Bi/Ch 110 Introduction to Biochemistry Fall 2014 Professor John H. Richards 184 Braun, x6040 Course Schedule: Lectures: 11:00 AM-12:00 PM - Tues/Thurs - 147 Noyes Lecture: 2:00-3:00 PM - Wed - 147 Noyes Recitation: 3:00-4:00 PM - Wed - 147 Noyes Website: http://chemistry.caltech.edu/courses/ch110/index.html Text: Berg, Tymoczko, Stryer, Biochemistry, 7th Edition (You can purchase this from Caltech's Online Textbook website: http://bookstore.mbsdirect.net/caltech.htm) The course will be directed towards the study of protein structure and function and aspects of intermediary metabolism. Lectures will focus on interesting highlights of these topics and will be relatively independent of material in the textbook. Grading: 40% on 7 problem sets; 50% on exams (20% midterm; 30% final), and 10% on active participation in discussions. Schedule of Problem Sets and Exams: Out Due Returned Problem Set 1 2 October 7 October 9 October Problem Set 2 9 October 14 October 16 October Problem Set 3 16 October 21 October 23 October Problem Set 4 23 October 28 October 30 October Midterm 29 October 4 November Problem Set 5 6 November 11 November 13 November Problem Set 6 13 November 18 November 20 November Problem Set 7 20 November 25 November 2 December Final 4 December Credit will be given for each assigned problem submitted, provided that all work is shown. The exams will be weighed as follows: 20% on the midterm; 30% on the final. The final will include material from the first half of the term. Both questions on lecture material and problems similar to those given as homework will be included. Recitation sections will provide opportunities for asking questions and having extended discussions about the lecture material as well as discussing papers from the original literature. On many Wednesdays the first hour will involve lectures on supplementary material such as modern techniques for manipulating DNA (cloning, sequencing, synthesis, in vitro mutagenesis) and proteins (synthesis both chemical and biological, purification, determination of properties).Outline of Lectures Lecture Date Topic 1 Tuesday, September 30 Introduction 2 Wednesday, October 1 Amino Acids, Proteins / Secondary Structures: Helices and Sheets 3 Thursday, October 2 Tertiary Structures of Globular Proteins 4 Tuesday, October 7 Protein Folding 5 Wednesday, October 8 Enzyme Kinetics 6 Thursday, October 9 Mechanisms of Enzyme Action 7 Tuesday, October 14 Control, Allostery, Hemoglobin 8 Wednesday, October 15 Regulation / Proteosome 9 Thursday, October 16 Membranes 10 Tuesday, October 21 Structure Reveals Function - Chaperones (Prof. A. Hoelz) 11 Wednesday, October 22 Structure Reveals Function - Chaperones (Prof. A. Hoelz) 12 Thursday, October 23 EPO / Biotechnology 13 Tuesday, October 28 λ Phage-Cell Control (Prof. C. Parker) 14 Wednesday, October 29 λ Phage-Cell Control (Prof. C. Parker) Thursday, October 30 MIDTERM 15 Tuesday, November 4 Intermediary Metabolism—Reaction Types 16 Wednesday, November 5 Glycolysis (Embden-Meyerhof Pathway) 17 Thursday, November 6 Pentose Phosphate Pathway, Gluconeogenesis, Photosynthesis 18 Tuesday, November 11 Tricarboxylic Acid Cycle 19 Wednesday, November 12 Metabolism of Fatty Acids, Lipids 20 Thursday, November 13 Basis of DNA Diagnosis / Forensics 21 Tuesday, November 18 Harvesting Energy: "Oxidative Phosphorylation" /mitochondrion 22 Wednesday, November 19 DNA Structure Function (Prof. J. Campbell) 23 Thursday, November 20 Chromosome Structure Function (Prof. J. Campbell) 24 Tuesday, November 25 Electron Transfer in Biochemistry Thursday, November 27 Friday, November 28 Thanksgiving 25 Tuesday, December 2 Steroid Biosynthesis 26 Thursday, December 4 Review / FINALReading Lecture Text Chapters 1 Introduction 2, 3, 4 Stryer Chapter 2, 3.6, 6.1 5 Stryer Chapter 8 6 Stryer Chapter 9.1 7 Stryer Chapter 7.1-7.4, 10.1 8 Stryer Chapter 4.4-4.7; 10.2-10.3 9 Stryer Chapter 12 10 Hoelz refs 11 Hoelz refs 12 Stryer Chapter 14 13, 14 Parker refs Midterm 15 Stryer Chapter 15.1-15.4 16 Stryer Chapter 16.1-16.2 17 Stryer Chapter 20.1-20.5, 16.3, 16.4 18 Stryer Chapter 17.1-17.5 19 Stryer Chapter 22.1-22.6 20 Stryer Chapter 18.1-18.6 21 Stryer Chapter 19 22 Campbell refs 23 Campbell refs 24 Stryer Chapter 26.2-26.4 Thanksgiving 25 Review Collaboration The central point of any education is for you to learn individually. Solving problem sets by teams, in my view, can defeat this objective. On the other hand, to set a policy of absolutely no collaboration can lead to unproductive frustration in cases where a hint or some slight help from a classmate could open the way to a successful solution. Accordingly, my policy is somewhat complex. You may seek help on a particular problem but only after you have made a significant individual attempt to solve it (i.e., 15 minutes of serious effort) and even then the help should be more in the form of a suggestion than in simply copying someone else’s solution.Teaching Assistants Office hours Extension Email Heather Curtis (Head TA) Mondays, 8-9 PM SFL, 2nd floor x5951 [email protected] Alejandra Olvera Sundays, 7-8 PM SFL, Room 220 x6451 [email protected] Richard Mosesso Fridays, 11 AM-noon SFL, 1st floor x4162 [email protected] Evan Zhao (undergrad) Mondays, 10-11 PM SFL, room 3-2 [email protected] Lawrence Wang (undergrad) Mondays, 9-10 PM SFL, room 3-2 [email protected] Grading and Homework Policy: The problem set is due in class (by noon) the morning of the due date. Late homework will be penalized 10 points per day. During office hours, the TAs will be able to answer questions regarding all the problems in the set. Please try to limit the length of the answers on your work. In an essay answer, points will be deducted for incorrect statements, even if the correct answer is buried in the text. If you wish to appeal a score on graded work, list the number of the question and your specific concerns on a cover sheet attached to your problem set or test. Deliver grade appeals and excuses for late work to the