Colorado State University Department of Biochemistry BC Principles of Biochemistry Fall Semester 2013

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1 Colorado State University Department of Biochemistry BC Principles of Biochemistry Fall Semester 2013 Instructor: Aaron Sholders Ph.D. Office: MRB 231 Phone: This is the best way to get a hold of me. Office Hours: Monday 2:00 4:00PM. What does this mean? What this means is that I will pretty much guarantee that I will be in my office during this time (unless I state otherwise in class) and you can stop by with no appointment. What it does not mean? It does not mean that this is the only time you can meet with me. If you have a question or a concern, then come see me. If you want a guarantee that I will be there then make an appointment with me. TA: Schedule: Kelsey Thompson klthomps@rams.colostate.edu Yates 104 MTRF 1:00PM-1:50 PM Prerequisites: CHEM 245 or CHEM 341 or CHEM 345; LIFE 102 or BZ 110 or BZ 120 Textbook: Course objectives: Principles of Biochemistry, 1 st edition, by Aaron J. Sholders, Great Rivers Technology Publishers. An access code for the book can be purchased at the bookstore or online at this URL: Objective #1: You should be able to think critically about biochemistry and be able to assess and interpret biochemical data. Biochemistry is a science concerned with the question how does this work? Or how does it do that? Of course this is at a molecular level and as such can be very hard to visualize. Therefore to be a good biochemist you need to know how to look at, interpret and critically assess data. I hope to help you in this endeavor. Objective #2: You should be able to define and recognizes major concepts and principles in biochemistry. You must understand that the field of biochemistry is so large and so complex that no one could ever understand and retain it all. I am going to help you define some biochemical concepts and I am going to try to stick to the principles. Understand though that I will use very detailed examples to help establish those principles for you. These examples come with a nomenclature of their own that is unique to that field of biochemistry and has been established in the primary journals. This is the case with much of biochemistry, the nomenclature and labeling is horrific. However, once you

2 learn the nomenclature of a certain system then the principles of biochemistry are very similar across topics. Objective #3: You should walk away from this class saying That is a cool subject I want to know more! This may be a bit idealistic but I do want to develop in you a sense of respect, reverence and awe for the wonderful intricacies and design of the cell and the macromolecules therein. Hopefully the questions we pose and seek to answer will develop in you a hunger to learn more. Blackboard: Attendance: Materials: Blackboard address: Everybody should be online, if you do not have access by the end of today write me an . This site will be used to post lecture materials, your grades, any assignment and most importantly quizzes!! Attendance to every class is strongly encouraged and will be a determining factor for your success in this class. If you miss a class, you will be held responsible for all material covered. Attendance to exams is absolutely mandatory. Obvious exceptions, such as a death in the family, hospitalization and extreme illnesses will be accepted and dealt with appropriately. I am going to give you several things to help you understand the logic of my presentations and they are listed below: 1. The Book a. Contains material that will be covered in the lecture plus a small amount of additional material. b. Has your graded quizzes (more on this below). c. Has practice quizzes. 2. Powerpoints a. In class I will be projecting a powerpoint presentation. I have also made a student version of these that will be excellent for taking notes on. 3. Study Guides a. These are very general questions directing your studying and your thinking and also include problems from your text. 4. Practice Exams a. My suggestion on these is to wait until you are done studying (about 2 days before the test ) and then take this without any assistance from your notes. b. If you do well then you are set. If you do poorly go through all the questions and understand WHY you got

3 one wrong and WHY you got one right. Assignments: So how are you going to assess me? In other words what am I going to require of you? 1. Chapter Quizzes 70 points a. These will be presented through the book. There will be a total of 14 quizzes equaling 70 points. The quiz will initial be used as a pre-quiz and will be a prereq for viewing the material in the chapter. You will then have access to the quiz a 2 nd time so that you can study using your class notes and chapter readings to help improve your score. Due dates for the final attempt on each quiz are listed on the schedule. 2. Exams points a. I am going to give four exams. Each one will be worth 100 points. How to Study: The question I am most often asked by students is How do I study for this class? As such I have decided to provide the answer up front so you can get started right away! The objective of studying is to learn the material that is being presented. Exams are designed to assess whether or not you have learned. So really the question is How do I learn in this class? I think the best way to do this is to come to class prepared. My suggestion is to review questions I have presented to you in the study guides and your initial chapter quiz attempt PRIOR TO THE DAY THAT THE MATERIAL IS COVERED. Seek to answer study guide questions by doing the reading I assign to you in the text. If you can t come to an answer you are satisfied with, no big deal, at least you have thought about the material before coming to class. Now when you come to class your mind will be better prepared to understand the material I am presenting and you will be much more able to pick out the important points in my lecture. Once the lecture is done, review your notes, review the chapter and maybe even listen to the lecture again and then reattempt to answer the questions in the study guide and take the quiz a 2 nd time. If you still can t come to an answer then come and see me and I will hopefully set you straight. In addition to this I also am providing several short answer questions and practice multiple choice questions for each chapter. Attempt to answer these questions using your notes and the chapter content. Once you are satisfied that you have the correct answer submit it and the correct answer will then be displayed.

4 Grades: Historically the class average in BC351 has hovered around the 79-80% range. As such I have never curved this course and I don t really expect to do so this semester. I also have never had to drop a lowest exam score for the class and again I don t expect to do this for this semester. Below is how your grades will be broken down. What this means is that you are guaranteed at least those grades if you have those percentages (I do use a +/- system and the break for those will be determined at the end of the semester.) Grade Percentage A % B 80-89% C 70-79% D 60-69% F below 60% Grade Breakdown: Assignment Points Counted 4 Exams (100 points each) Quizzes (5 points each) 70 Total 470 Extra Credit: I have decided to use iclickers this semester. I am going to give only participation points for the use of iclickers. If you participate in 80% of iclicker questions I will give you 5 points of extra credit. In order to receive this credit, you will need to register your iclicker remote online within the first week of class. To do this, go to clicker.colostate.edu/registration.aspx. Login with your ename and password. In the iclicker ID field, enter your remote ID and select the "Register" button. The remote ID is the number found on the back of your iclicker remote. iclicker will be used every day in class, and you are responsible for bringing your remote daily. In addition to iclickers I will also give 5 point extra credit to any student that completes 90% or more of the optional short answer and multiple choice questions found in each chapter. Academic Integrity: The definition for integrity is: the quality of being honest and having strong moral principles; moral uprightness In practice I feel that this is best defined as doing the right thing when no one is looking. It is my goal to be a man of integrity in every facet of my life. As such it is important for you to know what I feel that means for this course. The following is a list of what you should expect from me in

5 terms of academic integrity: 1. Make sure that what I teach is consistent with the most current knowledge in my field to the best of my ability. 2. To admit mistakes when made EVEN if they are not caught by students. 3. To treat each student with the dignity and respect they deserve based upon their status as a human being. 4. To understand and meet students needs particularly when circumstances beyond their control impact their academic performance. 5. Make sure that each student is given an equal opportunity to succeed in my course by: a. Providing the SAME study material for all students on each exam as seen on Blackboard. b. Providing access to student in both review sessions and my office hours. c. Providing every student with the SAME opportunity for extra credit assignments. d. Providing every student with identical exam score adjustments if needed. That is what you should expect from me what though do I expect from you? Here is a list of my expectation for you the student in terms of academic integrity: 1. I expect that you will work hard at my course and take full responsibility for the grade you receive at the end of the semester. 2. I expect that you will do all of your own work on both quizzes and exams. In other words you will not receive or use any unauthorized assistance on both quizzes and exams. a. For quizzes this simply means that you will not allow someone else to give you the answers or to take the quiz for you. You may use any other resource (lecture notes, the book, powerpoint presentation etc) at your disposal for these assessments. b. For exams this means that you will take it and you will not use ANY resources other than the information recalled from your brain. To prevent unauthorized information from being used in the exam mobile or other electronic devices, including calculators, are strictly prohibited c. For exams the study materials that I permit are those found on blackboard. Students MAY NOT use old exams or practice exams from previous semesters as I cannot ensure each student has access to them.

6 3. I also expect that you will not GIVE unauthorized assistance on quizzes or exams. 4. I expect you to be honest in all your communication with me. In summary my desire is that this class maintains a HIGH level of academic integrity consistent with the Student Code of Conduct. If an academic integrity breech is uncovered I reserve the right to take disciplinary action including, but not limited to, giving the guilty student a failing grade. End of the Semester: I know that there will be a handful of people at the end of the semester that need just a few points to get the grade they desire. The extra credit assignments listed above will be designated as THE mechanism to get these points. I WILL NOT NEGOTIATE GRADES AT THE END OF THE SEMESTER. It is my expectation that you will accept the grade assigned to you and take responsibility for YOUR work throughout the semester. Grade negotiation always leads to someone receiving special treatment and is a policy that I cannot abide as I desire to maintain an atmosphere of academic honesty and integrity. If you are concerned about your grade please come and talk to me DURING the semester when something can be done about it. Schedule: I have posted a lecture and exam schedule online. I always ask my classes to be FLEXIBLE as I often fall behind. We will see what we get through and how much fun we can have doing it!

7 Lecture Schedule SUBJECT TO CHANGE DATE DAY TOPIC TEXT QUIZ (DUE DATE) 8/26 M Introduction 8/27 T Laying Foundations Lecture 1 Chapter 1 1 8/29 R Laying Foundations Lecture 1 Chapter 1 1 8/30 F Laying Foundations Lecture 1 Chapter 1 1 (8/30) 9/3 T 9/5 R 9/6 F 9/9 M 9/10 T 9/12 R 9/13 F 9/16 M 9/17 T 9/19 R 9/20 F 9/23 M 9/24 T Molecular Interactions in a Biological Context Lecture 2 Acid/Base Chemistry and the Limits of Biological Life Lecture 3 Acid/Base Chemistry and the Limits of Biological Life Lecture 3 Amino Acids: The Building Blocks of Proteins Lecture 4 Chapter 2 2 (9/3) Chapter 3 3 Chapter 3 3 (9/6) Chapter 4 4 (9/9) (9/24)

8 9/26 R Enzymes: The Catalyst of Biological Life Lecture 6 Chapter 6 6 9/27 F Enzymes: The Catalyst of Biological Life Lecture 6 Chapter 6 6 9/30 M Exam I (Lectures 1-5) 10/1 T 10/3 R 10/4 F 10/7 M 10/8 T 10/10 R 10/11 F 10/14 M 10/15 T 10/17 R Enzymes: The Catalyst of Biological Life Lecture 6 Enzyme Kinetics: Measuring and Comparing Enzyme s Abilities Lecture 7 Enzyme Kinetics: Measuring and Comparing Enzyme s Abilities Lecture 7 Chapter 6 6 (10/3**) Chapter 7 7 Chapter 7 7 (10/7**) (10/17) 10/18 F Membrane Proteins and Transport Lecture 9 Chapter /21 M Exam II (Lectures 6-8) LAST DAY TO WITHDRAW 10/22 T Membrane Proteins and Transport Lecture 9 Chapter /24 R Membrane Proteins and Transport Lecture 9 Chapter /25 F Membrane Proteins and Transport Lecture 9 Chapter 9 9 (10/28) 10/28 M Bioenergetics and Metabolic Themes Lecture 10 Chapter /29 T Bioenergetics and Metabolic Themes Lecture 10 Chapter /31 R Bioenergetics and Metabolic Themes Lecture 10 Chapter 10 10

9 11/1 F Bioenergetics and Metabolic Themes Lecture 10 Chapter /4 M Bioenergetics and Metabolic Themes Lecture 10 Chapter (11/4) 11/5 T Carbohydrate Metabolism Lecture 11 Chapter /7 R Carbohydrate Metabolism Lecture 11 Chapter /8 F Carbohydrate Metabolism Lecture 11 Chapter /11 M Carbohydrate Metabolism Lecture 11 Chapter /12 T Carbohydrate Metabolism Lecture 11 Chapter /14 R Carbohydrate Metabolism Lecture 11 Chapter (11/14) 11/15 F Metabolic Control - Lecture 12 Chapter /18 M Exam III (Lectures 9-11) 11/19 T Metabolic Control - Lecture 12 Chapter /21 R Metabolic Control - Lecture 12 Chapter /22 F Metabolic Control - Lecture 12 Chapter (11/22) 11/23-12/1 Fall Break 12/2 M The Citric Acid Cycle- Lecture 13 Chapter /3 T The Citric Acid Cycle- Lecture 13 Chapter (12/3) 12/5 R Oxidative Phosphorylation Lecture 14 Chapter /6 F Oxidative Phosphorylation Lecture 14 Chapter /9 M Oxidative Phosphorylation Lecture 14 Chapter /10 T Oxidative Phosphorylation Lecture 14 Chapter /12 R Oxidative Phosphorylation Lecture 14 Chapter /13 F Oxidative Phosphorylation Lecture 14 Chapter (12/13) 12/16 M Exam IV (Lectures 12-14) 4:10-6:10PM