CHEM 315: BIOCHEMISTRY Fall, 1996 INSTRUCTOR: Dr. Diane Husic OFFICE: 303 Gessner Building OFFICE HOURS: Mondays 11:00 - 12:00 AM and 2:00 - 3:00 PM Wednesdays 12:00 - 2:00 PM Thursdays 12:00 - 1:00 PM PREREQUISITES: CHEM 234, 236; the organic chemistry prerequisite must be met to be enrolled in CHEM 315 REQUIRED Mathews, C.K. and van Holde, K.E., Biochemistry, TEXT: 2nd ed., Benjamin/Cummings Publishing Co., Inc., (1996, Menlo Park, CA). RECOMMENDED Efiok, B.J.S. (1993) Basic Calculations for Chem- TEXT: ical and Biological Analyses, AOAC International INTRODUCTION TO COURSE: For many of you, this will be the only biochemistry course you take during your undergraduate studies. Thus, this course is designed to introduce and survey the discipline of biochemistry. We also discuss biochemistry that appears in the news during the semester. The material covered in this course provides the groundwork necessary for further biochemistry and related courses. Several of the topics will also help to prepare you for standardized exams such as the MCAT or GRE tests. By the nature of the discipline, a large amount of material will be covered in this course, and biochemistry has never been considered a easy course! My expectations, as you most likely have heard, are high for each student in this course. However, please do not be intimidated by this. Always feel free to come in for help. This will be my eighth year of teaching this course and I have consistently observed that those students who come in with questions in a timely manner do best in the course. You should expect to study a minimum of 6 hours per week for this course. Reading the chapter material prior to attending the lectures is useful. Working through suggested problems is also important. Students who wait until the last minute to study for an exam quickly realize that the amount of material is overwhelming and typically perform poorly. Approximately once per week, I will provide an outline of topics covered in lecture with corresponding pages from the text to be read and sample problems from the book that will be useful in helping you to learn the material. Additional problem sets, designed to help develop important concepts, may be distributed periodically; solutions will be posted and/or discussed in class. This semester, I am introducing some new computer exercises via a web-site format. These exercises have been designed to supplement the lecture and text material. Besides allowing you to more clearly visualize complex molecular structures and molecular interactions, you may also gain some valuable computer and internet usage skills. Almost all of you are all enrolled in this course because it is required for your major, which should indicate the importance of the material and the necessity for you to work hard and do well. I hope that you each learn a lot of interesting science, develop an appreciation of the field of biochemistry, and perhaps even enjoy the course! Here's to a good semester together! EXAMS AND QUIZZES: Four exams are scheduled during regular class meeting times as listed below: Monday, September 30th Wednesday, October 30th Wednesday, November 20th Wednesday, December 18th (finals week) Brief quizzes will be given occasionally in order to keep everyone on track with the material. GRADING: Percent of course grade: Exam #1 15 % Exam #2 20 % Exam #3 20 % Exam #4 (cumulative final) 30 % Quizzes, assignments, computer work and class participation: 15 % In this course, the topics continually build upon previously learned material. This is important when considering how to prepare for exams. Assignments are designed to help reinforce concepts presented in the lecture and readings. Some will be graded; others will be for "practice". I do look at trends in grades over the semester; improvement in test grades over the duration of the course will be favorably noticed! Participation in class discussions, review periods, etc. is highly recommended and may be a factor in the determination of borderline grades at the end of the semester. TENTATIVE LIST OF TOPICS TO BE COVERED* Chapter 1 Introduction to Biochemistry Chapter 2 The Aqueous Environment Chapter 9 Carbohydrates Chapter 4 Nucleic Acids Chapter 5 Introduction to Proteins Chapter 6 Protein 3-D Structure Chapter 7 Protein Function and Evolution Chapter 10 Lipids and Membranes Chapter 11 Enzymes/Catalysis Chapter 12 Introduction to Metabolism Chapter 3 Introduction to Bioenergetics *Chapters referred to are from the required text: Mathews, C.K. and van Holde, K.E., Biochemistry, 2nd ed., Benjamin/Cummings Publishing Co., Inc., (1996, Menlo Park, CA). LECTURE OUTLINE AND ASSIGNED READINGS - WEEKS #1 & 2 (1996) I. Introduction to Biochemistry and Fundamental Principles Readings: Chapter 1. "The Scope of Biochemistry" pp. 2 - 20 (through "Summary") Lecture Outline: A. What is Biochemistry and why is it an important field of study? B. A short historical perspective C. Biochemistry as a chemical science: 1. the chemical elements of living matter 2. macromolecules (biological polymers) D. Biochemistry as a biological science: 1. the distinguishing characteristics of living matter 2. the basic unit of life: the cell 3. organelles II. The Aqueous Environment Readings: Chapter 2. "The Matrix of Life: Weak Interactions in an Aqueous Environment" pp. 25 - 48 See also Chapter 2 of Efiok's text, pp. 31-53 Suggested Problems: pp. 49 - 50, #2, 5, 6, 8, 10, 11 , 13, 14 Lecture Outline: A. Noncovalent Interactions 1. charge-charge interactions (ionic bonds) 2. dipole interactions a. hydrogen bonds b. van der Waals forces B. Water 1. structure 2. solvent properties 3. hydrophilic and hydrophobic interactions C. Ionic Equilibria 1. Acids/Bases 2. pH 3. Buffers 4. the Henderson-Hasselbalch equation D. Interactions Between Macroions in Solution LECTURE OUTLINE AND ASSIGNED READINGS - WEEKS #3 - 5 (1996) INTRODUCTION TO BIOMOLECULES III. Amino Acid and the Primary Level of Protein Structure 1. General Structural Features/Classification by R-groups 2. Stereochemistry 3. Ionization Properties (acid-base chemistry) 4. Separation and Detection Techniques (ion exchange Chromatography, electrophoresis, ninhydrin reaction, etc.) 5. Formation and Properties of the Peptide Bond Readings: Chapter 5. "Introduction to Proteins: The Primary Level of Protein Structure", pp. 129 - 146 (Up to "From Gene to Protein") Tools of Biochemistry 2A, pp. 50 - 54 Tools of Biochemistry 5B-D, pp. 156 - 163 Suggested Problems: pp. 49 - 50, #12, 13 and 16 p. 151, #2, 3 - 6, 9 EXAM #1 -- September 30, 1996 1995 (to be updated) B. Carbohydrates 1. General Structure/Classifications 2. Formation of Hemiacetals 3. Isomeric Forms of Carbohydrates 4. Modified Sugars 5. Glycosidic Linkages and Disaccharides 6. Introduction to Polysaccharides and Complex Carbohydrates Readings: Chapter 11. "Carbohydrates", pp. 298 - 320 Suggested Problems: pp. 322 - 323, #1(a,b), 3, 6, 7, 12, 13 IV. Proteins A. An Introduction 1. The Peptide Bond 2. Peptides (structure, function and special properties) 3. Protein Functions 4. Protein Purification Techniques 5. Protein Sequencing Techniques Readings: Chapter 6. "An Introduction to Proteins", pp. 134 - 143, 146 - 156 Suggested Problems: pp. 157 - 159, #5, 6 (or 7), 8 - 12 B. Structure Readings: Chapter 7. "The Three Dimensional Structure of Proteins", pp. 160 - 182, 190 - 192 Suggested Problems: pp. 195 - 197, #1, 6, 11, 12, 13 VI. Nucleotides and Nucleic Acids General Structure and Properties of Nucleotides Phosphodiester Linkages Nucleic Acid Structures Nucleic Acid Chemistry Analysis of Nucleic Acids Readings: Chapter 12, pp. 324 - 355 Suggested Problems: pp. 357 #3, 6, 8, 9 The Relationship Between Genes and pp. 150-155 Proteins - The Genetic Code Suggested problems: p. 156 #6,7 page 3. V. Higher Levels of Protein Structure CH 6: pp. 171-176, 179-191 VI. Protein Functions Myoglobin/Hemoglobin CH 7: pp. 216-228; 236-248 Suggested problems: p. 255 #2-4 VII. Introduction to Enzymology Catalysis CH 10: pp. 339-345, 348-362 Cofactors pp. 365-376 Suggested problems: p. 377 #1,4,5 VIII. Regulation CH 11: pp. 381-401 Suggested problems: p. 402 #1,2,9 IX. Introduction to Metabolism/ CH 12: pp. 404-424 Suggested problems: p. 86 #4-6, 11 p. 425 #3 XI. Glycolysis CH 13: pp. 433-458 Suggested problems: p. 466 #1,2,5 XII. TCA Cycle (Krebs Cycle) CH 14: pp. 467-491 XIII. Electron Transport CH 15: pp. 504-525, 531-533 Suggested problems: p. 536 #2, p. 537 #10 XIV. Misc. other topics as time warrants A. Glycolysis B. TCA Cycle (Krebs Cycle) C. Electron Transport VI. Misc. other topics as time warrants A. Biochemistry of Photosynthesis B. Fatty Acid Oxidation C. Catabolism of Polysaccharides/Pentose Phosphate Pathway D. Membranes 1. Structure 2. Introduction to membrane transport