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9/2/14 1 of 7General Biology 111Fall 2014Lecturer & Coordinator:InstructorProf. Brian WhiteKiley Brownoffice: W-3-003 (617) 287-6630 W-2-074 (617)287-6608(ISC-4450 – 4th floor)e-mail: brian.white@umb.edukiley.brown001@umb.eduoffice hours: Wednesdays 2:00-3:00*You should contact Kiley with& by appointmentquestions about the course*Where can I find things on the web?• Blackboard https://umb.umassonline.net/ this site has the after class and administrativematerials:o Class Notes & Class Video – posted after each classo Exams and solutions – posted after each examo iClicker registrationo Grades• World-Wide Web Site: http://intro.bio.umb.edu this site has a link to the On-Line LabManual, Blackboard, and the Bio 111 SPOC• The Bio 111 SPOC (see links on Blackboard and the course web site) this site has materialsto help you get ready for each class:o Video, readings, practice problems, tutorials, etc.o Information about each examRequired Materials:1. Lab Manual: The Lab Manual is essential for performing the lab activities; the lab manualalso contains pre-labs, worksheets, etc. You can purchase a 3-ring binder with the LabManual from Quinn Reprographics (Quinn LL-024). It is also available for free downloadon the course website. I strongly advise you to buy the printed version. You must bringyour lab manual to every lab session.2. Lecture Handouts & A Problems Approach to Introductory Biology (APAIB) For each class,there is an essential handout with figures, questions, data, etc. APAIB contains practiceproblems (both on paper and computer-based) will be used in lab, class, and at home andprovide essential practice with the material for the exams. You can purchase a 3-ringbinder with both the Lecure Handouts and APAIB from Quinn Reprographics (Quinn LL-024). Both are also available for free download on the SPOC and course website,respectively. I strongly advise you to buy the printed version. You must bring LectureHandouts and APAIB to every class session.3. iClicker Transmitter: All students must have an iClicker transmitter (see later for details)and bring it to each lecture. These are available from many sources including the UMBBookstore. Please note that you will need to be able to read the serial number of youriClicker in order to register it; so, if you buy a used iClicker, be sure that you can read the8-character serial number on the back of it. Any of the different iClicker models(“iClicker”, “iClicker +” or “iClicker 2”) will work just fine in Bio 111. You must bringyour clicker to every class session.

9/2/14 2 of 7Other RequirementYou must sign up for a free account at the 7.00x_UMass SPOC. “SPOC” stands for “SmallPersonalized On-Line Course” – more on what this means later. You will need access to this toprepare for class sessions, labs, and exams. You should go to the “SPOC” link on Blackboardor the course web page and sign up for a free account ASAP. You must use your UMB e-mailto register. You will not get credit for your SPOC work if you do not register exactly asdescribed.• What is it? In the spring of 2013, I worked with a team of about 20 people at MIT todevelop a Massively Open On-line Course (MOOC) called “7.00x”. This course covers thematerial in Bio 111 and includes lectures, supporting videos, problem sets, and exams. Iextensively re-organized these materials to create a custom version for Bio 111; this is the“7.00x_UMass SPOC”.• How to use the SPOC materials: The SPOC materials are organized by class “sessions”:o All of the materials are accessible from the “Courseware” tab.o Before each class session:! Watch the lecture and answer the “Core” and “Challenge” questions. The Corequestions are easier and you have two tries to get them right. The Challengequestions are harder; you have an unlimited amount of tries to get them rightand, after your first try, you can look at the answer. They are due by 11:00AMon the day of the corresponding class session and will not be accepted late.! You may find it useful to look at the questions before watching the video. Thatway, you can have an idea what to watch for.o In class, we will go over questions and problems including those from APAIB.o After class, to prepare for the exam, go over the problems including the APAIBproblems and “Extra Practice Problems” until you are confident that you can solveproblems like these.o Looking at the answers. For all of these problems, including those in APAIB, wehave provided detailed solutions. These solutions are an essential part of learningthe material; you are strongly encouraged to read them carefully. However, youshould only read them after you have tried to write out an answer to the question.• Can I work with others on the SPOC problems? It depends on which type of problem:o Core Problems: These must be done on your own. You may not discuss answerswith other students or post them on the web, etc.o Challenge Problems: You are encouraged to talk with other students about these.• What if I have questions? You should try the following in this order:o Look on the “Wiki” tab of the SPOC to see if this has been answered.o Search the “Discussion” on the SPOC to see if this has been answered.o Post a question to the SPOC’s “Discussion” – see the “Forum Guidelines” on theSPOC’s “Course Info” tab.o E-mail your question to the course instructor.Optional TextbookThe 7.00x SPOC has two built-in free on-line textbooks, so will not likely need a paper and inktextbook for this class. If you find that the on-line textbook is not what you need, any of thepopular introductory-level college books (“Biology” by Campbell is one example) will beuseful.

9/2/14 3 of 7Course ScheduleDate In-Class Activity Lab & [Due Date]W 3-Sep 01 Introduction 00: Computer Help SessionF 5-Sep 02: Building MoleculesM 8-Sep 03: Drawing Molecules 01: Chemical StructuresW 10-Sep 04: Hydrogen BondsF 12-Sep 05: Reading MoleculesM 15-Sep Exam 1: Making Molecules 02: ChromatographyW 17-Sep 06: Protein Structure; ApproximateF 19-Sep 07: Protein Structure; Real [Lab report due week of 9/22]M 22-Sep Exam 2: Reading Molecules 03: Protein StructureW 24-Sep 08: ThermodynamicsF 26-Sep 09: Enzymes[Lab Report due week of 9/29]M 29-Sep Exam 3: Proteins 04: AmylaseW 1-Oct 10: Glycolysis, etc.F 3-Oct 11: Pathways[Lab Report due week of 10/6]M 6-Oct Exam 4: Enzymes &c. 05: GFP I: PurificationW 8-Oct 12: Basic GeneticsF 10-Oct 13: Sex-linkageM 13-Oct Columbus’ Day 06: Genetics Practice ProblemsW 15-Oct 14: Pedigrees I& VGLIF 17-Oct 15: Pedigrees IIM 20-Oct Exam 5: Genetics I 07: Aipotu I: Genetics &W 22-Oct 16: Proteins & GeneticsBiochemistryF 24-Oct 17: Genetics Limitations[Lab Report due week of 10/27]M 27-Oct Exam 6: Genetics II 08: PTC I: DNA extraction & PCRW 29-Oct 18: Genes are DNAArabidopsis PhenotypesF 31-Oct 19: DNA Structure & Replication [Lab Report due week of 11/3]M 3-Nov 20: Transcription & Translation 09: VGL ChallengesW 5-Nov 21: IntronsF 7-Nov 22: Mutations[Electronic Lab Report due in class]M 10-Nov Exam 7: Gene Expression NONEW 12-Nov 23: IntegrationF 14-Nov 24: Recombinant DNA IM 17-Nov Exam 8: Integration 10: GFP II: TransformationW 19-Nov 25: Recombinant DNA IIF 21-Nov 26: Recombinant DNA IIIM 24-Nov Exam 09: Recombinant DNA NONEW 26-Nov 27: GenomicsF 28-Nov ThanksgivingM 1-Dec 28: Genetic Disease I 11: Aipotu II: Biochemistry &W 3-Dec 29: Genetic Disease IIMolecular BiologyF 5-Dec 30: Genetic Disease III[Lab Report due week of 12/8]M 8-Dec Exam 10: Genetic Disease 12: PTC II: Gel ElectrophoresisW 10-Dec 31: Viruses & HIVF 12-Dec 32: HIV Treatment

9/2/14 4 of 7Other course details:Course Blackboard site: Bio 111 also has a site on Blackboard (https://umb.umassonline.net/).This site has links for the iClicker registration, recorded class sessions, and many of yourgrades. It also has links to the lab discussion boards and data blogs.Discussion Section: Tuesdays 12:30 - 1:20 in W-2-032. I will lead a group discussion of theweek’s material as a tutorial for you and an opportunity for me to understand how you arelearning the material. Attendance is encouraged but not required.Tutor-led Study Groups: There are several tutors to help students in Bio 111. Tutoring is freeand open to all students. The tutors will lead weekly study group workshop sessions wherethey will go over that week’s APAIB problems as well as answer questions. Regularattendance is strongly encouraged.Class Session Video I make a digital audio & video recording of each class session and postthese Blackboard. DANGER: these are not a substitute for attending class!!!Class Session Notes from this year. I am using a Tablet PC to write notes on the screen. Aftereach lecture, I will post these notes on the course website.iClicker Beginning with the second class session, at the beginning of each session and thenseveral times during the class, I will ask a short multiple-choice question to make sure that youare able to apply the material we are working with (note that the exams will not be multiplechoice).You will submit your answer as described below; you will receive credit for eachanswer you submit, whether it is correct or not. Answers are due during the lecture on theday the question was asked; no late answers will be accepted; there are no make-ups formissed iClicker questions.Using an iClicker This looks like a small TV remote control. You transmit your answerto the receiver in Lipke and the computer logs your answer.You will need to register your iClicker serial number so you can get credit. You dothis by going to the course Blackboard site, clicking on the “Register your iClicker” link, andfollowing the directions there. You should not register through iClicker.com.Course Policies:Class Sessions: Class Sessions meet in Lipke Auditorium: Mon, Weds, Fri 12:00 to 12:50;regular attendance is expected. Extra copies of some handouts can be found on the coursewebsite, the SPOC, and outside W-3-003.Lab Sections: Lab sections meet in W-2-030, -031, and -032. Some labs involve hands-onactivities; others involve problem-solving exercises. Lab sections will be assigned before thefirst week of class; you may not switch sections after that time. Attendance in lab is expected.In an emergency, you may make up a missed lab by attending another section thatmeets during the same week with the permission of the TA; TAs may refuse entry to studentsonce the section is full. You may attend only one make up lab section per semester; after that,if you attend a lab other than the one to which you have been assigned, you will be allowed toattend that lab but your pre-lab and any other materials due in that lab will not be graded.You must read the lab manual before lab. Some labs have pre-lab exercises based on thelab manual; these are due at the start of lab and will not be accepted late. You will not beadmitted to lab unless you have a copy the lab manual and a completed pre-lab with you.

9/2/14 5 of 7The lab sections are as follows:Section Time Room Section Time Room1 Tu 9:30 - 12:30 W-2-030 8 We 1:00 - 4:00 W-2-0302 Tu 9:30 - 12:30 W-2-032 9 We 1:00 - 4:00 W-2-0323 Tu 2:00 - 5:00 W-2-030 10 We 5:30 - 8:30 PM W-2-0314 Tu 2:00 - 5:00 W-2-031 11 Th 9:30 - 12:30 W-2-0305 Tu 2:00 - 5:00 W-2-032 12 Th 9:30 - 12:30 W-2-0326 We 8:30 - 11:30 W-2-030 13 Th 2:00 - 5:00 W-2-0307 We 8:30 - 11:30 W-2-031 14 Th 2:00 - 5:00 W-2-032Note: lab sections are very full - if you do not fill out and sign a student information sheetat the first lecture, your space in lab will be given to another student even if you areregistered for the class.Exams:• There will be eleven exams: ten 50-minute exams given in class during the semester and acomprehensive 3-hour final exam.• There will be no make up exams. No conflict exams will be given.• If you arrive more than 5 minutes late to an exam, but before the first person has finishedthe exam, you may be given as many minutes as you were late as extra time after the exam.• A subset of the students will be asked to take the exam in a nearby location to relieve thecrowding in Lipke.• The final exam will be scheduled during the semester.• You may bring a single 8.5 x 11 sheet of paper with whatever you want on it to each examand four such pages to the final exam.• Exam Re-grades: Occasionally, we make mistakes when grading. If you feel that yourexam was graded in error, you can request a re-grade. Instructions and notes for regrading:• Re-grades must be in writing; because different TAs graded different questions, neitheryour TA nor I can re-grade your exam “on the spot”.• When asking for a re-grade, you should include the following:o Your whole exam. Do not mark on it in any way. In order to prevent cheating,we xerox or scan some or all of the exams; any marks made on your exam after itwas graded and given to you in lab may be interpreted as cheating. Studentswho alter their answers and submit these altered answers for a re-grade willreceive a grade of “F” for the course and a letter will be sent to the Dean ofUndergraduate Education notifying him/her of the incident.o A note on a separate piece of paper (attached to your exam) explaining whatneeds to be re-graded. Don’t simply say, “Re-grade question 3”; you shouldexplain why your answer deserves more credit than we gave. If it is an additionerror, explain which numbers were added up incorrectly.o Re-grade requests that do not follow these rules will be returned without review.• Re-grade requests must be turned in to your TA or Brian White within 2 weeks of thedate the exam was handed back in lab.• Re-graded exams will be returned in lab about 2 weeks later.

9/2/14 6 of 7Grades: Your final grade will be calculated as follows:• There are 700 points available in the course:o 250 points for your 10 hour exams 1-5 (25 points each)o 100 points final examo 150 points Lab: Your lab grade will be totaled (max = 425) and scaled to a maximumof 150 points (multiplied by 150/425); see breakdown that follows.o 150 points SPOC; this will be the “Total” shown on the “Progress” page of the SPOCscaled to 150 points.o 50 points iClicker: Your iClicker points will be totaled and scaled to 50 points.• However, your overall grades are based on a 600-point scale which is approximately:o 516-544 = A- 545-600 = Ao 426-455 = B- 456-485 = B 486-515 = B+o 336-365 = C- 366-395 = C 396-425 = C+o 246-275 = D- 276-305 = D 306-335 = D+o 0-245 = F• Thus, you have a 100-point “safety net” for missed assignments, etc. with one exception:because iClickers are such an important part of the course, if you do not register youriClicker, your final score will be divided by 2 when calculating your grade.Lab GradesDone at home & handed in at start of labPre-labs 12 x 10 pts = 120Chromatography Report 25Protein Structure Report 20Amylase Report 25Aipotu I Report 25VGL Electronic Report 20Arabidopsis Report 20Aipotu II Report 30GFP Transformation Report 10Work done entirely in labSmall Molecules Worksheet 20Protein Structure Checkoff 20GFP I Checkoff 10Aipotu I Checkoff 20PTC I Checkoff 10VGL Challenges Checkoff 10GFP II Checkoff 10Aipotu II Checkoff 20PTC II Checkoff 10Total: 295Total: 130Grades will be posted as they become available on Blackboard or the SPOC as appropriate.Due dates:o 7.00x SPOC Assignments They are due at 11:00 AM on the date indicated and will not beaccepted late for any reason. There are no make-ups for SPOC assignments. Do not beconfused by the due times that are listed in the SPOC – they are in GMT (Greenwich Mean Time),which is 4-5 hours ahead of our time zone.o Lab reports are due as indicated in this syllabus or as modified by your TA. In cases wherethere is a conflict between when the Lab Manual says that a report is due and when thesyllabus or TA says so, your TA is the final source; the syllabus is next. In certain cases, andonly with the permission of your TA, lab reports may be turned in to the TAs mailbox inthe Biology office (W-3-021) by 5:00 PM on the day that they are due. In ALL other cases,late reports will NOT be accepted* – do not assume that we will grant you an exception. Ihave very limited flexibility; if you need an exception, it can only be granted if you come tome in advance.* Each student will be allowed to turn in one and only one lab report one week late for amaximum of ½ credit. Specifically, if the lab report is turned in between 1 and 7 days late(relative to the student’s assigned lab section meeting time), the student’s lab report will begraded; the score received will be ½ of the grade earned. Each student may do this onlyonce per semester.

9/2/14 7 of 7⇒ If you have computer problems with your lab report, you have several options forturning it in on time (in each case you are responsible for making sure that your TA receivesyour report):1. Turn in a partially complete report on time.2. Bring your report to your TA on disk (only with your TA’s permission).3. E-mail your report to your TA as an attachment (only with your TA’s permission).4. Fax your report to the Biology office (617 287-6650); attention: your TA (only withyour TA’s permission).It is always good practice to keep backup copies of lab reports on other disks to guardagainst hard drive crashes.Snow days: If class is cancelled due to snow, check the SPOC, course web site, or my officephone for announcements. In general, snow days before exams will not cause the exams to bemoved; if a snow day falls on an exam day, the exam will be held in the next class period.Incompletes: Incompletes will only be granted under certain special conditions. To receive anincomplete, you must be doing well in the course and the work to be completed must be awell-defined unit of the course. An incomplete must be arranged in advance of your absenceat a meeting in person with Brian White.Academic Conduct: Students are required to adhere to the Code of Student Conduct, includingrequirements for the Academic Honesty Policy, delineated in the University of MassachusettsBoston Graduate Studies Bulletin and relevant program student handbook(s).http://www.umb.edu/life_on_campus/policies/code In this course, penalties foracademic misconduct, including plagiarism (copying from another student, a book, or theinternet), are strictly enforced. It is my policy to make the consequences of being caughtcheating on a given exercise much more severe than the consequences of not turning in thatparticular exercise.Acommodation for Students with Disabilities: Section 504 and the American with DisabilitiesAct of 1990 offer guidelines for curriculum modifications and adaptations for students withdocumented disabilities. If applicable, you may obtain adaptation recommendations from theUMass Boston Ross Center 617-287-7430. You need to present and discuss theserecommendations with me within a reasonable period, prior to the end of the Drop/Addperiod.If you are using adaptive software with Blackboard Vista, please contact the instructorfor information regarding the software’s interface with the LMS.