BIO 3513 Spring 2019 Syllabus PDF

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Biochemistry BIO 3513 Syllabus Spring 2019 Instructor: James P. Chambers, Ph.D., Professor of Biochemistry ([email protected]) PLEASE READ CAREFULLY WELCOME to Bio 3513, Introductory Biochemistry. This is a chalk/blackboard lecture course. Success in this course is premised upon time honored and proven classroom skills and activities: 1) attending class (mandatory), 2) paying attention during class, and 3) careful study of lecture notes and outside preparation. Thus, to insure achieving student expectations and success, students must purchase a textbook , attend class, take notes, work all assigned problems in a timely meaningful manner , and commit the needed time, i.e., a minimum of 10 hours/week in addition to classroom lecture time. Listed for your perusal are a few unsolicited comments by some of your contemporaries who took to heart the above advice while taking the course: Student #1: Hello Dr. Chambers, I just wanted to let you know that I sincerely enjoyed your biochemistry class last semester and feel like it has been one of the best classes I've taken at UTSA. I'm sure you're aware of your intimidating nickname "Chainsaw Chambers" among students, but even in spite of that, I have eagerly sent my friends your way to take biochemistry because of how much I gained from your lectures and this course. Student #2: Your course fascinated me more than any other course I have taken here at UTSA because it pieced together the concepts of my other science courses and really brought medicine to life. I received an A in your course, which took a lot of effort but it was honestly the most excited I've been about studying for any course I've ever taken! Many of my friends who took other biochem courses got A grades but when we get together to compare notes it was very apparent to me who knew the most. You really prepare your students. Student #3: Hi Dr. Chambers, I recently had occasion to rummage through the pile on my desk in my old lab (I recently switched positions due to my prior PI moving to another university) and

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Pulled out my big, bright, red Stryer textbook. Of all the textbooks I read and bled over in college, this was the one that I kept. I dug through it, curious to see where I'd left bookmarks and what bits of notes were shoved here and there (I did actually need it as a reference for a few years) and I came across the syllabus from Fall 1999, when I took your class. Boy, you were one tough guy. But you know what? Thank God you were, because in the now 18 years I've been working in labs (I did in high school and through college) there is nothing I did in a class that was harder than the real-life, actual thinking I've done as a technician and now lab manager. Textbooks and lectures do not prepare you for things like serial electron microscopy and the creation of developmental models, or composing sections in papers. What does is being told that only hard work and simply showing up -mentally and physically. I'm a well-respected member of UT's research staff now (I've been here for 12 years), and have solid relationships in several departments and across disciplines. Only a handful of professors at UTSA helped make that happen and I'm proud to say that you were one of those very few. I only got a C in your class, and at the time that bothered me a bit. It doesn't matter at all now, of course, but the neat thing is that I actually learned so much from your lectures and know how to find what I need when I have biochem questions put to me by the undergraduates and graduate students I supervise and train. Like you say, brains, textbook, and chalk equal learning, and I hope that I like you can instill the hard-work attitude and enthusiasm necessary to do real science. I might just hang on to my Stryer. And your syllabus. Thanks so much, Dr. Chambers for your probing, pushing, shoving, and tireless dedication. There are other biochem courses but there is only one like yours. Student #4: Hi Dr. Chambers, I just wanted to let you know that I was just accepted into Medical School yesterday, and will be starting this coming Fall. I appreciate the wisdom and encouragement you shared with me throughout biochem, as well as all that I learned in class. I feel very confident entering this next level most in part due to your dedication, drive, and mastery in teaching this really important course. Student #5: Dr Chambers,

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Thank you very much! I really enjoyed learning biochemistry from you and appreciate your professionalism and approach to the class. You are a shining example of what your mentor inspired you to be and I know he is proud. I also wanted to let you know I got into both VCU and UTHSCSA dental schools! Since we are happy, personally and professionally here, I'll be starting dental school at the HSC next summer! I look forward to keeping you updated on my progress. Student #6: Hel l oDoct orChamber s ! Ij ustwantt osayt hanky ousomuchf oranamaz i ngsemest er .Il ear nedso much!Ihav ement i onedt oy out hatIam pr emed,andt ooky oubecaus eIhear d t haty ouwer et hebes tf orpr eppi ngf ort heMCAT,andIwasnotdi s appoi nt ed.I can' tt el ly ouhowhappyIam t ohav eanear nedanAi ny ourc l ass.Iputal otof effor ti nt ot hecl ass ,andi t ' soneoft hecl as sesI ' m mostpr oudoft ohav eear ned t hatAi n.Agai n,t hanky ousomuchf ort hegr eatsemest er ! St udent#7: Hi Dr. Chambers: I just wanted to thank you for this past semester of Biochemistry. It was certainly the most challenging, and best class that I've taken here at UTSA. I am better for it as I go on (hopefully) to medical school. I appreciate your time and dedication to make your students excellent. ________________________________________________________________ Office Hours: 5:15 PM, M/W, Flawn 2.03.08. Sunday Evening Biochemistry Review: This review is offered by the Instructor gratis to help students. It is not mandatory. BSE 3.106, 7:00 PM. Clinical Seminars: These seminars are offered by Dr. Chambers gratis as an enrichment for interested students. Attendance at these seminars is not mandatory. TBA Teaching Assistant: Elizabeth Moreno-Smiley ([email protected]) Textbook: Biochemistry: A Short Course-Tymoczko, Berg and Stryer, Third Edition

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Prerequisites: Chem. 2203 and Chem. 2242; Bio 2313 is also recommended Course Objective This is a Chemistry course with biological/human disease relevant applications requiring facile use of fundamentals learned in General and Organic Chemistry. The objective of this course is to examine key chemical concepts underlying Biochemistry, i.e., structure/function, metabolism, and bioenergetics. Course Description This course is a demanding, one semester course in Biochemistry that attends to the basic conceptual needs of pre-professional students seeking matriculation/transitioning into Medical, Dental, and Veterinary curricula. Execution of the Course Prior to the start of class: Once roll is taken, all electronics must be turned off and properly stowed away. The only exception to this is the retaking of roll at the end of the class. The use of Laptop computers for the purpose of taking notes will not be allowed. Attendance: Attendance is mandatory regardless of one’s membership in Mensa, and/or savant, genius, Albert Einstein acuity-like status. As such, you may be able to master this material in Dr. Chambers’ absence and consider attending class as unnecessary. If the case, you need to withdraw immediately and take a different course. Attendance will be taken the first few minutes prior to the lecture. Therefore, it is important to be in class on time. TopHat is the program that we will use for rapid roll taking. All students must register no later than January 23, 2019 for this program at TopHat.com. The respective ‘join codes’: M/W Section 0.001 (733173) and M/W Section 0.002 (678679). Students must have either an I-Phone, I-Pad, Cell phone of any kind, or laptop computer for participating/responding. Once attendance is electronically, the respective join codes will be closed. if you are tardy, you will be counted absent. Do not leave class early-often times, we will retake the roll and/or administer class quizzes at the end of class. Dr. Chambers understands fully that events do occur outside of one’s control, e.g., TDY assignments if military, accidents, illness, death of a family member, children becoming sick, etc. Therefore, it is imperative that if you are experiencing difficulties outside of your control or if an emergency arises, you must notify Dr. Chambers of such developments. We are dedicated to helping students and will work with students experiencing unforeseen difficulties. Class Quizzes: Quizzes will be administered via TopHat either at the beginning/end of class, i.e., after taking roll or just prior to the end of class.

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Assigned problems: Working all of the assigned problems in a timely manner, i.e., concurrent with the respective lectures is very important. This is how you will become facile with 1) the fundamental concepts being presented in the respective lectures, and 2) important supporting material that is not covered in class. Assigned homework problems will not be graded but have a great tendency to appear on Examinations. Thus, it is to your great advantage to work and study the assigned problems in a timely fashion as we cover the related topics. Learning objectives: Prior to each lecture, ‘Learning Objectives’ will be reviewed serving as a roadmap as to where we are and where we are going, helping the student to focus on and integrate the key principles being presented. Examinations: There are three ‘in class’ examinations including the Final Examination. On all examinations, you must show all work, i.e., calculations, pathways, etc. to receive credit for your response. In order to take the Examinations you must bring with you 1) a standard calculator, and 2) ParSCORE test form compatible with Scantron 48/TSM-50 answers per side (the form must allow you to ‘bubble in’ your Banner ID #). Please do not use old, wrinkled, soiled, erasure laden ParSCORE Test Forms. If used, your examination will not be graded correctly indicating that you did not take the Examination (cf. above). You must know your student ID Number. THIS IS NOT YOUR SS#. The Instructor will diligently try to adhere to the examination (Examinations 1 and 2) schedule listed below; however, if extenuating circumstances arise, e.g., coverage of a specific body of information, may necessitate modification of the examination schedule. The Final Examination (Examination 3) date (subject to student verification) is not set by the Instructor and cannot be changed. The Final Examination is cumulative and is counted twice. A word of warning-if you have an ‘A’ on the first two Examinations, and do poorly, i.e, make less than a 'B' on the Final Examination, you will receive a ‘C’ in the course. This is a consequence of the weighted nature of the Final Examination. This is by design. You must make an ‘A’ on the Final Examination to obtain an ‘A’ in the course. Regardless of the average of the two previous examinations, e.g., a ‘D, C, B’, if the student makes an 'A' on the Final Examination, the student will be assigned as final course grade the Final Examination grade, i.e., an ‘A’ provided the student has taken all examinations, and attended class regularly (please see Instructor Discretion). Therefore, it is to the student’s advantage to attend class regularly, and continue to work hard for the Final Examination regardless of scores on Examinations 1 and 2. Examinations 1 and 2 will be returned during class. If for some reason you take an examination and receive a score of ‘0’ (suggesting a grading error) indicating that you did not take the examination, YOU MUST notify the Instructor immediately. The Final Examination will not be returned to the student nor is it reviewable by the student following completion of the course. However, if you should have any

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question regarding the Final Examination, please notify Dr. Chambers such that he can examine the Final Examination to insure that no error/miscalculation has occurred in grading the Final Examination and/or the grade for the course. Course Grade: Shown below is the grading scale used in this course. A = 89.5+ % B = 79.5-89.49 % C = 60-79.49 % D = < 59.5 % F = Failure to take all three examinations, excessive absences, e.g. 6+, and Instructor Discretion if applicable. Midterm Grades: In general these grades are useless and are not meaningful considering the above explanation of course grading policy. They will be based upon whatever information we have at the time of submission. Thus, these grades have no bearing on your performance in the course. However, if a student has not adhered to the rules of engagement regarding the execution of this course, e.g., texting in class, participating in social media, excessive absences, etc., at the Instructor’s discretion ( cf. Instructor Discretion ), the midterm grade may take on significant meaning as to one’s continuation in the course. Instructor discretion: At the discretion of the Instructor , a grade can be lowered by the Instructor. For example, if you choose to text, talk, participate in social media, be disruptive, etc., subsequent to being warned by the Instructor regarding such activities, your grade will be lowered without any warning/discussion at the discretion of the Instructor. Examination Schedule As previously stated, ALL Examinations will be given in ParSCORE format and all answers must be recorded on ParSCORE Test Forms compatible with Scantron 48/TSM Scanners-50 answers per side, (available in the UTSA Bookstore). Examination #1-February 13, 2019 Examination #2-April 3, 2019 Examination #3-FINAL EXAMINATION-See ASAP Examination Schedule for the date, place, and time. You must verify! Make-up examinations are strictly up to the discretion of the Instructor. Make-up examinations are given ONLY in the Department of Biology Office according to a set schedule.

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The Instructor Dr. Chambers is Professor of Biochemistry, Department of Biology, The University of Texas at San Antonio. He has taught Biochemistry going on 50 years at Undergraduate, Graduate, and Professional School (Medical and Dental School) levels. Dr. Chambers is a consummate professional, recipient of numerous teaching and research awards. The Instructor encourages students to make known any and all concerns regarding issue(s) germane to the execution of this course by contacting the Department of Biology (Main Office, BSE 1.601, 458-4511) and/or contacting the Dean of the College of Sciences (BSE 2.110, 458-4450). Course Evaluation Attendance is critically important to succeeding in this course. Evaluating a course that you did not faithfully attend is not helpful nor ethical. Therefore, only students who have attended the course on a regular basis will be encouraged to participate in the survey of the course. The course will be surveyed objectively in anonymous fashion according to the Syllabus which describes in detail the execution of the course, the expectations of the Instructor as well as the implied/understood expectations of the student. This semester, the course evaluation will be conducted April 1-15. The survey will be conducted in class, and only those participating in class will be given participation points. University Policy on Dishonesty Students are expected to be above reproach in scholastic activities. Students who violate University rules on scholastic dishonesty are subject to disciplinary penalties, including the possibility of failure in the course and dismissal from the University. Please become familiar with Regents’ Rules and Regulations, Part One, Chapter VI, Section 3, Subsection 3.22. Since scholastic dishonesty harms the individual, all students, and the integrity of the University, policies on scholastic dishonesty will be strictly enforced. Chapter topics will be covered in the order shown. Chapter 2: Water, and weak bonds. Assigned Problems: 1-20, and 22. Chapter 3: Amino acids. Assigned Problems: 3-15. Chapter 4: Protein three-dimensional structure. Assigned Problems: 1-10, 12, 13, 15, and 16.

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Chapter 9: Hemoglobin, an allosteric protein. Assigned Problems: 1, 5-6, 8-10, 12-15, 18 and 19. Chapter 6: Basic concepts of enzyme action. Assigned Problems: 1-3, 5-14, 16-20. Chapter 7: Kinetics and regulation. Assigned Problems: 1, 3, 4, 6-8, 10, 14, 15, 17, 22, and 23. Chapter 8: Mechanisms and inhibitors. Assigned Problems: 2, 3, 5-7, 10, 11, 13, and 16. Chapter 10: Carbohydrates. Assigned Problems: 2-8, 12, and 13. Chapter 11: Lipids Assigned Problems: 1-3, 5-10, 12, 13, 15. Chapter 12: Membrane structure and function. Assigned Problems: 1-7. Chapter 15: Metabolism: basic concepts and design. Assigned Problems: 5-14, 15, 16, 18, 19, 21, and 22. Chapter 16: Glycolysis. Assigned Problems: 2-9, 11, 14, 16, 17, 20, 21, and 23. Chapter 17: Gluconeogenesis. Assigned Problems: 1-10, 12, 13, 17, 23, and 25. Chapter 18: Preparation for the cycle. Assigned Problems: 1-6, 8, 9, 11, 13, and 14. Chapter 19: Harvesting electrons from the cycle. Assigned Problems: 2-5, 8, 10, 11-14. Chapter 20: The electron-transport chain. Assigned Problems: 1, 4, 6-8, 10, and 11. Chapter 21: The proton-motive force. Assigned Problems: 2-4, and 11. Chapter 24: Glycogen degradation. Assigned Problems: 1-4, 6, and 7. Chapter 25: Glycogen synthesis.

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Assigned Problems: 1, 2, 4-6, 8, and 12. Chapter 26: The pentose phosphate pathway. Assigned Problems: 1-9. Chapter 27: Fatty acid degradation. Assigned Problems: 3, 5-8, 10-12. Chapter 28: Fatty acid synthesis. Assigned Problems: 1-4, 6-8, 11, 12, 14, and 17. Chapter 30: Amino acid degradation and the urea cycle Assigned Problems: 8-10, and 12. Chapter 31: Amino acid synthesis Assigned Problems: 11, 12, 14, 17, 18, and 23. Chapter 32: Nucleotide metabolism. Assigned Problems: 1, 4-6, 8-15.

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Sample Examinations-please note the ParScore format and be aware that there are errors in these drafts. These examinations give you a flavor for the types of questions, and the format that you will encounter. Examination 1 1. Calculate the hydrogen ion concentration [H +] in blood plasma, pH = 7.40. A. B. C. D. E.

1.6 x 10-2 M 3.9 x 10-8 M 2.5 x 10-7 M 5.0 x 10-7 M 1.0 x 10-5 M

2. Which of the following statements is true? A. The φ and ψ angles about the α-C of amino acids in a polypeptide determine the path of the polypeptide because all combinations of φ and ψ angles are allowable. B. If the pH of a diabetic’s blood is 6.9, the [H +] is less than 10-7.4M C. In the formation of the ES complex, the water becomes highly ordered about the substrate thus the Second Law of Thermodynamics is violated. D. The Hydrogen bond is about 10 % covalent in nature due to the overlaps in the bond orbitals, and about 90% electrostatic. E. The Second Law of Thermodynamics states that the entropy of the universe decreases in all spontaneous processes. 3. Consider the following reaction: Glucose 1-phosphate ↔ Glucose 6-phosphate After the reactants and products were mixed and allowed to reach equilibrium at 25 0C, the concentration of each compound was measured: [Glucose 1-phosphate]eq = 0.01 M [Glucose 6-phosphate]eq = 0.19 M The ΔG0’ = A. B. C. D. E.

+4.5 kJmole -1 -2.4 kJmole -1 -7.4 kJmole-1 +7.0 kJmole-1 +3.0 kJmole -1

4. Calculate the pH of a dilute solution that contains a molar ratio of potassium

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acetate to acetic acid (pKa = 4.76) of 2:1. A. B. C. D. E.

3.76 4.76 5.46 4.28 None of the above

5. In a highly basic solution, pH = 13, the dominant form of alanine (R group in parentheses) is: A. NH2-HC-(CH3)-COOH B. NH3+-HC-(CH3)-COOH C. NH-HC-(CH3)-COOD. NH2-HC-(CH3)-COOE. NH2-HC-(C+H3)-COO6. A dye that is an acid and that appears as different colors in its protonated and deprotonated forms can be used as a pH indicator. Suppose that you have a 0.001 M solution of a dye with a pK a of 7.2. From the color, the concentration of the protonated form is found to be 0.0002 M. Assume that the remainder of the dye is in the deprotonated ...