BCHM 461 Biochemistry I Section 0101 TuTh 8 00 9 15 am Chemistry 1402 Spring 2003 Prof David Fushman Office Room 1121 Agriculture Life Sciences Surge Bldg 296 x53461 fushman wam umd edu much preferred to phone Please restrict telephone inquiries to office hour times except in emergencies Email is welcome anytime Office hours Tuesday 3 00pm 4 00pm Thursday 11 00am 12 00noon Teaching Assistant Ms Ranjani Varadan Office hours Monday 4 5pm Wednesday 4 5pm Room 1122 Agriculture Life Sciences Surge Bldg x58710 ranjani wam umd edu Course Description Biochemistry is the study of the molecular basis of life Biochemistry 461 is an introductory course that will focus on basic concepts in biochemistry and will provide the vocabulary and grammar needed to pursue further course work and research in this field We will cover the four major classes of biological molecules proteins carbohydrates lipids and nucleic acids The emphasis will be on the chemical properties and three dimensional structure of these molecules in relationship to their biological function Textbooks Required Lehninger Principles of Biochemistry 3rd edition by Nelson and Cox Recommended The Absolute Ultimate Guide to Lehninger Principles of Biochemistry 3rd edition by Osgood and Ocorr The publisher s web site http www worthpublishers com lehninger that accompanies the Lehninger textbook contains interactive tutorials to further illustrate the class material study aids links to protein data bases and suggestions for further reading about some topics Additional recommended sources on reserve in the Chem library no need to buy them Biochemistr y 2nd edition by Voet and Voet Biochemistry 3rd edition by Mathews van Holde and Ahern There is a course homepage at http gandalf umd edu BCHM461 where you will find a copy of the syllabus practice problems study hints and extra materials Some of these materials will be posted as we proceed with the course You are welcome to email your questions and comments I do not guarantee individual responses but errors or common points of confusion will be addressed in class p 1 Course Outline The exact order of topics and the number of lectures on each may change 1 Introduction 2 lectures The molecular logic of life Biomacromolecules Composition and principles of organization Energy and principles of bioenergetics 2 Water 3 lectures Non covalent interactions Properties of water Acid base properties pH buffering capacity 3 Protein structure and stability 8 lectures Amino acids structures nomenclature chemistry Primary structure the peptide bond sequence homology and evolution synthesis Methods for protein purification and analysis Secondary structure helices sheets turns Ramachandran plot structure prediction Tertiary structure protein motifs structure classification Quarternary structure Protein folding and dynamics Methods for protein structure determination Ch 1 Ch 3 pp 53 65 69 73 Ch 1 pp 9 12 Ch 14 pp 490 499 Ch 4 pp 82 84 86 91 pp 83 91 pp 95 107 Ch 5 pp 115 126 pp 126 129 150 153 pp 130 150 pp 159 169 pp 170 177 182 188 pp 171 172 188 191 pp 191 198 pp 178 181 4 Protein function 8 lectures Protein ligand interactions Oxygen binding proteins Quantitative analysis of protein ligand interactions Cooperativity allostery Enzymes how they work Enzyme kinetics Michaelis Menten equation Lineweaver Burke plots Enzyme inhibition mechanisms Examples of enzymatic reactions Ch 8 pp 257 266 Ch 8 pp 266 269 Ch 8 pp 269 289 5 Carbohydrates and glycobiology 2 lectures Ch 9 6 Nucleotides and Nucleic Acids 2 lectures Ch 10 7 Lipids and Membranes Ch 11 12 2 lectures Ch 7 pp 203 221 Ch 7 pp 206 209 Ch 7 pp 214 216 Ch 8 pp 243 257 Note that Chapter 3 in Lehninger includes a short review of some basic chemical principles structures and reactions I will not go over this material in the lecture but I urge you to review it yourself especially if it has been some time since you last saw these topics p 2 Examinations will be given on the following dates I Tuesday February 25 II Tuesday March 18 III Tuesday April 29 Final exam Wednesday May 21 10 30am 12 30 pm These exam dates are firm The quiz dates will be announced on a previous lecture or earlier Grading Policies Each exam during the semester will be worth 100 points and the final exam will be 150 points Exams during the semester will include only the material covered since the previous exam but will inevitably draw on information from earlier in the semester The final will cover the entire course material The exams will include material covered in the lectures and in the corresponding sections of the textbook Problem sets given as homework are optional however completing them is likely to be very helpful in your preparation for the exams All midterm exams will be 75 min long and will be given in the lecture hall Chem 1402 You will be allowed to use calculators for computation only Two of your three mid term exams with the highest scores will count toward the final grade In addition you will be given five 10 15 minutes quizzes each worth 20 points You will be notified about their date in advance Your final letter grade will be based on your total score calculated as a sum of your scores on all quizzes on the two out of the three mid term exams and on the final exam maximum 450 points Grading will be done on a curve based on the overall distribution of the class scores You will be guaranteed an A if your total score is 85 or better a B if it is 60 or better and a C if it is above 30 of the class Final grading will then be done using the grading system as follows The cut offs for A B etc grades will be determined first Then each letter range will be divided into three groups all students whose scores are in the upper third of e g B range will be given a B those in the middle will receive a B and the lower third will receive a B and so on Regrades If you think a mistake has been made in grading your work you must submit it to me for regrading no later than one week after the date on which the work was returned to the class with a written explanation of your reasons for desiring a regrade The entire exam is subject to regrading which often decreases the total score After that the grade will be considered final Arithmetic errors in the grading can be corrected without regrading Make up exam policy Do not miss any of the exams or quizzes If you miss an exam you will have a score of 0 on the exam until it is made up Only students with legitimate excuses as determined by the