Lehninger Principles of Biochemistry, 6th ed

Duane W. Sears General Biochemistry, MCDB W 108A ‐ (Syllabus using Nelson and Cox, 6th ed., 2012) Summer Session (2015) EDIT LINK IN PDF by COPY/PASTE to eliminate the problem with the hyphens in the original link created in the PDF file. Technical Information @ http://mcdb‐webarchive.mcdb.ucsb.edu/sears/biochemistry/MCDB‐W‐108A/MCDBW108A‐Information.htm #Wk Date Lec. # Required Reading Topics Updated as of Saturday, May 23, 2015 THEME I: Basic Properties of Amino Acids and Proteins & Analysis of Reversible Ligand Binding Reactions 1 M Aug. 3 T 4 1 Protein Structures and Functions (For more info, see the Course Introduction video & slides on GauchoSpace, Wk 0) 2A Basic Amino Acid Properties 2B: AA Stereochemistry @@ NC Ch 3 pp. 75‐81; **WWBH‐Ch 2 Prblms: 2.1‐7, 10‐11, 14‐18 W R 5 6 3A Reversible Ligand‐Binding Reactions. 3B: Buffers NC Ch 2 pp. 45‐74; Ch 5 pp. 157‐166; &&RLBR pp. 1‐16 4A. Multivalent Reactions 4B Equilibrium Perturbation by Microenvironment NC Ch 3 pp. 81‐5; RLBR pp. 21‐30 THEME II: Strategies for Isolating Proteins F 2 M 7 10 5 On the Trail of Recombinant Human Erythropoietin (rhuEPO), Isolation and Characterization 6 Distinguishing Recombinant from Native Human EPO T 11 7A Sickle Cell Anemia 7B. Discovery of Sickle Cell Hemoglobin NC Ch 5 pp 172‐174; L. Pauling Science 110: 543 (1949) ##BF Ch 1 pp. 1‐12; Ch 11 pp. 452‐62; 472‐92; Ch 12 pp. 502‐12 W R F 3 M T 12 13 NC Ch 3 pp. 85‐94 NC Ch 3 pp. 94‐96 THEME III: Strategies for Characterizing Protein Sequences and Conformations 8 AA Sequences of Hb A and Hb S NC Ch 3, pp. 96‐109; BF Ch 2, 13‐8; WWBH Ch 3; V. Ingram, Nature 180:326 (1957) 9 3‐D Structure Determination of Myoglobin and Hemoglobin NC Ch 4 pp. 115‐43; BF Ch 2 19‐34 14 >> Midterm Review<< 17 10A Proteins Stability and Folding 18 20 10B Constraints on Protein Folding and Conformation NC Ch 4 pp. 143‐152 th
MIDTERM #1, Tue. Aug. 18 ‐ Online exam proctored on campus (TBA) or proctored by registering with ProctorU. THEME IV: Analysis of the Regulation of O2 Transport by Hemoglobin W R F 4 M 19 11 20 12 21 13 24 14 NC Ch 5 pp 157‐72; BF Ch 3 (all); RLBR pp. 30‐40; $$Martin Ch 4‐6 Mechanism of Cooperative O2 Binding by Hemoglobin NC Ch 5 pp. 157‐72; BF Ch 2 pp. 19‐32; BF Ch 3 pp. 45‐53 Metabolic Regulation of Hb O2 Transport NC Ch 5 pp. 168‐72 BF Ch 4 pp. 61‐71; Ch 5 pp. 91‐109; & Ch 7 pp. 169‐77 14A Fine‐tuning Hb Function. O2 Binding and Transport by Hb 14B Hemoglobinopathies and Hb Variants NC Ch 5 pp. 168‐172; BF Chs 3, 5, 14, & 17‐ selected pp THEME V: Analysis of Enzyme Kinetics and Reversible Enzyme Inhibition T W R 25 15 General Properties of Enzymes NC Ch 6 pp. 186‐206; WWBH Ch 8 26 16A Michaelis‐Menten (MM) Kinetics 16B. Kinetic Constants & Plots WWBH Ch 8 27 17 Mechanisms of Enzyme Inhibition NC Ch 6 pp. 207‐213; WWBH Ch 8 Problems: 8.1‐9, 11‐12, 15‐22, 24‐26 THEME VI: Specific Mechanisms of Enzyme Catalysis F 5 M 28 18 31 19 T Sept 1 20 Structure and Catalytic Properties of Chymotrypsin NC Ch 6 pp. 212‐218; WWBH Ch 7 Catalytic Mechanisms of Chymotrypsin and Serine Proteases NC Ch 6 pp 212‐218; WWBH Ch 7 Problems: 7.1‐17, 21 Catalytic Mechanism of Lysozyme, a Glycosidase NC Ch 6 pp 220‐223; Ch 7 pp. 257‐258; WWBH Ch 7 nd
W 2 MIDTERM #2, Wed. Sep. 2 ‐ Online exam proctored on campus (TBA) or proctored by registering with ProctorU. R 3 21 Catalytic Mechanisms of Aspartyl and Cysteine Proteases NC Ch 6 p. 213, pp. 218‐19 THEME VII: Biological Strategies for Regulating Enzyme Activity F 6 M 4 22 Introduction to Enzyme Regulation 7 LABOR DAY T W 8 23 9 24 R 10 Friday 11 NC Ch 6 pp. 226‐236; Ch 27, pp. 1147‐1149 Allosteric Feedback Regulation of ATCase NC Ch 5 pp. 168‐170; Ch 6 pp 226‐228; Ch 22 pp. 915‐916; WWBH Ch 7 Differential Regulation of Isozyme Catalyzed Reactions NC Ch 14 pp. 563‐565; Ch 15 p. 602 >> Final Exam Review<< FINAL, Fri. 11th ‐ Online exam proctored on campus (TBA) or proctored by registering with ProctorU. @@ TEXT: (NC) –D.L. Nelson & M.M. Cox, Lehninger Principles of Biochemistry, WH Freeman. Recommended: 6th ed. (2012) Optional: 5th ed. (2008). Posted on GauchoSpace (GS ‐ @ https://pilot.gauchospace.ucsb.edu/courses/ ) &&(RLBR) – Reversible Ligand Binding Reactions – D. Sears **(WWBH) W. B. Wood, J. H. Wilson, R. M. Benbow & L. E. Hood, Biochemistry: A Problems Approach, 2nd ed., 1981 – Chs 2‐3 & 7‐8 ##(BF) ‐ KF Bunn & BJ Forget, Hemoglobin: Molecular, Genetic & Clinical Aspects, 1986 – Chs 1‐5, 7, 11, 12 $$ L. Martin All you Really Need to Know to Interpret Arterial Blood Gases, 2nd ed. Lippincoltt, Williams, & Wilkins, 1992 ‐ Chs 1‐6s Instructors: Prof. D. Sears [email protected], TAs: Kyle Swentowsky [email protected], & Eric Valois [email protected] Syllabus MCDB W 108A (NC 6th ed).docx Page 1 of 2 5/23/2015 Duane W. Sears General Biochemistry, MCDB W 108A ‐ (Syllabus using Nelson and Cox, 6th ed., 2012) Summer Session (2015) Course Examination Schedule – Times, Locations, and Options MIDTERM #1: Tuesday, August 18th Duration: 1.5 hours Computer lab opens: 4:20 PM Earliest exam start time: 4:45 PM Latest exam start time: 6:00 PM (The exam closes at 7:30 PM) On‐campus location: TBA SMS 1303 or 1304 Off‐campus option: Register at least 72 hr in advance with ProctorU ‐ http://www.proctoru.com/ (cost, $25.00) . MIDTERM #2: Wednesday, September 2nd Duration: 1.5 hours Computer lab opens: 4:20 PM Earliest start time: 4:45 PM Latest start time: 6:00 PM (The exam closes at 7:30 PM) On‐campus location: TBA SSMS 1303 or 1304 Off‐campus option: Register at least 72 hr in advance with ProctorU ‐ http://www.proctoru.com/ (cost, $25.00) . FINAL EXAM: Friday, September. 11th Duration: 3 hours Computer lab opens: 11:30 AM Earliest start time: 11:45 AM Latest start time: 1:30 PM (The exam closes at 5PM.) On‐campus location: TBA Phelps Hall 1517, 1518, 1525, or 1526 Off‐campus option: Register at least 72 hr in advance with ProctorU ‐ http://www.proctoru.com/ (cost, $33.75) . Review Session Schedule – Times, Locations, and Options Instructor‐led review sessions will be held on five Friday afternoons in LSB 1001  You are invited to attend if you are near campus. Friday August 7th @ 3:30 PM Friday August 14th @ 3:30 PM Friday August 21st @ 3:30 PM Friday August 28th @ 3:30 PM Friday September 4th @ 3:30 PM A final review session will be held on Thursday afternoon at in LSB 1001 the day before the final exam.  Again, you are invited to attend if you are near campus. Thursday September 10th @ 12:00 PM All review sessions will be broadcast as streaming videos, which will also be recorded and posted on GauchoSpace afterwards in case you are unable to attend or watch the broadcasts, or if you wish to review the material covered later on. Syllabus MCDB W 108A (NC 6th ed).docx Page 2 of 2 5/23/2015