Ch6-120210 - CHEM 350: Introduction to Biological Chemistry...

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Unformatted text preview: CHEM 350: Introduction to Biological Chemistry Brian Lee, Ph.D. [email protected] Office: Neckers 146G or 324 Phone: 453-7186 Ho urs: 9:30am to 10:30am or by appointment Website: https:/ /online.siu.edu Textbook (required, U.S. edition only) Fundamentals of Biochemistry, 3rd Ed., Voet, Voet & Pratt. Study Guide (recommended) Student Companion to Fundamentals of Biochemistry, 3rd Ed. Help Desk Tuesday 6:30 to 7:30 pm in Neckers 218 Thursday 5:00 to 6:00 pm in Neckers 410 Announcements Undergraduate Research Opportunities Research for credit (such as CHEM 396 or CHEM 496) Student worker ($8.00 per hour) (http://www.siu.edu/~fao/jobs/) Undergraduate Assistantships (http://www.siu.edu/~fao/jobs/) McNair Scholars Program (http://www.siu.edu/~mcnair) REACH Awards Competition (http://www.siu.edu/~reach/) Summer Research Experiences for Undergraduates (REU) http://www.nsf.gov/crssprgm/reu/reu_search.cfm For other REU programs, search the National Science Foundation site: http://www.nsf.gov/crssprgm/reu/index.jsp Students must contact the individual sites for information and application materials. NSF does not have application materials and does not select student participants. A contact person and contact information is listed for each site. Assignments Read Chapter 7 Protein Function Chapter 7 Problems Student Companion site for Voet, Voet & Pratt http://bcs.wiley.com/he-bcs/Books?action=index&bcsId=4274&itemId=0470129301 Second Midterm Exam, Wednesday February 29th Chapters 6 through 9 All exams are cumulative Help Desk Tuesday 6:30 to 7:30 pm in Neckers 218 Thursday 5:00 to 6:00 pm in Neckers 410 Grades are posted on SIU Online Exam 1 – raw score (4 pts per question) Curved Exam 1 – tentative curved score (ave. 75%) A sample Exam 1 with answers marked is posted. Appeals for exam grading due Monday Your appeal must be in writing and describe either: 1) Why your answer is correct. 2) Why the answer key is incorrect. Studying for Biochemistry 1) Rea d the chapter before lecture 2) Go to class, ask questions 3) Read the chapter, review problems and lecture slides 4) Use the past quizzes and exams to test yourself 5) Ask questions (office hours or help desk) Quiz and test question are designed to assess more than simple knowledge and comprehension (like MCATs). How do you apply knowledge or analyze ideas? What holds a protein together (section 4)? How do proteins fold into the correct structure (section 5)? Protein Stability -Hydrophobic effect -Electrostatic interactions -Disulfide bonds -Metal ion coordination -Flexibility Protein denaturation and renaturation(1) Heating - affects protein conformation, a sharp transition in dicates that the polypeptide chain unfolds simultaneously (cooperatively) - loss of weak interactions (2) pH - alters ionization states of residues affecting charge distribution and H-bonds (3) Detergents - affect non polar residues interfering with hydrophobic interactions 4) Chaotropic agents (guanidinium ion and urea) organics that increase solubility of non polar substances in water affecting the hydrophobic interactions. Chaotropic agents Reducing agent Reduce disulfides with ß-mercapto-ethanol Christian Anfinsen’s refolding experiments with ribonuclease A in 1957, showed that a protein could be unfolded and refolded back to 100% native structure. RNase A has 4 disulfide bonds. The probability to randomly reform the correct bonds is 1 7 1 5 11 1 = 3 1 105 Random refolding would produces less than 1% native structure Anfinsen’s Hypothesis Proteins can fold spontaneously into native conformations under physiological conditions. The amino acid sequence dictates the tertiary structure. Levinthal’s Paradox (Cyrus Levinthal 1969) If protein folding requires exploration of all conformational space, given an estimated sampling of 1013 conformations per second, RNase A (124 residues) would never find the correct conformation 10124 t = 13 10 sec 1 = 10111 sec = 3 10103 years The age of the universe is only 20 billion years (2 x 107 years) Model 1: Hierarchical folding (1) Local segments of secondary structure (Evidence of weak secondary structure in unfolded state) (2) Longer range interactions (3) Co mplete folding Model 2: Hydrophobic collapse (1) Spontaneous collapse mediated by hydrophobic interactions: “molten globule” (2) Elements secondary structure exist in molten globule state (3) Initial tertiary interactions are non-native weaker interactions (4) Native interactions are formed Protein folding is a most likely combination of both models 1 and 2. The actual “pathway” to folding may vary from one protein to another. Funnel (or Ski slope) Model of Protein Folding Unfolded protein is in a high energy state an d has a high degree of conformational entropy. Native structure is a low energy state. Folding is entropically driven by the release of water molecules. Hydrophobic effect. Protein disulfide isomerase (PDI) catalyzes the exchange of disulfide bonds to eliminate non-native conformations Peptide prolyl cis-trans isomerase (PPI) catalyzes the conversion of the peptide bond between cis and trans Assisted folding (1) Molecular chaperones (DnaK, DnaJ, GroEL) (2) Protein disulfide isomerase (PDI) (3) Peptide prolyl cis-trans isomerase (PPI) Heat shock protein Hsp70 (DnaK) Protects the cell from aggregation of unfolded proteins. Allows protein to find native conformation. Chaperonins (GroEL/GroES) large multi-subunit complex encapsulates unfolded protein and promote native structure amyloids are aggregates of unfolded proteins that form tangles or plaques that lead to cell death. prion proteins can transmit disease between individuals and across species (from cows or deer to humans by consumption). ...
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This note was uploaded on 03/26/2012 for the course CHEM 350 taught by Professor Lee during the Spring '08 term at SIU Carbondale.

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