Ch7-120213 - 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 Oxygen binding alters the structure of the tetramer so the structures of deoxyhemoglobin and oxyhemoglobin are different. T-state (tense) low affinity deoxyhemoglobin R-state (relaxed) high affinity oxyhemoglobin Oxygen binding shifts the Fe2+ into the plane of the ring. This changes the electronic state of the porphyrin ring which is why the color of blood goes from blue to red in the presence of oxygen. T-state proximal His F8 0.1 Å shift in Fe-N bond R-state 0.6 Å shift porphyrin proximal His F8 Oxygen coordinates with a bent geometry to Fe2+ and a distal histidine Steric clash between the proximal His F8 and the porphyrin ring inhibits oxygen binding to the T state. The whole F helix must move to reorient the His F8 imidazole ring and thus prevent steric clash. Both the flattening of the porphyrin ring and the contraction of the N-Fe2+ bond lead to a large change in the F helix position and orientation. The F helix movement changes the interface between the and protomers (subunit communication) Ion pairs between 12 subunits stabilize the T-state (deoxy) In the transition from T to R states, some residues move up to 6 Å. Note: the “knobs” of His97 and Thr41 prevent intermediate conformations, e.g. shifting gears (T <-> R). The communication between subunits is called cooperativity. Oxygen binding by one subunit effects the neighbor subunit. T-state (tense) low affinity deoxyhemoglobin R-state (relaxed) high affinity oxyhemoglobin Myoglobin binding to oxygen yields a rectangular hyperbola. pO 2 YO2 = pO2 + P50 Hemoglobin binding to oxygen is affected by cooperativity between subunits. The binding curve is sigmoidal in shape. Dashed line is hyperbolic curve with same P50 as Hb Oxygen dissociation curves of Mb and of Hb in whole blood. Oxygen binding to hemoglobin is described by a sigmoidal (S-shaped) curve. A sigmoidal curve is diagnostic of a cooperative interaction between binding sites. Cooperativity lowers binding affinity at lower pO2 in tissues without effecting the affinity in lungs. Models of Cooperative Binding Concerted Model assumes an all-or-nothing transition between T an d R states. Ligand binding in “lock-and-key” fashion. Sequential Model follows the “induced fit” hypothesis. Ligand binding can change the conformational state. T state R state The reversible binding of O2 to myoglobin (Mb) is described by : Mb + O 2 MbO 2 With an dissociation constant Kd and fractional saturation YO2: YO 2 [O 2 ] pO 2 = = [O 2 ] + K d pO 2 + P50 The above equation accurately describes a rectangular hyperbola. How do we describe cooperative binding? What equation will describe a sigmoidal binding curve? Hill Equation- Hill assumed that hemoglobin (Hb) bound n molecules of O2 in one step, with infinite cooperativity giving the equilibrium reaction: n P + nL PL n Kd [P][L] = [PL n ] From the (dissociation constant) KD and rearranging similarly to the equation for myoglobin the result is the Hill equation, which describes the degree of saturation of Hb as a function of pO2. n [L] Y= n [L] + K d Rearranging and taking the log of both sides yields a linear equation, where Kd = [L]n0.5 (concentration at 50% saturation): [ L]n = Kd 1Y Y log Y 1Y = n log[ L] log K d HILL PLOT: The Hill equation can be used to graphically determine n (Hill constant or coefficient). Note pO2=P50 at log Y 1Y =0 n = 1 non-cooperative (myoglobin) n > 1 + cooperative (hemoglobin) n < 1 - cooperative (very rare) log Y 1Y = n log pO 2 n log p n50 The Bohr Effect Hemeglobin releases protons when binding oxygen HbH+ + O2 -> Hb-O2 + H+ lungs So oxygen affinity increases when the pH increase (lungs) And oxygen affinity decreases when the pH decreases (tissue) Carbonic anhydrase: CO2 + H2O -> H+ + HCO3increases H+ in tissue which is absorbed by Hb when O2 released tissue Structural Source of the Bohr Effect His-146 is protonated in the T state. The electrostatic interactions involving His-146 help to stabilize the T state. All of these interaction are disrupted in the R state. The Bohr Effect This proton is released by the transition to the R state Salt Bridge The salt bridge increases the pKa of His-146 to pH 8.0 So that His-146 will be protonated at the pH of blood (7.2) CO2 Transport and the Bohr Effect CO2 binds to the N-terminal amino groups of proteins carried in the blood which releases a proton 95% of CO2 is transported as bicarbonate 5% of CO2 is transported as carbamate Only 10% of CO2 is released per circulatory cycle Half of this comes from carbamate Chloride ion stabilizes the protonation of the N-terminus in the T state which prevents carbamate formation CO2 Transport and the Bohr Effect Carbonic anhydrase and oxygen binding to hemoglobin are coupled through release and acceptance of a proton. high pH low pH ...
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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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