Chemistry 3130L Syllabus Spring 2015 Course Information Introduction to Biochemistry Lab (CHEM 3130L) 1 credit hour Course Meetings Section 01 Tuesday 1:15 - 4:05 pm NCF 316 Johanson Instructors Dr. Kelly Johanson NCF 301H x 7610 kjohanso@xula.edu Dr. Terry Watt NCF 314 x 5271 tjwatt@xula.edu Office Hours M 11:30 am - 2:30 pm T 9:30 am - 11:30 am W 11:00 am - 12:00 pm T 10:45 am - 11:45 am W 2:00 pm - 5:00 pm R 4:15 pm - 5:15 pm F 9:00 am - 10:00 am Section 02 Wednesday 2:00 - 4:50 pm NCF 316 Johanson Section 03 Thursday 1:15 - 4:05 pm NCF 316 Watt Section 04 Friday 2:00 - 4:50 pm NCF 316 Watt If these times are not convenient, contact your instructor for an appointment. You may also attend another instructor’s office hours. Required Textbook Fundamental Laboratory Approaches for Biochemistry and Biotechnology, 2nd edition. Ninfa, Ballou, & Benore, 2009 (Wiley). Recommend Textbook Essential Biochemistry, 3rd edition. Pratt & Cornely, 2013 (Wiley). Course Description A selection of experiments covering the isolation of biochemical substances and the study of their properties. This course will enable the student to readily perform isolations of a number of types of biochemical substances, and to determine their properties and concentrations while gaining some skills in the use of common laboratory techniques and instruments. Course Prerequisites Grade of C or better in CHEM 2220/2240L; CHEM 3130 (co-requisite) Course Objectives CHEM 3130L is a thematic selection of experiments in biochemistry primarily focused on biomolecular properties. The goals of this course are to expose the students to techniques commonly used in a biochemistry lab and to develop the skills needed to express the results of an experiment in a scientifically appropriate manner. Students should learn how to use micropipettors, make buffers, set up a PCR, run agarose and polyacrylamide gels, use a microplate reader, estimate pKa values, and use Microsoft® Excel to make graphs and tables. In addition, students should leave the class with the ability to calculate dilutions, concentrations, absorbances using Beers Law, and enzyme kinetic values. Students should also be familiar with the techniques and equipment used in protein purification. Finally, students will learn how to combine the results from a series of experiments into a manuscript following the guidelines of the journal Biochemistry. Class Structure In the first five weeks of the semester, you will spend approximately half of the laboratory period performing an experiment with both supervision and input from the instructor and the other half discussing data analysis and scientific writing techniques. During the later part of the semester, you will be expected to plan and execute several experiments with minimal input from the instructor. 1 Blackboard Your instructor will use Blackboard throughout the semester to post experimental protocols, grade written assignments, post copies of handouts and assignments, and contact students by email. You should make a habit of checking Blackboard for course materials on a regular basis and should verify that your account is set up to receive emails from Blackboard. You will also be expected to complete pre-lab assignments and upload written work to Blackboard. All Blackboard assignments will be prepared and posted by the instructor well in advance of the due date. You should plan to complete these assignments with enough time to spare in case computer issues arise at the last minute. Unless the University Blackboard system is down for an extended period of time (i.e., more than 12 hours), due dates will not be changed nor will late assignments (including pre-labs) be excused due to computer issues. Be aware that the Blackboard auto-save feature does not work if your network connection is unreliable, so you should be sure to manually save your pre-lab assignments periodically as you work through them. If you are having difficulties accessing your Blackboard account or uploading documents, please see ITC to resolve the issue. Your instructor will not be able to provide technical assistance. You are also responsible for accessing Blackboard using an appropriate device; in some circumstances, smart phones and tablets will restrict your ability to work with Blackboard and you will need to use a computer. Class Attendance You should attend each class and be on time. You are responsible for all notes, assignments, handouts, instructions, etc. given during your absence. If you need to miss a class for a legitimate reason (severe illness, university sponsored event, etc.), you must notify your instructor before the missed class period and make every effort to attend another section. You must obtain permission both from your instructor and the instructor of the other section before attending. If you arrive late or miss a class without sufficient justification, you will not be allowed to make up the quiz for the day, and you may not receive permission to make up the lab. No make-up sessions will be offered; the only opportunity to make up a missed class is the other scheduled sections that have not yet completed the experiment. Participation You are expected to be prepared for lab (which includes wearing appropriate attire and completing all reading assignments), pay attention during pre-lab lectures, share the in-class workload equally with your lab partner, remain engaged during the entire lab period (e.g., no use of social media or texting during a lull in activity), and clean up before leaving lab. You must wear closed-top shoes (no part of the top of the foot or sock visible), have a lab coat or other protective clothing, and have protective eyewear. Lab coats must be worn at all times in the lab if your clothes do not completely cover your legs to your knees and completely cover your torso (sleeveless is acceptable). Extensively ripped clothing is not appropriate without a lab coat. You should also bring a USB drive to every class so that you can save your data. Your instructor may deduct points if you fail to meet expectations, are late to class, or miss a class. In addition, failure to ensure that both the lab drawers you utilize during class are back in their original condition at the end of every class will result in penalties, as will the use of materials from unassigned lab drawers without the explicit permission of your instructor. Lab Notebooks You are required to maintain a laboratory notebook. The notebook is a place where all your data and calculations are recorded along with any relevant observations. This notebook is not to be used for class notes – only information about the experiments should be recorded in your notebook. You should have this notebook with you during every class session, and should write in it during experiments to ensure that you have a record of what you did. A composition notebook or a notebook from a previous class can also be used, but not a notebook concurrently in use for any other purpose or course. The notebook should include a purpose for the lab and outline of the procedure, including all relevant calculations and any changes made during the experiment. Pasting a printed copy of the protocol in the lab notebook is not an acceptable substitution for the purpose or method nor is copying the protocol word-for-word from the handout on Blackboard. The notebook should also include a summary of the results (including any tables and/or figures generated as 2 part of the data analysis). This summary should be handwritten in your notebook. While it is acceptable and encouraged to paste in copies of graphs, charts, and extensive tables, it is not acceptable to simply staple in the entire typed results or any other typed analysis completed as part of an assignment. Please read the section in the lab manual and/or ask your instructor if you have questions about how to keep a lab notebook. All notebook entries must be written in pen. The notebook will be checked at random during the semester. If you do not have your notebook in class during a random notebook check, you will receive a zero for that check. Experimental Protocols All experimental protocols will be available on Blackboard at least two weeks prior to the scheduled lab date, and you are encouraged to look through the protocols well in advance of each lab. Each protocol will contain information about calculations that need to be performed prior to lab and any other information necessary for the pre-lab. As the semester progresses, the protocols will become less detailed and you will be expected to rely on your lab notebook for experimental details and to prepare your own experimental procedure. Although your instructor will give some additional explanations of techniques and data analysis during the pre-lab lecture, you should contact your instructor prior to lab if you do not understand how to complete the required calculations or are very confused about the purpose of the lab. Your instructor will expect you to walk into lab each day with these calculations completed and with a general understanding of that day’s purpose. You will have a chance to practice these calculations in the online pre-lab assignments described below. Failure to complete pre-lab calculations and other preparation may result in the inability to complete experiments within the allotted class time. Online Pre-labs Pre-lab exercises can include questions about the purpose of the lab, experimental details of the lab, analysis of your data, reading assignments, and calculations that should be completed prior to beginning the experiment. The information needed for the completion of the pre-lab exercise can be found in the protocol and assigned reading. The first part of each pre-lab will require you to enter information necessary for the completion of the lab. This portion of the pre-lab quiz must be completed by 5:59 pm (morning lab sections) or 11:59 pm (afternoon lab sections) on the evening prior to your scheduled lab, and you may only complete this portion only once. Your instructor will review and grade this part of your pre-lab between the submission time and the start of your class, generally by late evening for morning lab sections or midmorning for afternoon lab sections. You can then review your score (and submitted answers) before class by clicking on the grade in the Blackboard Gradebook. The second part of each pre-lab will question you about general calculations and other background information. This portion of the pre-lab can be completed at any time prior to the start of class. You will be able to re-take this second portion of the pre-lab as often as you would like prior to class to increase your score; only this highest score is recorded. Failure to complete the pre-lab prior to class will result in a zero; there is no opportunity to make-up a pre-lab exercise. Pre-lab submissions by email will not be accepted. The pre-lab part 2 questions will be available for additional practice and review prior to the exam; the questions will not be worth additional points when practiced. Written Assignments Details of each assignment will be provided in the information sheet for each week. You are expected to use the schedule at the end of this syllabus to keep track of your assignment due dates. Your instructor may discuss the details of each assignment in class, but you are responsible for all assignments based solely on the provided written information even if assignments are not discussed during class. It is your responsibility to keep up and turn in your work on time. The list of assignments and the associated point values is the same for all lab sections, although due dates are specific to each section based on class meeting time. Assignments come in a variety of types. A few 10 point assignments focus on learning how to present particular types of information. Most assignments are worth 15 points and focus on data analysis; completion of these assignments will greatly assist with preparation of the final paper. Two 20 point assignments make up a lab practical at the end of the semester, and part of the grade for those assignments 3 will be based on in-class performance. One 30 point lab report will also be due. All assignments are to be submitted online using the designated Blackboard link, which may also require submission of your work to TurnItIn. Assignments will not be accepted by email or on hard copy. All assignments must be your own work; it is never acceptable to copy any work from another student, even your lab partner. Your instructor will grade your work online and provide comments if appropriate; it is your responsibility to look at the graded work for any comments by your instructor using the TurnItIn interface. Your instructor may leave comments in the grade report for the assignment and/or on the document itself within the TurnItIn interface. If you do not understand how to view these comments, please seek help early in the semester. (Two hints: placing your mouse cursor over a comment will expand it to show more detail, and you can click-and-drag comments to more clearly determine which text a particular comment refers to.) Note that the TurnItIn interface for mobile devices, including tablets, does not provide full functionality and may restrict your ability to view feedback. It is your responsibility to view feedback with an appropriate computer. Failure to correct issues pointed out by your instructor in early assignments will lead to significantly lower grades on later assignments. Note that assignments may be submitted multiple times until 15 minutes before class on the due date. The last version uploaded will be the one graded. You can take advantage of this feature to ensure that a draft is uploaded well in advance of the due date, and then upload a final version later if necessary. This will help you avoid late penalties in the event of technical difficulties uploading close to the beginning of class. However, be aware that revised versions cannot be uploaded after the time the assignment is due, even though it is still possible to upload a first version (with a late penalty). Written assignments routinely require the use of a spreadsheet program for data analysis. Appropriate programs include Microsoft Excel (but not “Excel Starter Edition”), Libreoffice Calc, and Openoffice Calc (the latter two being freely available to download). Note that many other commonly available spreadsheet programs lack necessary features and are not adequate for this course, including Apple iWorks Numbers. Quizzes Quizzes will focus on calculations you should have completed as part of the data analysis for a previous lab and/or those necessary for the current lab. Pre-lab exercises provide opportunities to practice the calculations that may appear on quizzes. Late attendance will result in a missed quiz unless you have a valid excuse approved by your instructor in advance. Exam There will be a comprehensive final exam given on the date indicated on the course schedule. Note that this exam will be given in the evening, and you should plan work schedules accordingly. All sections of 3130L will take the final exam at this time. You will be given two hours in which to complete the exam. Exams will not be returned, but you may arrange an appointment with your instructor to view your exam after exam grades are posted. Final Paper You will write up the results of Weeks 6-11 as a manuscript using the format for the journal Biochemistry (http://pubs.acs.org/journal/bichaw). You will be given many opportunities throughout the semester to complete and receive feedback on portions of this manuscript. Specific guidelines for each section of the manuscript will be provided in handouts and discussed during class. Each student must submit their own, original work. The due date and time for the manuscript is listed in the schedule at the end of this syllabus. As with other written assignments, this manuscript will be submitted electronically. Course Grading It is possible to earn a maximum of 1070 points, but percent grades will be calculated out of 1000 points. Assignments. Assignments are individually worth five to thirty points, for a total of 225 points. Pre-labs. There will be ten 20-point pre-labs (combined part 1 & part 2) for a total of 200 points. 4 Quizzes. There will be nine 20-point quizzes during the semester, for a total of 180 points. Exam. There is one 150 points exam. Final paper. This paper is worth 200 points. Lab notebook. The notebook is worth 50 points. Participation. Following the given participation guidelines is worth up to 65 points. Final Total Points and Grade Distribution Letter Grade A B C D F Minimum Percent 90% 80% 70% 60% < 60% Point Range 900-1070 800-899 700-799 600-699 0-599 Course Policies Attendance Swipe your ID in the card readers when entering the classroom. If you forget your ID or arrive more than 10 minutes after class has begun, your attendance will not be recorded. Failure to attend a lab session without an excuse approved by your instructor in advance will result in an automatic 5 point deduction from your participation total. If you are completely unprepared for lab, especially on days where a protocol assignment is due, you may be asked to leave and make up the class as an unexcused absence. Late Assignments All assignments are due by the beginning of class and must be submitted electronically by that time. For most assignments, submissions after the deadline will receive an automatic 5 point deduction with an additional 10% deduction will be applied per day starting 24 hours after the original deadline. For both the final manuscript and lab practical written assignment, a late penalty of 1% per hour following the deadline will be applied instead. Once the total possible points reaches zero for any assignment, the assignment will no longer be accepted. If you have an emergency that prohibits you from turning in work on the due date, you must immediately notify your instructor and provide the appropriate documentation within one week of the original due date. Graduating seniors will receive a grade of zero for any assignments that are not submitted before Quiet Day, even if the total late penalty would not yet automatically mean zero points (spring semesters only). Written Assignments After Missing Class Most written assignments require that you have completed an in-class experiment to generate data. If you miss a class due to an unexcused absence, you will be unable to complete the corresponding assignment. Your instructor will not accept an assignment based on data from a class that you missed unless you have received special permission in advance. Collecting Your Graded Work Your instructor will return all graded work as quickly as possible. It is your responsibility to collect your graded quizzes if you are not available to pick them up in class. Assignments submitted electronically will also be graded electronically, and may be viewed using the TurnItIn interface in Blackboard. Your instructor may choose to place graded quizzes outside of her/his office for easier pickup. If you do not want your graded work placed in a common area, please notify your instructor by email. 5 Calculators Bring a non-programmable calculator capable of logs (including natural logs and antilogs), exponents, and scientific notation to class every day. (Calculators that round off very small values instead of switching to scientific notation will lead you to calculation errors.) On quizzes and exams, cell phones and multimedia devices may not be used as calculators, sharing of calculators is not permitted, and you should not assume that your instructor will have a spare calculator. Electronic Devices Silence cell phones for the duration of the class period. If there is a situation that requires that you be able to answer your cell phone during a class, please inform your instructor before the class. If you use your phone during class (including text messaging), you may be asked to leave; an exception will be made if the phone is used strictly as a timer or clock during appropriate experiments. Some classes will require the use of computers, but the computers should be used only for classwork. Regrade Requests Grades on assignments/quizzes may be disputed up to one week after being returned or being made available for pickup. Grade errors on online assignments must be brought to the instructor’s attention within one week of the grade entry. Re-grade requests must be in writing with a detailed explanation for the request. Re-grades may result in a grade higher or lower than the original grade. It is your responsibility to keep track of your grades and notify your instructor immediately if you feel that you are missing a quiz or assignment grade. Sample Data You may require sample data from your instructor if an experiment does not produce any data. You may request this data for any experiment under the following guidelines: (i) the data analysis must clearly indicate that sample data was used and why; and (ii) you may receive a 5% point deduction on the assignment for using sample data if use of the data is not sufficiently justified (this corresponds to 10 points for each set of sample data if required for the final paper). Poor quality data is not usually a sufficient justification to request sample data. Keep this in mind when preparing for labs and working on experiments; it is usually easier to analyze and write about good quality data. Any assignments prepared using sample data (or data obtained from another student) due to an unexcused absence and/or without prior permission from your instructor will not be graded. Biochemistry Lecture If you are concurrently taking Introduction to Biochemistry lecture (CHEM 3130) but considering dropping the lecture, you must discuss whether or not you should remain in lab with your lab instructor. All lab students are assumed to have fundamental knowledge from lecture at each stage of the semester, and students who drop lecture but remain in lab have a very high failure rate. Evacuation Policy In the event that classes are canceled due to a hurricane evacuation, assignments and course materials will be posted to Blackboard. Please log on to the Blackboard site as soon as possible after the evacuation. Health or Disability Concerns If you have special needs, please make an appointment to speak to your instructor to discuss any appropriate accommodations. Academic Misconduct The CAS Academic Integrity Policy will be followed in this course. According to the policy, academic misconduct includes, but is not limited to, the following: 1. Using unauthorized materials in completion of an exam, quiz, or assignment. 6 2. Assisting or gaining assistance from an unauthorized source during an exam, quiz, or assignment. 3. Providing assistance to another student in a manner not authorized by the instructor. 4. Obtaining an examination or assignment in an unauthorized manner. 5. Using material from a source without giving proper citation. 6. Fabricating or altering data. 7. Submitting work to one class that is substantially similar to work submitted for another class without prior approval from the instructors involved. 8. Submitting written work that is not completely one’s own or allowing others to submit one’s work. 9. Destroying or altering the work of another student. 10. Committing any other violation of academic integrity as described in this syllabus. Specific examples of academic misconduct in this class include: the use of a cell phone during an exam or quiz for any reason (even as a calculator); talking during an exam or quiz; using anything other than explicitly authorized materials on a quiz or exam; attempting to read from another student's quiz or exam; copying class assignments, including sharing files to analyze or present data; using data that you did not collect in a report without proper attribution; submitting a lab report that contains information from a website or other source without proper attribution; working with others on any assignments (in or out of class) when not authorized; submitting a lab report that contains information from a previous semester. You are responsible for arriving on time for all quizzes or exams, as you will not be permitted to begin after any other student has left the room. You are responsible for all written materials on, under, and near your seat during quizzes and exams, so it is in your best interest to ensure that the desk surface is clear of writing and that no extraneous papers are within your line of sight (both when you begin and finish). Cell phones should always be off and inside a bag during a quiz or exam; your instructor will not give you the benefit of the doubt if a cell phone is used or visible. The CAS policy makes no distinction between the person receiving unauthorized assistance (copying an assignment) and the person providing the assistance (allowing work to be copied); both actions are academic misconduct. All cases of academic misconduct will be reported to the CAS Dean's Office per Xavier's Academic Integrity Policy. Any case of academic misconduct on assignments will result in a grade of zero for the assignment and may result in a grade of F for the entire course. Premeditated academic misconduct during an exam (for example, using a cell phone to text or preparing a “cheat sheet”) will result in the student being asked to leave immediately and in a failing grade for the course. 7 Lab Schedule (Tuesday, Section 1) A (Y) in the pre-lab column indicates that you will need to complete an online pre-lab prior to the start of lab. A (Y) in the quiz column indicates that there will be a quiz given at the start of the lab period. Date Week Experiment Jan 13 1 Pipetting Jan 20 2 Spectrophotometry Jan 27 3 Buffers and pKa Feb 3 4 PCR Feb 10 5 Restriction digest Feb 17 No class: Mardi Gras break Feb 24 6 Protein purification Mar 3 7 Specific activity: phosphatase Mar 10 8 Specific activity: invertase Mar 17 9 SDS-PAGE and Optimal pH Mar 24 10 Invertase kinetics Mar 31 Apr 7 Apr 14 Apr 17 Apr 20 Apr 21 Apr 24 11 12 13 No class: spring break Non-linear kinetics analysis Manuscript workshop Pre-lab Quiz Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Exam at 6:00 pm Due at 11:59 pm Lab practical: phosphatase kinetics Due at 1:15 pm 8 Assignment Due Pts Week 1 notebook Week 2 report Week 3 report Abstract of research paper 10 15 15 10 Weeks 4+5 report Week 6 report Week 7 report Week 8 report Week 9 report Protocol for week 10 30 15 15 15 15 10 Week 10 report Week 11 report Protocol for week 13 draft 15 15 5 Manuscript Protocol for week 13 200 20 Week 13 results 20 Lab Schedule (Wednesday, Section 2) A (Y) in the pre-lab column indicates that you will need to complete an online pre-lab prior to the start of lab. A (Y) in the quiz column indicates that there will be a quiz given at the start of the lab period. Date Week Experiment Jan 14 1 Pipetting Jan 21 2 Spectrophotometry Jan 28 3 Buffers and pKa Feb 4 4 PCR Feb 11 5 Restriction digest Feb 18 No class: Mardi Gras break Feb 25 6 Protein purification Mar 4 7 Specific activity: phosphatase Mar 11 8 Specific activity: invertase Mar 18 9 SDS-PAGE and Optimal pH Mar 25 10 Invertase kinetics Apr 1 Apr 8 Apr 15 Apr 17 Apr 20 Apr 22 Apr 25 11 12 13 No class: spring break Non-linear kinetics analysis Manuscript workshop Pre-lab Quiz Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Exam at 6:00 pm Due at 11:59 pm Lab practical: phosphatase kinetics Due at 2:00 pm 9 Assignment Due Pts Week 1 notebook Week 2 report Week 3 report Abstract of research paper 10 15 15 10 Weeks 4+5 report Week 6 report Week 7 report Week 8 report Week 9 report Protocol for week 10 30 15 15 15 15 10 Week 10 report Week 11 report Protocol for week 13 draft 15 15 5 Manuscript Protocol for week 13 200 20 Week 13 results 20 Lab Schedule (Thursday, Section 3) A (Y) in the pre-lab column indicates that you will need to complete an online pre-lab prior to the start of lab. A (Y) in the quiz column indicates that there will be a quiz given at the start of the lab period. Date Week Experiment Jan 15 1 Pipetting Jan 22 2 Spectrophotometry Jan 29 3 Buffers and pKa Feb 5 4 PCR Feb 12 5 Restriction digest Feb 19 6 Protein purification Feb 26 7 Specific activity: phosphatase Mar 5 8 Specific activity: invertase Mar 12 9 SDS-PAGE and Optimal pH Mar 19 10 Invertase kinetics Mar 26 Apr 2 Apr 9 Apr 16 Apr 17 Apr 20 Apr 23 Apr 26 11 12 13 Non-linear kinetics analysis No class: spring break Manuscript workshop Pre-lab Quiz Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y TBA Exam at 6:00 pm Due at 11:59 pm Lab practical: phosphatase kinetics Due at 1:15 pm 10 Y Assignment Due Pts Week 1 notebook Week 2 report Week 3 report Abstract of research paper Weeks 4+5 report Week 6 report Week 7 report Week 8 report Week 9 report Protocol for week 10 Week 10 report 10 15 15 10 30 15 15 15 15 10 15 Week 11 report Protocol for week 13 draft 15 5 Manuscript Protocol for week 13 200 20 Week 13 results 20 Lab Schedule (Friday, Section 4) A (Y) in the pre-lab column indicates that you will need to complete an online pre-lab prior to the start of lab. A (Y) in the quiz column indicates that there will be a quiz given at the start of the lab period. Date Week Experiment Jan 16 1 Pipetting Jan 23 2 Spectrophotometry Jan 30 3 Buffers and pKa Feb 6 4 PCR Feb 13 5 Restriction digest Feb 20 6 Protein purification Feb 27 7 Specific activity: phosphatase Mar 6 8 Specific activity: invertase Mar 13 9 SDS-PAGE and Optimal pH Mar 20 10 Invertase kinetics Mar 27 Apr 3 Apr 10 Apr 17 Apr 17 Apr 20 Apr 24 Apr 27 11 12 13 Non-linear kinetics analysis No class: spring break Manuscript workshop Pre-lab Quiz Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y TBA Exam at 6:00 pm Due at 11:59 pm Lab practical: phosphatase kinetics Due at 2:00 pm 11 Y Assignment Due Pts Week 1 notebook Week 2 report Week 3 report Abstract of research paper Weeks 4+5 report Week 6 report Week 7 report Week 8 report Week 9 report Protocol for week 10 Week 10 report 10 15 15 10 30 15 15 15 15 10 15 Week 11 report Protocol for week 13 draft 15 5 Manuscript Protocol for week 13 200 20 Week 13 results 20