Biochemistry and Molecular Biology 462

Advanced Biochemistry II – BMB 462 Course Information and Lecture Schedule SPRING SEMESTER 2015 9:10 - 10:00 A.M., M W F 1281 Anthony Hall

Instructors Dr. Jon Stoltzfus (Course Coordinator) Dr. Monique Floer Dr. Lee Kroos

Course Objectives BMB 462 is the second semester of the undergraduate series BMB 461-2 which provides an introduction to biochemistry at the advanced undergraduate level. BMB 462 continues the study of metabolism begun in BMB 461 and then examines the transmission and expression of the genetic material in bacterial and eukaryotic cells. At the conclusion of this course, successful students will be able to: • Explain the roles of common membrane components and predict how the membrane will change based on changes in these components. • Explain how signals are transduced in cells, categorize specific parts of signal transduction cascades based on general signal transduction principles, and predict how changes in a signaling system will alter the signaling process. • Discuss the processes used to metabolize lipids, amino acids, and nucleotides, explain the function of individual reactions in these processes, and connect these processes with central metabolic pathways. • Explain the mechanisms used to regulate cellular metabolism and predict how changes in these regulatory mechanisms will impact cellular metabolism. • Explain the roles of nucleotides and nucleic acids in cells based on the structures of these molecules and predict how changes in these structure alter their functions. • Explain how biomolecules store and transfer information and how this information is recognized and used by cells. • Diagram the processes used to synthesize, repair, and recombine DNA and compare the structure and function of key proteins involved in these processes. • Diagram the processes used to create various cellular RNAs and compare the structure and function of key proteins involved in these processes with proteins used to synthesize, repair, and recombine DNA. • Diagram the processes needed to synthesize and target proteins and discuss the structure and function of key molecular machines involved in these processes. • Explain how gene expression is regulated using classic examples of gene regulation as models, categorize specific examples of regulation by general regulatory mechanism, and predict how changes in a regulatory system will alter gene expression. • Design a basic DNA cloning experiment incorporating the general processes used in cloning DNA.

Textbook Nelson, D.L. and Cox, M.M. Lehninger Principles of Biochemistry, 6th ed. (2013). W.H. Freeman, New York. 1198 pages. Specific reading assignments and end of chapter problems are intended to reinforce and develop further the subjects introduced during the lectures. You may expect some exam questions to be formulated directly from the textual reading and problems.

Lecture Notes Instructors will post lecture notes in D2L. These notes are based on the textbook, so most of the figures and information they contain can also be found in Lehninger. These notes contain most figures discussed during lecture and are designed to aid your note taking during lecture and while reading the text. They are not a substitute for regular lecture attendance and reading the textbook. It is highly recommended that you print these lecture notes and read the assigned reading in the text prior to lecture, taking notes while you read. Then bring your notes to lectures to help fill in areas that were confusing when you first read them in the text.

Clickers This course will use i-clickers to facilitate active learning. Clickers may be registered at the beginning of lecture any time during the first two weeks of the semester. If you have not registered your clicker by the end of two weeks you may not receive credit for previous clicker questions. During a typical lecture you will have one or more opportunities to answer questions using the clicker. You will receive 9/10th of a point for sending in any answer and an additional 1/10th of a point for sending in the correct answer. Some questions are designed to generate discussion and may not have a single correct answer. In this case, you will receive one point for any answer. Prior to each exam your score will be adjusted as follows. Your Score = Points Earned/(Possible Points * 0.9) This will adjust your score upward so that if you earned 90% or more of the possible points you will receive full credit. Clicker points for the entire semester are worth 4% of your final grade. It is your responsibility to understand the feedback lights on your clicker and verify that your answers are received. It is also your responsibility to check the clicker spreadsheet in D2L on a regular basis to verify that your points are being recorded correctly. If your clicker malfunctions, please notify the TA immediately. It is your responsibility to bring your clicker to class each day and if you forget to bring your clicker or miss class for any reason, you will receive no points for that day. There are no make ups for clicker points. You must attend class and use your clicker to receive points: having a friend bring your clicker is a breach of academic integrity and will be treated as such. Because you only need 90% of the possible points to earn full credit, you can miss class occasionally for emergencies, religious days, or other commitments without seriously impacting your clicker scores.

Recordings This semester we are providing audio-video recordings of the lectures. The purpose of these recordings is to allow review of lectures as you study. These recordings are not a substitute for attending lectures and taking notes. You should not depend on these recordings: some lectures may not be available or may be of poor quality due to technical difficulties and the server streaming the recordings may go down at inopportune times. The recordings will typically be posted on D2L within 24 hours of each lecture.

Office Hours Questions concerning subjects covered in the lectures, assigned reading, or homework may be discussed with the individuals listed below at the times and places shown. Note that office hours are not intended to substitute for attendance at lectures. If you have missed a lecture, please view the lecture recording (see Recordings above) prior to attending scheduled office hours.

Instructor Information

Lectures

Office and Office Hours

Dr. Jon Stoltzfus Phone: 432-8775 e-mail: [email protected]

Lectures 1-21

Dr. Monique Floer Phone: 353-3247 e-mail: [email protected]

Lectures 22-27

Dr. Lee Kroos Phone: 355-9726 e-mail: [email protected]

Lectures 28-41

305 Biochemistry Bldg. M 12:00-1:00 P.M. Th 9:30-10:30 A.M. F 2:00-3:00 P.M. or by appointment 410 Biochemistry Bldg. Th 4:30-5:30 P.M. F 4:30-5:30 P.M. or by appointment 422A Biochemistry Bldg. M & F 10:15-11:15 A.M. or by appointment 101 Biochemistry T 5:30 to 6:30 P.M. Th 4:30 to 5:30 P.M.

Michael McAndrew e-mail: [email protected]

Electronic Resources and Communication D2L will be used to post lecture notes, lecture recordings, grades, and other general course information. It will also be used for e-mail and a general discussion board. LON-CAPA will be used for online assignments and for discussions pertaining directly to those assignments.

LON-CAPA Homework Homework for BMB 462 is available through LON-CAPA (http://loncapa.msu.edu/). Log on using your MSU Net ID and password. This homework covers some of the concepts you need to know but is not exhaustive. It should give you a feel for the types of things you are expected to know on the exam. It is also recommended that you work the problems available at the end of each chapter in the text. The LON-CAPA problems over the course of the entire semester are worth 8% of your final grade. You are authorized and encouraged to work together and help each other learn how to solve the homework problems but you must log on and solve your own homework problems to receive credit. Postings on the discussion board that describe the thought process or techniques you used to solve a problem or other information that will help classmates learn to solve problems are authorized and encouraged. Simply posting answers is not allowed, is a breach of academic integrity, and will be treated as such. Please read Discussion Board Etiquette file in LON-CAPA for more information.

Missed Assignments and Technical Issues with LON-CAPA On occasion, technical issues related to the online homework may occur. Dr. Stoltzfus will attempt to assist you in resolving such issues. However, as long as access to LON-CAPA through the computer labs on Michigan State University’s campus is available, technical difficulties with your computer or your internet service providers are not excuses for missing the homework. Unless there are technical problems with LON-CAPA, the MSU network, or the MSU computer labs there will be no homework extensions. You are encouraged to record the LON-CAPA receipt number when you complete each assignment as a record that you have completed that assignment.

Examinations Exams will be held in the same room as lectures, 1281 Anthony Hall. Exams will consist of multiple choice and/or free response questions at the instructor's discretion. All exams are cumulative because concepts on each exam rely heavily on concepts previously covered in the course. Exams I-III will commence at 9:10 A.M. and will terminate at 10:00 A.M. Exam IV will commence at 8:15 A.M. and will terminate at 9:30 A.M. Each exam contributes to your final course score based on the percentage of lectures covered by that exam as described in the section on grades. Academic honesty is expected. As discussed in the Spartan Life Student Handbook General Student Regulation Part 1, PROTECTION OF SCHOLARSHIP AND GRADES: “The principles of truth and honesty are fundamental to the educational process and the academic integrity of the University; therefore, no student shall: 1.01 claim or submit the academic work of another as one’s own. 1.02 procure, provide, accept or use any materials containing questions or answers to any examination or assignment without proper authorization. 1.03 complete or attempt to complete any assignment or examination for another individual without proper authorization. 1.04 allow any examination or assignment to be completed for oneself, in part or in total, by another without proper authorization.” Exams are an individual effort and you should neither give nor receive help during an examination. Policies to ensure academic integrity will be strictly enforced. Any instance of academic dishonesty will result in a failing grade for the exam and may result in a failing grade for the course.

Absences With the exception of technical problems originating in LON-CAPA or the MSU network, there are no extensions on LON-CAPA homework. There will be no makeup or adjustments to clicker scores for days you miss class except in the case of extended illness. If you miss an exam for any reason, it is your responsibility to contact the instructor within 24 hours of the missed exam. You may or may not be offered a makeup exam depending on the circumstances. Make-up exams are administered at the instructor’s convenience, typically within 72 hours of the original exam. Make-up exams typically consist of essay questions but instructors retain the right to offer multiple choice makeup exams in some circumstances.

Grades Your grade in BMB 462 will be determined by your performance on the following assessments:

Assessment

%

Date

Exam I Exam II Exam III Exam IV Clickers LON-CAPA Homework

19% 17% 22% 30% 4% 8%

February 6 February 27 April 3 May 5 See the "Clickers" Section for Details See the "LON-CAPA Homework" Section for Details

This grading scale shows the percentage or the rank (as calculated from the overall distribution of undergraduate scores using the "percentrank" function in Excel) you must earn at the end of BMB462 to guarantee a particular grade. Please be sure you understand the difference between your percentage and your rank when considering your grade. Whichever scale gives you the higher grade will be used for final grades. Grades for graduate students will be determined from the undergraduate distribution.

Grade 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.0

Percentage Rank ≥ 92.00 ≥ 84.00 ≥ 78.00 ≥ 70.00 ≥ 62.00 ≥ 56.00 ≥ 50.00 < 50.00

≥90.00 ≥75.00 ≥55.00 ≥35.00 ≥20.00 ≥10.00 ≥ 5.00 < 5.00

Extra Credit You will have one opportunity near the end of the course to earn extra credit in BMB462. The extra credit opportunity is an online research survey and course evaluation at the end of the course. The purpose of the extra credit is to give you the opportunity to ensure that if you are within 0.5% of a cutoff for a particular grade that you will earn the higher grade. The purpose of the extra credit is not to make significant changes in the grade you earn from other assessments. See D2L for more details.

Honors Option You may elect to take BMB 462 with the H-option provided you are progressing at the 3.0 level or higher. If you are considering an H-option you must send Dr. Stoltzfus an e-mail before January 21 making your intentions known. On January 23 at 8:30 A.M. in 1281 Anthony Hall there is a mandatory meeting with Dr. Stoltzfus to discuss scientific literature and research procedures in the context of the honors assignment. More information about the honors option is available in D2L.

BIOCHEMISTRY AND MOLECULAR BIOLOGY 462 LECTURE SCHEDULE SPRING 2015

Date

Inst.

1/12 1/14 1/16 1/19 1/21 1/23 1/26 1/28 1/30 2/2 2/4 2/6 2/9 2/11 2/13 2/16 2/18 2/20 2/23 2/25 2/27 3/2 3/4 3/6 3/9 to 3/13 3/16 3/18 3/20 3/23 3/25 3/27 3/30 4/1 4/3 4/6 4/8 4/10 4/13 4/15 4/17 4/20 4/22 4/24 4/27 4/29 5/1 5/5

JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS JS MF MF MF MF MF MF LK LK LK LK LK LK LK LK LK LK LK LK LK LK

Lect. #

Topic

Assigned Reading Pages

Pages 357-370 Course Introduction and Fatty Acids Lipid Structures and Properties Pages 370-380; 845-847; 874 Membrane Structure and Properties Pages 385-402 No Class – Martin Luther King Day 4 Membrane Structure and Properties Pages 385-402 5 Membrane Transport Pages 402-427 6 Signaling Pages 433-472 7 Signaling Pages 433-472 8 Lipid Catabolism Pages 667-688 9 Lipid Catabolism Pages 667-688 10 Fatty Acid Anabolism Pages 833-845 EXAM ONE: Lectures 1 - 9 In Anthony 1281 11 Fatty Acid Anabolism Pages 833-845 12 Glycerolipid and Sphingolipid Anabolism Pages 848-859 13 Cholesterol Metabolism Pages 859-867 14 Amino Acid Metabolism Pages 695-717; 719-721 15 Amino Acid Metabolism Pages 881-894; 902-910 16 Metabolic Integration Pages 929-960 17 Metabolic Integration Pages 929-960 18 Nucleotide Chemistry and Metabolism Pages 977-978; 281-287; 306-308; 910-925 EXAM TWO: Lectures 10 - 17 In Anthony 1281 19 Nucleotide Metabolism Pages 910-925 20 Gene Transmission and DNA Structure Pages 29-39; 977-978; 287-302 21 DNA Structure Pages 287-292 No Class - Spring Break Chromosome Structure 22 Pages 979-1003 23 DNA Replication Pages 1009-1033 24 DNA Replication Pages 1009-1033 25 DNA Replication Pages 1009-1033; 1085-1094 26 DNA Repair & Recombination Pages 299-302; 1027-1052 27 DNA Repair & Recombination Pages 1027-1052 28 RNA Structure & Function Pages 977-978; 293-296; 34-35 29 Transcription Pages 1057-1060 EXAM THREE: Lectures 18 - 27 In Anthony 1281 30 Transcription Pages 1060-1064 31 Transcription Pages 1064-1069 32 RNA Processing Pages 1069-1075; 1082-1083; 1092-1094 33 RNA Processing Pages 1075-1081; 1084-1085 34 Translation Pages 1103-1110 35 Translation Pages 1113-1123 36 Translation Pages 1127-1139 37 Protein Targeting and Degradation Pages 1139-1149 38 Regulation of Gene Expression Pages 1155-1165 39 Regulation of Gene Expression Pages 1165-1174 40 Regulation of Gene Expression Pages 1175-1186 41 DNA Cloning – Class Meets in BPS1410 Pages 313-332 FINAL EXAM: Lectures 28 - 41 In Anthony 1281 from 8:15 A.M. to 9:30 A.M. 1 2 3