CH369_Syllabus51780_F11(3) - CH369: Fundamentals of...

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Unformatted text preview: CH369: Fundamentals of Biochemistry Fall 2011 Unique #51780: 3:30 ­5:00 pm in WEL 2.224 What is biochemistry? Study of the structure and properties of molecules in living organisms and how those molecules are made, changed, and broken down. “Organic chemistry is the chemistry of carbon compounds. Biochemistry is the study of carbon compounds that crawl.” — Mike Adams Often seen quoted, though without source, for example, in Vassilis Mougios, Exercise Biochemistry (2006) “Now, a living organism is nothing but a wonderful machine endowed with the most marvellous properties and set going by means of the most complex and delicate mechanism.” — Claude Bernard An Introduction to the Study of Experimental Medicine (1865), trans. Henry Copley Green (1957), 63 Instructor: Dr. Gail Grabner (aka “Dr. Grabner” or “Dr. G”) WEL 5.266c 471 ­1982 Please keep in mind that emails received after 5 pm may not be answered until the following day. Office Hours: TAs/Office Hours: Tu: 10:30 ­11:30 am Th: 10:30 ­11:30 am Or by appointment Nicola Cole: Office hours: Mon 11:00 am ­Noon Eta Isiorho: Office hours: Fri 10:00 ­11:00 am Max Rubinson: Office hours: Wed 2:00 ­3:00 pm Location: All office hours will be held in WEL 4.238 Senior PLUS Preceptor: Kaitlin Whelan: I. Course 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. 1 Revised 8/24/2011 II. Course Aims and Objectives: 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 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 coordination and control. The degree of biological sophistication that allows you to read this document and (hopefully) make sense of it is truly amazing! Specific Learning Objectives: Throughout this course, you will see several recurring themes, which are: • The structure of a biological molecule always, ALWAYS relates to its function. • The function of a given molecule relates to its contextual role in the cell or organism. • There is always a degree of coordination of pathways and processes, which means there is ALWAYS some level of regulation. • Understanding the structure of a molecule also allows us to detect and measure it in meaningful ways – both qualitatively and quantitatively. • There is a certain flow of information within the cell and therefore an order to certain molecular events. • There are often redundancies in molecules or processes, in order to ensure that “life” keeps happening. 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 be able to: • Recognize the basic structures of biological molecules and be able to identify their functional groups • Understand and evaluate thermodynamic properties in order to understand if and how biochemical reactions occur • Apply the general principles of the Central Dogma of biology to the investigation and understanding of cellular processes • Understand basic protein architecture and how to use biochemical tools and techniques to analyze protein structure • Explain how enzymes function as catalysts and quantitatively measure their effectiveness • Recognize the different ways that enzymes can be inhibited and predict if and how that inhibition can be overcome • Recognize the general structure of lipids and understand how this contributes to their function in the cell 2 Revised 8/24/2011 Understand the thermodynamics and mechanisms of membrane transport and predict the flow of molecules in and out of the cell • Recognize the basic structure of carbohydrates and understand their role in molecular and cellular structure and function • Recognize many of the metabolic pathways of the cell and understand how they are regulated and integrated in the cell • Understand how chemical energy is generated through oxidative phosphorylation and how this process is regulated • Explain the process and significance of converting light energy into chemical energy • Understand the processes of lipid metabolism and how that impacts human health • Understand the mechanism of DNA replication and be able to relate this to DNA damage and repair • Summarize the processes that eventuate in the synthesis of RNA and protein • BE ABLE TO COMMUNICATE IN THE LANGUAGE OF BIOCHEMISTRY • BE ABLE TO UNDERSTAND AND APPLY THE PRINCIPLES OF BASIC SCIENTIFIC INVESTIGATION Course Activities to Meet Learning Objectives: We will be discussing material in lecture and – more importantly – you will be discussing things among yourselves in study sessions. You will also get practice in working through problems by using the WileyPlus system and by completing homework assignments in Sapling Learning. There will also be some in ­class assignments to complete as well as opportunities to earn extra credit. (See Section IV for specifics on course assignments.) III. General Course Format and Procedures: Lecture will be used as a time to emphasis major points in the assigned chapter(s) and to build an understanding of the material through explanation, in ­class quizzes (iclickers), and other in ­class assignments. Make sure you bring your “building materials” with you by: 1) reading the material in advance; 2) ALWAYS having a working iclicker with you; and 3) ALWAYS having something to write with and on. These in ­class assignments are not just a measure of attendance, but will also provide me with feedback on how well the concepts are being assimilated and how I can better help you to grasp them. IV. My Suggestions Learning is a very dynamic process – so don’t be surprised if it becomes challenging and even uncomfortable at times. All logical minds delight in reaching a conclusion and eliminating or reducing uncertainties, but this will not happen overnight – so please don’t get frustrated and give up! Please make use of instructor office hours and help sessions (mine and the course TAs), as well as the preceptor ­led study sessions – in order to facilitate and emphasize learning. If you find yourself struggling at ANY point – don’t suffer in silence! We are all here to help you – so be sure to let us know if you have questions or concerns. There is an important caveat I must add, though – that we will not simply give you the answers to your questions. Instead, our united goal as instructors is to help you find the answers and to make sense of them – we’re not interested in simply training “parrots.” Biochemical systems are very complex and can be confusing and difficult to grasp. If you find yourself confused about a topic – it often helps to ZOOM OUT. Look at the big picture to see common patterns; then once you have that clear, you can focus in on more of the details. There is an architecture in nature, and if you organize and build learning by moving from the simple to the more complex – your neurons will thank you! • 3 Revised 8/24/2011 V. Course Requirements 1. Attendance and punctuality a) Regular attendance – in body AND mind – is expected at all class meetings and random attendance will be taken throughout the semester by various means. b) Please be on time – late arrivals and early departures can be very disruptive to the instructor and to the other students. 2. Code of conduct a) I promise to make class as interesting and informative as possible, so please make every effort to be attentive. Please do no waste class time by texting, sending emails, reading newspapers, watching YouTube, sleeping, etc. – I’d rather that you stay home rather than distract other students who are truly interested in learning. b) If you have trouble hearing due to such distractions, quietly ask the person to stop. If this doesn’t help, let me know. c) Please be respectful of others – instructors as well as fellow students – in all comments and questions. This respect should be manifest in word, in tone, and in conduct. 3. Religious Holy Days By UT Austin policy, you must notify me of your pending absence at least fourteen days prior to the date of observance of a religious holy day. If you must miss a class, an examination, a work assignment, or a project in order to observe a religious holy day, I will give you an opportunity to complete the missed work within a reasonable time after the absence. 4. Course Readings/Materials a) Essential Biochemistry, 2nd edition, Pratt and Cornely – available as a new softcover at the Coop. The new 2nd edition is very similar to the 1st edition, but the order of the chapters is changed – some are merged, some are separated. If you want to use the first edition – be aware that there are differences and you will have to pay closer attention in class to catch anything not in the first edition. b) Sapling Learning: Homework assignments will be available at this web site and must be completed online. (See note under Section 5 regarding homework.) Students will need to set up an account and pay for this service ($29.95) using the above URL, but enrollment will be done en masse when I forward the class roster to Sapling. Please note that this will mean that no homework can be completed using any name other than one enrolled in this course. c) iclicker 2 If you already have an iclicker1 device, it should still work with the new iclicker2 base unit and software. iClickers will be used in class for various purposes and for extra credit . Please be sure to have your clicker starting on the first day of class and make sure it has been properly registered in Blackboard. Click on the link for Blackboard Tools on the left border. Click on the link for “Register Your i>clicker remote ID” and follow the prompts. Please keep in mind that you can’t receive credit for in ­class quizzes if your clicker isn’t properly registered. d) Students will also need a scientific calculator for taking exams. (See note under Section 3 regarding exams.) e) We will not be using the WileyPlus resources for this course, since not all students have ready access. It is, however, an excellent way to get more practice if it is available to you. Students who have recently purchased the 2nd edition of the Pratt and Cornely text are granted free access. 4 Revised 8/24/2011 5. Assignments, Assessment, and Evaluation a) Graded homework for each chapter (22, total) will be assigned through Sapling Learning for a maximum of 60 points (4 points each, highest 15 will be counted). The homework assignments will help to assess your understanding of the chapter material, as well as provide practice in working through example problems. Please be careful to note the due dates and times for each homework assignment. Because there are multiple opportunities to earn credit for homework assignments, late submissions will NOT be allowed. b) Four exams (100 points each) will be given, and the lowest exam score will be dropped. No make up exams will be given for interviews, weddings, or personal events of any kind. In the case of a documented illness, a make up exam may be considered. (See Section 8 for Exam Rules.) c) The comprehensive final is scheduled for Thursday, December 8 at 9:00 am to Noon and will be worth 140 points. Be sure to check your calendars NOW for any conflicts. There will be no early finals due to interviews, weddings, early flights, etc. You should plan to drop the class if you cannot take the final. d) There will also be in ­class assignments associated with each lecture, worth a maximum of 30 points (24 quiz/assignments worth 2 points each, accumulate up to 30 points). Students who simply “click in” will receive 1 ­point credit; full credit is given for correct answers. These will be mostly in the form of iclicker quizzes, as noted on the schedule. These are intended to keep students up to date on the readings and will also provide feedback on how well concepts have been grasped. These assignments and quizzes are not intended to be difficult – doing well will simply mean reading the chapter in advance and paying attention in lecture. Please keep in mind, however, that “clicking in” for someone else is a violation of academic integrity and will be dealt with accordingly. 6. Exam Rules Exams will are scheduled in the evening from 7:00 ­9:00 pm in order to accommodate two sections. There will be no scheduled lecture on exam days. Exams WILL NOT be individually rescheduled or postponed except for documented medical reasons. Assigned seating will be used during exams. Please check Blackboard for your assignment the day before the exam. Thurs, Sept. 15, Chapters 1 ­5 Thurs, Oct. 6, Chapters 6 ­10 Thurs, Oct. 27, Chapters 11 ­15 Thurs, Nov. 17, Chapters 16 ­19 Final: Dec. 8, 9:00 am  ­ Noon (comprehensive chapters 1 ­22) a) b) c) d) e) Seating will be assigned for each exam and final. Backpacks, notebooks, books, papers, etc. will be placed in the front of the room. Students will not talk during the exam except to the instructor or TAs. Remove hats and caps during the exam – 5 points will be deducted for wearing one. No graphing calculators or programmable hand held devices or any electronic equipment of any sort (e.g. Palm Pilots, phones, cameras, computers, scanners etc) – use of one will result in confiscation and a loss of 30 points on the exam. f) You may use a simple scientific calculator, e.g., TI ­36S Solar Calculator (~$15) or learn to use the log tables for pH and buffer problems. g) No cell phones or pagers or any other electronic equipment – turn them off and place at front of room! 5 Revised 8/24/2011 7. Important Academic Dates a) Sept 9: Last day to drop b) Oct 19: Last day to change Pass/Fail status c) Nov 1: Last day to drop with approval 8. Use of Blackboard in class a) In this class I use Blackboard—a Web ­based course management system with password ­protected access at —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 Blackboard at the ITS Help Desk at 475 ­9400, Monday through Friday, 8 a.m. to 6 p.m., so plan accordingly. b) Please note that with Blackboard 9.1, the instructor no longer controls whether or not email notices are sent when new items or announcements are posted on the web site. After entering Blackboard, click on the Notifications Dashboard tab. Click on any of the buttons labeled “Edit Notification Settings.” On this page, you can edit an individual course or you can edit “Courses I Am Taking” – I recommend you do the latter. Use the page that pops up to change your notification settings. VI. Additional Resources 1. PLUS (Peer ­Led Undergraduate Studying) a) This course will make use of the PLUS program to enhance student familiarity and proficiency in biochemistry. The PLUS program benefits both faculty and students enrolled in their classes. Students in PLUS ­supported courses have a more positive overall experience in the class and typically perform better than their peers. Faculty has the opportunity to get to know a select group of highly motivated students throughout the semester – and these benefits come with only a minimal time commitment (less than 1 hour a week) and at no cost! You can read more here: b) Students who are interested in participating in this program as a preceptor will find the application form on the Announcements page in Blackboard. c) There are regular PLUS study sessions scheduled each week (see schedule in Blackboard) that will be monitored by selected preceptors. The topic of the each of the study sessions during the week will not vary and students are welcome to attend any one of these sessions during any week. d) To encourage student participation, students who attend and participate in the study sessions will have the opportunity to earn extra credit points (see Section 2 below) through online quizzes in Blackboard. 2. Extra credit Several opportunities will be given to earn extra credit points, up to a maximum of 8 points, as follows: a) Quizzes will be available bi ­weekly in Blackboard, which will consist of 5 questions related to the topics of the PLUS study sessions for the week. Each question will be valued at 0.2 points for a total of 1 point of extra credit for each quiz. You may take as many of these quizzes as you like, but keep in mind that there is a maximum number of extra credit points that can be accumulated. Quizzes will open 15 minutes after the end of a given study session and will remain open for 30 minutes. They will be password ­protected, and the password will be announced at the study session immediately preceding the quiz. Please note that the passwords will differ 6 Revised 8/24/2011 depending on the study session (e.g. the Tues PW will differ from the Wed PW). The intent is to ensure that students actually attend the study session before taking the quiz. b) There may also be certain iclicker questions used in lecture that may count as extra credit points. c) In the interest of encouraging creativity and fun, students may also earn extra credit by performing one of the songs from “The Biochemists’ Songbook” by Harold Baum (1 ­2 points). These are topic ­related, so you must check with me first so that I can allow time in lecture. (Yes, you will be performing for the whole class.) There is no need to buy a copy of the book – I can get you the info you need. You can also check out the MP3 recordings of these songs here: If you believe in “safety in numbers” – you can perform one of these songs as a group of up to 4 students. d) Opportunities for extra credit may be modified during the course of the semester. 3. Interactive animations and a cool ­ish amino acid game may be found at: The amino acid game is a great way to learn the structures of the 20 common amino acids. VII. Grading Procedures 1. Your total accumulated points will be comprised of the following: Unit exams: 300 points Final exam: 140 points Homework: 60 points In ­class quizzes: 30 points TOTAL: 530 points 2. Course grade totals are NOT curved – what you see is what you get. Grades are NOT determined by percentage, but by total accumulated points. A total of 476 points is a B+, but fractions are rounded to the nearest whole number; e.g. 476.5 or above will be rounded to 477 (A ­). The full range of course grades (plus and minus) will be used, as follows: A: 493 ­530 C: 387 ­407 A ­: 477 ­492 C ­: 371 ­386 +: 461 ­476 B D+: 355 ­370 B: 440 ­460 D: 334 ­354  ­: 424 ­439 B D ­: 318 ­333 +: 408 ­423 C F: <318 3. It has been observed that if you score well below 50 on the first exam it is highly unlikely that you will score better on subsequent exams. This generally means you have too heavy a course load or are distracted by something in your personal life and do not have the time necessary to keep up with the material. Please pay careful attention to the drop dates and should illness or personal issues cause you to fall behind, immediately contact a College of Natural Sciences counselor (471 ­4536, WCH 1.106) and let me know. Generally these kinds of issues affect more than one class and the counselors can help you figure out which classes to drop. It is much better to drop the class than end up in trouble at the end of the semester. 7 Revised 8/24/2011 VIII. Academic Integrity University of Texas Honor Code The core values of The University of Texas at Austin are learning, discovery, freedom, leadership, individual opportunity, and responsibility. Each member of the university is expected to uphold these values through integrity, honesty, trust, fairness, and respect toward peers and community. Students who violate University rules on scholastic dishonesty are subject to disciplinary penalties, including the possibility of failure in the course and/or dismissal from the University. Since such dishonesty harms the individual, all students, and the integrity of the University, policies on scholastic dishonesty will be strictly enforced. Students are encouraged to study together and to discuss information and concepts covered in lecture and the sections with other students. However, this permissible cooperation should never involve one student having possession of a copy of all or part of work done by someone else, in the form of an e ­ mail, an e ­mail attachment file, a diskette, or a hard copy. Collaboration is not allowed on any of the graded course assignments, except on allowed in ­class assignments. Students are expected to do their own work during exams. Talking or discussion is not permitted during the examinations, nor may you compare papers, copy from others, or collaborate in any way. Any collaborative behavior during the examinations will result in failure of the exam, and may lead to failure of the course and University disciplinary action. IX. Other University Notices and Policies Use of E ­mail for Official Correspondence to Students • All students should become familiar with the University's official e ­mail student notification policy. It is the student's responsibility to keep the University informed as to changes in his or her e ­mail address. Students are expected to check e ­mail on a frequent and regular basis in order to stay current with University ­related communications, recognizing that certain communications may be time ­critical. It is recommended that e ­mail be checked daily, but at a minimum, twice per week. The complete text of this policy and instructions for updating your e ­mail address are available at : . Documented Disability Statement Any student with a documented disability who requires academic accommodations should contact Services for Students with Disabilities (SSD) at (512) 471 ­6259 (voice) or 1 ­866 ­329 ­3986 (video phone). Faculty are not required to provide accommodations without an official accommodation letter from SSD. (Note to Faculty: Details of a student’s disability are confidential. Faculty should not ask questions related to a student’s condition or diagnosis when receiving an official accommodation letter.)  Please notify me as quickly as possible if the material being presented in class is not accessible (e.g., instructional videos need captioning, course packets are not readable for proper alternative text conversion, etc.).  Please notify me as early in the semester as possible if disability ­related accommodations for field trips are required. Advanced notice will permit the arrangement of accommodations on the given day (e.g., transportation, site accessibility, etc.). 8 Revised 8/24/2011  Contact Services for Students with Disabilities at 471 ­6259 (voice) or 1 ­866 ­329 ­3986 (video phone) or reference SSD’s website for more disability ­related information: Behavior Concerns Advice Line (BCAL) If you are worried about someone who is acting differently, you may use the Behavior Concerns Advice Line to discuss by phone your concerns about another individual’s behavior. This service is provided through a partnership among the Office of the Dean of Students, the Counseling and Mental Health Center (CMHC), the Employee Assistance Program (EAP), and The University of Texas Police Department (UTPD). Call 512 ­232 ­5050 or visit IX. Letters of Recommendation Letters of recommendation will include your class grade, ranking in the class, and your level of participation as judged by extra credit (including attendance days) and homework turned in, etc. I generally only answer questions on forms that may be answered based on grades. You should come to office hours several times during the semester so that I may get to know you better if you want additional remarks. Remember there are 300+ in the class. X. Tentative Course Schedule: All readings refer to chapters in the Pratt & Cornely text. Students are STRONGLY encouraged to read the relevant pages BEFORE the scheduled lecture to be of highest benefit. Lecture is the best time to ask questions and clarify key points in order to build your understanding – but you can’t build unless you first look at the blueprint! Lecture topics may need to be adjusted from time to time – to best serve the needs of the students. Because of this possibility, exam material may also be altered – but the exam dates will remain fixed. Any changes will be announced in Blackboard at the earliest possible time. Lecture notes will be posted in Blackboard AFTER class. DATE TOPIC READING 8/25 Course intro; Chemical Basis of Life Ch 1 8/30 Aqueous Chemistry Ch 2 9/1 Molecular Biology Overview Ch 3 9/6 Protein Structure Ch 4 9/8 Protein Function Ch 5 9/13 Features of Enzymes Ch 6 Sept 9 Last Day to Drop  ­ ­ Sept 15 EXAM 1* Ch 1 ­5 9/20 Enzyme Kinetics Ch 7.1 ­7.2 9/22 Enzyme Inhibition Ch 7.3 9/27 Lipids & Membranes; Passive Transport Ch 8; Ch 9.1 ­9.2 9 Revised 8/24/2011 DATE TOPIC READING 9/29 Active Transport; Signaling Ch 9.3 ­9.4; Ch 10 10/4 Carbohydrates Ch 11 Oct 6 EXAM 2* Ch 6 ­10 10/11 Overview of Metabolism Ch 12 10/13 Glucose Metabolism Ch 13 10/18 Citric Acid Cycle Ch 14 Oct 19 Last Day to change Pass/Fail  ­ ­ 10/20 Oxidative Phosphorylation Ch 15 10/25 Photosynthesis Ch 16 Oct 27 EXAM 3* Ch 11 ­15 11/1 Fatty Acid Metabolism Ch 17.1 ­17.2 Nov 1 Last Day to Drop w/ Approval  ­ ­ 11/3 Synthesis of Other Lipids; Nitrogen Assimilation; Amino Acid Biosynthesis Ch 17.3; Ch 18.1 ­18.2 11/8 Nucleotide Biosynthesis; Amino Acid Catabolism & N Disposal Ch 18.3 ­18.5 11/10 Regulation of Fuel Metabolism Ch 19 11/15 DNA Structure, Replication, & Telomeres Ch 20.1 ­20.3 Nov 17 EXAM 4* Ch 16 ­19 11/22 DNA Repair & Packaging; Transcription Initiation Ch 20.4 ­20.5; Ch 21.1 Nov 24 THANKSGIVING HOLIDAY  ­ ­ 11/29 RNA Polymerase & RNA Processing Ch 21.2 ­21.3 12/1 Translation Ch 22 Dec 8 FINAL EXAM: 9:00 am  ­ Noon Ch 1 ­22 *Exams are scheduled in the evening in order to accommodate two sections. There is no lecture scheduled on the day of the exam. 10 Revised 8/24/2011 ...
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