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IBS601/BCH607: Biochemistry &
Metabolism/General Biochemistry Course ID: IBS601-001 This is the first half of a two semester course introducing graduate students to the molecules that comprise biological systems, the physical & chemical principles governing their behavior, and the methods used in their study. It is intended for doctoral students planning to enter a career in research in one of the biomedical sciences. Basic aspects of the carbohydrates and lipids are covered but the emphasis is on protein structure and function and metabolic control. Nucleic acid structure and function are covered in the second semester of the sequence. Course content The course will start with a series of lectures that will review undergraduate chemistry as used in the study of biological systems and introduce major biomolecular classes. The lecture on amino acids will begin an extended section on the structure and function of proteins. This section will first explore elements of protein structure. Basic aspects of protein function will follow, beginning with basic principles of binding interactions interweaved by mechanisms of regulation occurring at the protein level. We will begin with simple concepts and show how more complex behavior is built on these simpler beginnings with a focus on globin/O2, receptor/ligand and antibody/antigen interactions. Elements of chemical and biochemical catalysis will then be introduced, once again building on prior course topics. Throughout this section, quantitative treatments of biological phenomena will be emphasized, as will the chemical and thermodynamic bases of these behaviors. After completing the section on enzymology, there are seven lectures on experimental methodologies used in the study of protein function and structure. After these methods lectures, the emphasis of the course will be on metabolism and how it is integrated. Three lectures will focus on aspects of biomembranes and subcellular compartmentalization and transport. The thermodynamics and regulation of key pathways for energy production (glycolysis, citric acid cycle, & oxidative phosphorylation) will then be presented. The course will conclude with an overview of human metabolic control. Prerequisites Students taking this course should have at least a bachelor’s degree from an accredited university and have taken 1 yr of introductory (“freshman”) chemistry, 1 yr. of organic chemistry, and have advanced knowledge in general biology. More specifically, the student is expected to have a working knowledge of:
Text Most of the assigned readings will be in Voet & Voet, Biochemistry 3rd Edition, Wiley Press, but additional readings may be assigned for some topics not adequately covered by the text. The text contains far too much information; it is a very useful reference and, although expensive, you should really own your own copy. I still have (and use) the text with which I studied introductory biochemistry. Use the lectures and what the instructors tell you as guides as to what to pay particular attention to in the text. There is a fair amount of detailed information that you will be required to memorize, there is a lot more information with which you should have passing familiarity. The lectures will be more effective if the assigned reading is done prior to lecture. Blackboard (course website) IBS601 uses the University Blackboard system extensively. Announcements, this syllabus, the class lecture and exam schedule, lecture notes, reading assignments, answer keys, old exams, and instructor contact information are posted on this site (http://www.uky.edu/Blackboard). eQuestions Exams There are 4 exams this semester. Three of the exams occur during the semester and are held on Tuesday or Thursday evenings from 6:00-8:00—check the class schedule and be sure to keep these evenings open. The last exam is during finals week. Each exam is worth 100 points. The exams are technically not cumulative—they only cover the lectures as listed in the syllabus—but the information in class builds on prior lectures, so concepts introduced earlier in the course could show up on later exams if they pertain to the newer material. The exams are closed book. No notes, calculators or devices other than a pen or pencil will be permitted during the exam. If it appears that you will miss an exam, contact the course director at your earliest opportunity prior to the exam. Unexcused absences will result in a zero grade unless there was a consequential reason for the absence and concrete evidence that prior notification was unavoidable (emergency room report, arresting officer’s report, public statement by Gonzalez that you were held incommunicado due to suspicion of Patriot Act violations or other leftist leanings). Acceptable reasons for excused absences are: serious illness, illness or death of a family member, University-related trips, major religious holidays, or other circumstances agreed to by the course director. The student should be prepared to provide appropriate verification for an excused absence to the course director. Code names To help preserve confidentiality of test scores and grades, we will use code names instead of real names on all exams and homework assignments. Early in the semester, you will be asked to provide a 5 letter or digit “code name” to the course director. You will use that name all semester on exams and homework assignments instead of your real name. Except for the course director, faculty and graders will not have knowledge of the real identity of the code names. This will allow the faculty to return exams and homework assignments without students being able to see each others’ grades. Grading The final class grade is based on your combined performance on all tests relative to the class as a whole at the end of the semester. Grades will be calculated by two different grading systems; each student will receive the higher of the grades calculated by the two systems as their final grade for the course. In the first grading system, and the one most likely to be in effect, students with total scores one standard deviation or more above the class average will receive an “A” grade, scores less than one standard deviation above or more than one standard deviation below with receive a “B”. Students with total scores more than one standard deviation below the average, but less than two standard deviations below the average, will receive a “C”. Students with scores more than two standard deviations below the average will receive an “E”. There is no “D” for graduate students. On this scale, about 20% of the class will receive A’s, 60% B’s, 20% C’s. In the second grading system, any student obtaining final scores of 360 or more (>90% of the total) will receive an “A”, between 320 and 359 will receive a “B”, between 280 and 319 will receive a “C” with scores below that receiving an “E”. Interim grades based will be available throughout the semester, but these grades should be regarded only as estimates. Keys to exams will be posted on the class website after the last excused make-up exam has been turned in. If you question the grading of any exam, attach a written explanation as to why you think the grading was in error to the original exam and return it to the course director within 1 week of the posting of the key for possible regrading. Requests for regrading after this one week period will not be considered. Academic Integrity, Cheating and Plagiarism Plagiarism (willful, unattributed copying of another’s work) and other forms of cheating are considered unacceptable behavior for any student attending this University. The minimum penalty for either of these academic offenses is an “E” grade, with suspension or dismissal from the University also possible. Classroom Behavior, Decorum and Civility Students and faculty have the right to expect that all class activities will occur in a spirit of mutual respect for the opinions and rights of all participants. While all participants have the right to take reasoned exception and to voice alternative opinions, the accepted level of civility would not include attacks of a personal nature or statements denigrating another on the basis of race, sex, religion, sexual orientation, age, national/regional origin or other such irrelevant factors. Writing Skills Regardless of discipline, instructors have the right—and the obligation—to expect that students use English properly in all aspects of the course. (S.R.5.2.4.3). Instructors can ask students to rewrite papers, make writing style one of the grading criteria, and report a seriously deficient student to his/her college for remedial work. Other useful telephone numbers: IBS office: 323-0004 Molecular & Cellular Biochemistry Office: 323-5549 |
