BCH369_Syllabus56290_Fa14 - BCH 369 Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies Unique#56290 MW at 8:30-10:00 am in WEL 2.308 W

BCH369_Syllabus56290_Fa14 - BCH 369 Fundamentals of...

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Unformatted text preview: BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies Unique #56290: MW at 8:30-­‐10:00 am in WEL 2.308 W H A T IS B IO C H E M IS T R Y? Biochemistry is a branch of science involved in elucidating the structure, organization and function of living systems in molecular terms. It employs tools related to the disciplines of chemistry, biology, and physics and is therefore in many ways an interdisciplinary science. Yet biochemistry is its own distinctive discipline with regard to its emphasis on the structure and function of biological molecules. Note that in the physical sciences, such as chemistry and physics, the question of function is not relevant. An organic chemist may seek to understand the reactivity of various chemicals, but is not concerned with a particular purpose. Only in living systems does the question of function become relevant. Biochemistry is unique therefore in that it not only seeks to know the “what” – but also the “why.” In fact, THE most important question you will ask this semester is, “Why?” In the chemistry and physics courses you have had thus far you were mostly concerned with memorizing what was happening – and how, to a limited degree. With biochemistry – you will see that there is function and purpose in the myriad of chemical reactions that occur within the living cell. It is therefore less about memorizing and more about understanding – and this makes it endlessly fascinating to me. T E A C H IN G S T A F F Instructor: Dr. Gail Grabner (aka “Dr. Grabner” or “Dr. G”) WEL 5.266c 471-­‐1982 [email protected] Please be sure to specify the unique number of the section in which you are enrolled in your email correspondence. Office Hours: Mon, Tue, Thu: 12:00-­‐1:00 pm Or by appointment GTAs/Office Hours: Joshua Bryant: [email protected] Office hours: Tue 4:00-­‐5:00 pm Nicola Cole: [email protected] Office hours: Fri 9:00-­‐10:00 am Minhye Shin: [email protected] Office hours: Mon 11:00 am -­‐ Noon Location: ALL TA AND INSTRUCTOR OFFICE HOURS WILL BE HELD IN WEL 4.238 UGTAs: Ian Collier, Patrick Lawrence, Urvashi Mitbander, Quincy Zhuang Senior PLUS Preceptors: Kira Lowery, Ian Collier 1 Revised 8/18/14 BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies U S E O F C A N V A S IN C L A S S 1. We will be using Canvas as our web-­‐based course management system with password-­‐ protected access — to distribute course materials, to communicate and collaborate online, to post grades, to submit assignments, and to give you online quizzes and surveys. You can find support in using Canvas by calling the hotline at (855) 308-­‐2494. 2. The Home page contains the lecture schedule as well as hyperlinks to main pages within the Canvas site. a) The “Required Materials” page provides a list of all materials required for enrollment in BCH 369. b) The “Instructors” page provides a list of all teaching staff, as well as contact information and scheduled office hours. c) The “Web Resources” page contains a list of all external web links to be used for completing assignments, etc. It also contains a list, by chapter, of all additional links to animations or YouTube videos intended to enhance student grasp of the material. d) The “Lectures” page contains a list of all lecture-­‐related material – including chapter lecture files, class assignment worksheets, and access to unassigned lecture videos. There is also a link at the top of the page to provide access to lecture capture files. e) The “Exams” page contains the exam schedule, the exam review schedule, and information on how exams are graded. Information regarding unit exams as well as practice exams will be posted on this page as the semester progresses. f) The “PLUS” page contains information regarding the scheduled PLUS sessions and quizzes. Information will be added to this page as the semester progresses. g) The “Learning Tools” page contains links to documents intended to help students prepare for and take exams. In addition, all of the Learning Outcomes are posted here by chapter. These are the same as the study guides included in the custom edition of the text. 3. The materials used in this class, including, but not limited to, exams, quizzes, and homework assignments are copyright protected works. Any unauthorized copying of the class materials is a violation of federal law and may result in disciplinary actions being taken against the student. Additionally, the sharing of class materials without the specific, express approval of the instructor may be a violation of the University's Student Honor Code and an act of academic dishonesty, which could result in further disciplinary action. This includes, among other things, uploading class materials to websites for the purpose of sharing those materials with other current or future students. C O U R S E D E S C R IP T IO N , A IM S A N D O B JE C T IV E S Description This course is a one-­‐semester survey course designed for life science majors requiring only one semester of biochemistry. We will cover basic concepts about pH, biological buffers, bioenergetics, nucleotides, amino acids, proteins, enzymes, carbohydrates, lipids, intermediary metabolism, and molecular biology. The prerequisite for the course is 3 hours of organic chemistry with a grade of C or better. Aims Biochemistry is, in simplest terms, the study of the chemistry of living things. The general aim of this course, therefore, is to train students to understand biological processes and events by learning the logic of chemistry. It is far more than simply memorizing structures and pathways; the fascination of 2 Revised 8/18/14 BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies the field is to see how and why biological molecules are built the way they are and how this makes life possible – on many levels and with an amazing degree of coordination and control. The degree of biological sophistication that allows you to read this document and (hopefully) make sense of it is truly amazing! Learning Objectives: General • Learn the language of biochemistry • Be thoroughly familiar with the dynamic nature of all living systems • Understand and be able to apply the principles of thermodynamics to biological systems • Understand the principles that relate to spontaneity in biological systems and be able to predict whether or not a given reaction or process will be spontaneous • Know the basic compartments within a living cell and how they relate to basic biochemical systems • Understand and be able to apply the principles that govern the use of various techniques in the study of biochemical systems • Understand the basic principles that govern the interaction of various biological molecules • Understand the importance of balance in biological systems and the consequences of imbalance in terms of human disease In order to make sense of the material in this course, you should be asking at least some of the following questions ALL of the time: • HOW is this built or HOW does this work (structure/order)? • WHY is it built or WHY does it work this way (function)? o WHAT IF it worked a different way (order)? • HOW does this allow it to perform its role in the cell (context)? HOW does this interact with other molecules or processes (cross-­‐talk)? • HOW is this molecule or process activated or inhibited (regulation)? • HOW well does this work (redundancy)? • HOW can I know if this is happening (detection)? • HOW can I measure this (quantitative/qualitative analysis)? When you have completed the course you should: Water • Understand the intricate role of water in all living systems and how the various biological molecules interact in an aqueous environment • Understand the principles that relate to the influence of pH of living systems and the molecules that comprise these systems Structure and Function of Macromolecules • Understand the principle that structure always relates to function in biological systems • Be able to recognize the structures of basic biological molecules and identify their functional groups • Know and understand the types of chemical bonds present in biological molecules and their role in maintaining the structures of these molecules • Know and understand the nature and type of intermolecular interactions present in a given biological molecule 3 Revised 8/18/14 BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies • • • • • Be able to recognize oxidations and reductions of biological molecules and understand the role of temporary electron carriers Understand that small changes in form, structure, or energy content often relate to large overall effects Know the principles behind the role and effect of biological catalysts and be able to apply that understanding in the interpretation of experimental data Know the basic types of chemical reactions seen in biological systems and be able to recognize them Understand the nature and type of molecular interactions in communicating signals within living systems Transformation of Matter and Energy • Be able to recognize oxidations and reductions of biological molecules and understand the role of temporary electron carriers • Understand the basic principles of redox reactions and how they relate to energy transfer and utilization • Know the general principles governing the function and role of metabolic pathways • Understand, to some degree, the complex interactions of multiple metabolic pathways and the ways in which they are regulated Storage and Access of Genetic Information • Understand the nature of genetic material and how it is expressed into a functioning biological molecule and living cell Learning Objectives and aligned Course Objectives are given in greater detail according to textbook chapter in separate documents. These may be found on the course web site in Canvas. GENERAL COURSE FORMAT AND PROCEDURES I have three main goals as the instructor for BCH 369: 1) Help students learn to become independent learners 2) Help students learn to enjoy rather than dread biochemistry (yes – it’s possible!) 3) Help students learn to think like a biochemist YO U C AN G R O W YO U R O W N B R AIN As toddlers we learned our native language without formal instructions – we just assimilated it from our background influences. In fact, we all learn things every day without sitting in a classroom, though we often make use of printed or online resources to educate ourselves. Learning new things on your own initiative and without formal instruction in a classroom setting is as natural to humans as breathing – we do so constantly without giving it a second thought. In fact, this is one of the things that make us human – we assimilate information and grow our brains as a natural consequence of living out our lives. Somehow as we mature – we forget that we have this capacity and may begin to think of our intelligence as something that is fixed rather than dynamic. In this view, we are what we are and there’s nothing we can do about it. I took an IQ test, didn’t I? Doesn’t that mean I have a certain level of intelligence and that it can’t change? Let me give you a more specific example. The prerequisites for 4 Revised 8/18/14 BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies this course mean that you have taken general chemistry and at least one semester of organic chemistry. You’ve probably also taken some physics courses and may have also taken some biology courses. At this point – you may already have defined yourself as someone who “loves chemistry” or “hates physics” or maybe you think you’re “no good at biology.” Please note that these comments reflect this static view of intelligence. Research has shown that you can actually increase your intelligence – create more synapses and strengthen the ones you have. (See the course web site for an article on this.) This is great news! I can actually improve my brainpower – in a general way as well as in a specific subject. This means that I no longer have to adopt these negative self-­‐images I no longer need to define myself by my deficiencies. Instead, let us add a little word – “yet” – to our definition. Let’s say, “I’m no good at organic chemistry, YET.” What a difference a little word can make – because it represents a BIG concept! You can apply this same principle as you move along in this course. For instance, instead of saying – “I just can’t figure out this problem!” – say “I haven’t figured this problem out, YET!” If you practice and apply – you will actually create and strengthen your synapses. This means that problem solving will become easier and faster for you – that’s gotta help on exams, right? How do we accomplish this goal of growing our brains and becoming independent learners? As we enter the formal classroom, most of us adopt a strategy that would be classified as passive learning. It is often called the “sage on the stage” pedagogy. We got comfortable with the idea that the teacher would tell us what we needed to know – then we would go home and study. In most cases, this meant we memorized the material so that we could simply regurgitate it later. Then, we came back to the classroom so that we could take a quiz or exam and prove that we memorized the material. Some instructors – count yourselves lucky if you've had them – challenged us with questions that also assessed how thoroughly we actually understood what we’d memorized. Overall, this traditional model of the classroom means that the information gathering is done in class and the study is done at home. No doubt this this the model you have most commonly encountered – even here at UT-­‐Austin. FLIPPED C LASSR O O M M O D EL BCH 369 is NOT set up this way. Instead, information acquisition will be done at home and more in-­‐ depth study will take place during the class period. You will complete Learning Modules that will take you through the topics for the upcoming class period and take a short quiz to assess your understanding. Note that this moves lectures primarily out of the classroom and enables us to use that time for STUDYING and PROBLEM SOLVING. I hope you can see that by this method, you will do the easy part at home and the hard part – LEARNING – in a collaborative setting. Please keep in mind that the time you invest at home prior to class relates directly to our activities for the period. The time you invest in class is time you are using to LEARN the material and to STUDY for EXAMS. This will be especially important for a subject as challenging as biochemistry. You will find that by following this method, you will succeed where others have perhaps failed. Biochemistry is not a subject that can simply be memorized. You will have items – names, structures, mechanisms, etc. – that you will need to commit to memory. However, the most important aspect of the course is learning the connections between topics and to see how they are interrelated. Isn’t that how a living organism operates? Biological systems work in conjunction with one another – not in isolation. Regulation of pathways is a key theme in this course – so it is important to know the “Why?” related to the “How?” of cellular processes. In fact, THE most important question you will ask this 5 Revised 8/18/14 BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies semester is, “Why?” In the chemistry and physics courses you have had thus far you were mostly concerned with memorizing what was happening – and how, to a limited degree. With biochemistry – you will see that there is function and purpose in the myriad of chemical reactions that occur within the living cell. It is therefore less about memorizing and more about understanding – and this makes it endlessly fascinating to me. By adopting this approach, you will become less dependent on other people for your learning, and rediscover your ability to learn things on your own. You will be prepared to be a continuous learner, able to contribute something useful to the world in which you live. My purpose in adopting this approach is to achieve the three goals stated above. I trust you will see that you can become an independent learner, find biochemistry enjoyable, and actually understand the subject in a more meaningful way. B EFO R E C LASS Almost every class meeting will be focused around a central theme – though there will be sub-­‐topics associated with the general theme. To prepare for a class period, you will be given an assignment associated with a Learning Module. You will follow the assigned learning module and watch the embedded video content. Reading the associated pages in your text is ESSENTIAL to understanding the video content and assimilating the information. If you skip this step prior to watching the videos – it will take you MUCH longer to get through them. Among the video resources you’ll be given are videos from a playlist of YouTube videos I have created just for this course. Video lessons are meant to focus on a single topic and will generally be no more than 5-­‐7 minutes in length. Due to the complexity of a given topic, the video could be as long as 10 minutes – though this will be the exception rather than the rule. A key benefit to this approach is that you can watch the videos as many times as you like – and pause or rewind them when you need to. It also divides the subjects into more bite-­‐sized portions – a key factor in assimilating and processing the information. Although all of the content for the course is contained in these videos – not all of them are assigned as part of the learning modules. This is intended to keep the pre-­‐class work more time manageable – though you are responsible for the information contained in ALL of the videos. REMEMBER: you don’t have to watch all of the videos of the learning module in one sitting. This is another benefit of having short videos – you can watch one at a time and more easily fit them into your study schedule. If you only have a 15-­‐ minute window of time, you can watch at least one video – provided you have already read the text. As the last item in the module you will complete a short quiz on the video content, comprised of 7 multiple-­‐choice questions. These questions will assess your understanding of the material and will also provide you with feedback on potential problem areas. You are permitted unlimited attempts on these quizzes and your highest score will be recorded – based on the number of correct responses. However, you must score a minimum of 4 points in order to receive any credit for the quiz; scores of <4 points will be assigned a grade of “0.” The learning module, including watching the videos and completing the quiz, will be due one hour before class. This ensures that students are prepared for the day’s classroom activities. You will also complete a short survey each week composed of two questions: 1) to provide feedback on any concept or portion of the material that was still confusing to you; and 2) to indicate the subjects areas you found most interesting and why. Your response to these questions will guide the first portion of the next class period. In this way, I hope to address any outstanding questions you might have. These surveys are graded based solely on completion, but in order to receive credit for the surveys you MUST include a short, substantive answer for each question. Responses such as 6 Revised 8/18/14 BCH 369: Fundamentals of Biochemistry Fall 2014 Syllabus and Course Policies “Nothing,” or “Everything,” or “N/A” will NOT be given credit. This is your chance to let your voice be heard – because I read every single one of them! D U R IN G C LA SS The class period will be used primarily for problem solving. I will utilize the first 10-­‐15 minutes of one class period to address any outstanding questions from the surveys – focusing on the most common questions. The next portion of class wil...
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