabus and grading information is posted along with assignments and lecture videos. Discussion board forums are provided. Pay attention to all announcements. If you have used Stony Brook's Blackboard system previously, your login information (Username and Password) has not changed. If you have never used Stony Brook's Blackboard system, your initial password is your SOLAR ID# and your username is the same as your Stony Brook (sparky) username, which is generally your first initial and the first 7 letters of your last name. For help or more information see For problems logging in, go to the helpdesk in the Main Library SINC Site or the Union SINC Site, you can also call or helpme@ic.sunysb.edu. SOURCES OF HELP: 1. Administrative Questions Forum: There is a forum under your discussion board for all administrative questions all questions placed here will be answered within 24 hours. 2. TA s: Undergraduate TA s will monitor your discussion boards and assist you in critical thinking skills as applied to content. 3. Prof. Citovsky is available for live or web office hours, for any content-related questions. 4. Prof. Souza will answer any Blackboard-related and grading concerns regarding the discussion posts. 5. The access code, inside the textbook, provides access to the mastering biology website. which has chapter reviews, study guides, and interactive practice quizzes. If you do not have an access code, you can purchase one online from the website Americans with Disabilities Act: If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Disability Support Services, ECC (Educational Communications Center) Building, Room 128, (631) They will determine with you what accommodations, if any, are necessary and appropriate. All information and documentation are confidential. Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the

6 learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook. Academic Integrity: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty are required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at ALL ELECTRONIC EQUIPMENT, INCLUDING CELL PHONES ETC., SHOULD BE TURNED OFF AND PUT AWAY BEFORE ENTERING THE EXAM ROOM. BASED ON THE UNIVERSITY POLICY, A RINGING CELL PHONE DURING AN EXAM REPRESENTS ACADEMIC DISHONESTY. IF YOU ARE CAUGHT CHEATING, YOU WILL BE REPORTED TO THE ACADEMIC JUDICIARY COMMITTEE, AND YOU WILL RECEIVE AN F FOR THE COURSE.

7 COURSE SCHEDULE BIO 202 ONLINE SUMMER EXTENDED SESSION (Weekly Assignments referred to below are available through the Blackboard site under the ASSIGMENTS Button on the left menu) WEEK 1: May 29-June 3rd Assignment 1: Post for Orientation video and Lectures 1 or 2 by Thursday Second and Third Posts for Lectures 3, 4, 5 by Sunday 1A. Orientation Video 1. Echo Lecture 1: Atoms and Molecules in Biology Campbell Text: Chapter 2 2. Echo Lecture 2: Chemical Bonds, Functional Groups/Acids, Bases, ph and buffers Campbell Text: Chapters 3 and 4 3. Echo Lecture 3: Macromolecules 1: Lipids and Carbohydrates Campbell Text: Chapter 5 4. Echo Lecture 4: Macromolecules 2: Nucleic Acids Campbell Text: Chapter 5 5. Echo Lecture 5: Macromolecules 3: Protein Campbell Text: Chapter 5 WEEK 2: June 4-10th Assignment 2: Post for Lectures 6, 7, or 8 by Thursday Second and Third Posts for Lectures 9, 10, or 11 by Sunday 6. Echo Lecture 6: Protein structure, enzymes and catalysis Campbell Text: Chapter 8 7. Echo Lecture 7: Enzymes and regulation of enzymes Campbell Text: Chapter 8 8. Echo Lecture 8: Energy in Biology, ATP Campbell Text: Chapter 8 9. Echo Lecture 9: Cell Structure, organelles 1 Campbell Text: Chapter Echo Lecture 10: Organelles 2 Campbell Text: Chapter Echo Lecture 11: Cytoskeleton 1 Campbell Text: Chapter 6 WEEK 3: June 11-17th Assignment 3: Post for Lectures 12, 13, or 14 by Thursday Second and Third Posts for Lectures 15, 16, or 17 by Sunday 12. Echo Lecture 12: Cytoskeleton 2, intercellular connections Campbell Text: Chapter Echo Lecture 13: Membrane Structure Campbell Text: Chapter 6, Echo Lecture 14: Osmosis, transport across membranes Campbell Text: Chapter Echo Lecture 15: Cell communication and signaling 1 Campbell Text: Chapter Echo Lecture 16: Cell communication and signaling 2 Campbell Text: Chapter Echo Lecture 17: Cell communication and signaling 3 Campbell Text: Chapter 11

8 WEEK 4: June 18-24th Midterm Exam 1: June 19 th, 6:30-8:30 pm, Javits 110 Covering Lectures 1-14 Assignment 4: Post for Lecture 18 or 19 by Thursday Second and Third Posts for Lectures 20, 21, or 22 by Sunday Study for Exam! 18. Echo Lecture 18: Cellular respiration, glycolysis Campbell Text: Chapter Echo Lecture 19: Krebs cycle, fermentation, control of respiration Campbell Text: Chapter Echo Lecture 20: Photosynthesis 1 Campbell Text: Chapter Echo Lecture 21: Photosynthesis 2 Campbell Text: Chapter Echo Lecture 22: Chromosomes and cell division. Mitosis Campbell Text: Chapter 12 WEEK 5: June 25-July 1st Assignment 5: Post for Lectures 23 or 24 by Thursday Post for Lectures 25, 26, or 27 by Sunday 23. Echo Lecture 23: Cell cycle. Introduction to cancer Campbell Text: Chapter Echo Lecture 24: Meiosis Campbell Text: Chapter Echo Lecture 25: Mendel and the gene idea Campbell Text: Chapter Echo Lecture 26: Mendelian patterns in human inheritance Campbell Text: Chapter Echo Lecture 27: Chromosomal basis of inheritance Campbell Text: Chapter 15 WEEK 6: July 2-July 8th Assignment 6: Post for Lectures 28 or 29 by Thursday Post for Lectures 30, 31, or 32 by Sunday 28. Echo Lecture 28: Genetic variation: exceptions to Mendel s law Campbell Text: Chapter Echo Lecture 29: DNA: the genetic material Campbell Text: Chapter Echo Lecture 30: DNA replication Campbell Text: Chapter Echo Lecture 31: Transcription and RNA processing Campbell Text: Chapter Echo Lecture 32: Translation Campbell Text: Chapter 17 WEEK 7: July 9-July 15th Midterm Exam 2: July 10 th, 6:30-8:30 pm, Javits 110 Covering Lectures Assignment 7: Post for Lecture 33 or 34 by Thursday Second and Third Post for Lectures 35, 36 or 37 by Sunday Study for Exam!

9 33. Echo Lecture 33: Mutations, Bacterial Genetics Campbell Text: Chapter 17 & Echo Lecture 34: Regulation of eukaryotic gene expression Campbell Text: Chapter Echo Lecture 35: Introduction to protein structure Campbell Text: Chapter Echo Lecture 36: Eukaryotic genomes Campbell Text: Chapter Echo Lecture 37: Bacteria, viruses Campbell Text: Chapter 19 WEEK 8: July 16-July 22 nd Midterm Exam 3: July 20 th, 6:30-9:30 pm, Javits 110 Covering Lectures CUMULATIVE FINAL EXAM (Lectures 1-42): concurrent with above Midterm 3 Assignment 8: Post for Lectures 38, 39, 40 or 41 by Thursday Post for Lectures 42 and Farewell by Sunday 38. Echo Lecture 38: Biotechnology 1 Campbell Text: Chapter Echo Lecture 39: Biotechnology 2 Campbell Text: Chapter Echo Lecture 40: Fertilization and early development Campbell Text: Chapter 21, Echo Lecture 41: Mechanisms of Development 1 Campbell Text: Chapter 18, Echo Lecture 42: Mechanisms of Development 2 Campbell Text: Chapter 20, 47