General Biochemistry I
General Biochemistry I BCHS 3304
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This 12 page Class Notes was uploaded by Elody Boehm on Saturday September 19, 2015. The Class Notes belongs to BCHS 3304 at University of Houston taught by James Briggs in Fall. Since its upload, it has received 68 views. For similar materials see /class/208347/bchs-3304-university-of-houston in Biochemistry and Molecular Biology at University of Houston.
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Date Created: 09/19/15
Chapter 1 Problems Assigned 1 514 Book Ch 1 prob 6 Does the entropy increase or decrease in the following processes a N2 3H2 9 2NH3 Decrease Ammonia b HZNCONH2 H20 9 CO2 2NH3 Increase Urea Ammonia c 1M NaCl 3 9 05M NaCl Increase coo coo d HCOH gt HCOPOa392 No Change HZC OPO3392 H2C OH 3phosphoglycerate 2phosphoglycerate Chapter 1 Problems Book Ch 1 prob 7 Consider a reaction With AH15 kJmol and AS50 JmolK Is the reaction spontaneous a at 10 C b 80 C Recall AGAHTAS and if AGlt0 reaction is spontaneous a AG15 kJmol 27310K X 50 JmolK X l kJ1000 J 085 kJmol NO b AG15 kJmol 27380K X 50 JmolK X l kJ1000 J 265 kJmol YES Chapter 1 book 9 Calculate AGO for the reaction A B S C D at 25 C when the equilibrium concentrations of A 10 uM B 15 uM C 3 uM D 5 uM Is the reaction exergonic or endergonic under standard conditions AG RT ln Keq RT ln CDAB K601 3X10396M5X10396M10X10396M15X10396M AG 83l45 JKmol298K In 01 5705 Jmol AG 57 kJmol Not spontaneous since free energy is positive endergonic Chapter 1 book 10 AGO for the isomerization reaction Glucoselphosphate GlP gt glucose6phosphate G6P is 71 kJmol Calculate the equilibrium ratio of GlP to G6P at 25 C Keq G6PGlP Keq also e39AGO RT G6PG113 e71 kJmol1000 JkJ83145 JmolK298 K Note above that I am converting the change in free energy into units of Jmol since R is in JmolK G6PGlP 176 GlPG6P 0057 Chapter 1 book 14 Two biochemical reactions have the same K60l 5X108 at temperature T1 298K However Reaction 1 has AHO 28 kJmol and Reaction 2 has AHO 28 kJmol The two reactions utilize the same reactants Your lab partner has proposed that you can get more of the reactants to proceed via Reaction 2 rather than Reaction 1 by lowering the temperature of the reaction Will this strategy work Why or why not No Reaction 2 absorbs heat positive enthalpy and will be more disfavored at lower temperature Reaction 1 gives off heat and lowering the temperature will favor this reaction Chapter 1 Problems 0 Briggs 1 How many angstroms are there in a nanometer IA 103910m lnm 10399m 10399m1 nm1 A 103910m 10 All nm 2 How many kJmol are there in 1 kcalmol 1 kcalmol 4184 kJmol 4184 kjmet 4184 k 1 kcazmet 1 kcal 3 What is the de nition of a spontaneous process A spontaneous process is one that occurs Without input of additional energy from the surroundings the free energy is negative 4 Draw a carboxylic acid group g C 0 OH C R OH Chapter 1 Problems Briggs Given a AGO of 25 kJmol and a temperature of 25 C what is the equilibrium constant Recall AG0 RTan eq In Keq AG0 RT AG0 RT an 251dmol1000Jkl 8g 83144JmolK298K an 2500Jm0l 1009 W 24777Jm0l Keq 036 Chapter 2 Problems Assigned 1 3 4 610 1215 18 Book Ch 2 Prob 1 Identify the potential hydrogenbond donors and acceptors Acceptor Drill Donor 2 Acceptor H Acceptor C O O N1 6 IN AcceptorN I Acce tor gt 3 H IEI RI 0 1 2 Donor HN N NH 2 Acceptor H Acceptor H 3 Donor D0110r Donor Donor Chapter 2 Prob 2 Companion Which gas in each of the following pairs would you expect to be more soluble in water a Oxygen and carbon dioxide Carbon dioxide is more polar OO vs OCO b Nitrogen and ammonia Ammonia is more polar NEN vs NH3 c Methane and hydrogen sul de Hydrogen sul de is more polar CH4 vs HSH Chapter 2 Briggs problem 1 In the molecular structure below match up the functional group type in the list to the left with the molecule on the right Hydroxyl HYdrOXYI 39 OH Sullh dr 1 Amino Amlno y y Sullhydryl H2N CstH Carboxyl 0 E d Ester 11 0 Acyl H2CO H NH2 Ether Etherl CH Amido 3 Glycogen 01 14 linked Dglucose with 01 16 linked branches every 814 residues Glycogen granules also contain the enzymes that catalyze glycogen synthesis and degradation as well as regulatory proteins Highly branched structure permits rapid glucose mobilization through the simultaneous release of the endbranch glucose units Glycogenolysis Requires three enzymes 1 Glycogen phosphorylase catalyzes glycogen phosphorolysis bond cleavage by the substitution of a phosphate to yield GlP releases a glucose unit only if it is at least five units away from a branch point 2 Glycogen debranching enzyme breaks glycogen s branches making other glucose residues accessible to glycogen phosphorylase 3 Phosphoglucomutase converts GlP to G6P Glycogen phosphorylase degrades Glycogen to G1P Glycogen phosphorylase is a dimer of identical 842 residue subunits that catalyzes the rate controlling step in glycogen breakdown Allosterically inhibited by ATP G6P and glucose Allosertically activated by AMP A 30A long crevice on the surface of the phosphorylase monomer connects the glycogen storage site to the active site Since this crevice can accommodate a four or five sugar residues chain but cannot admit branched oligosaccharides it provides a clear physical rationale for the inability of phosphorylase to cleave glycosyl residues closer than five units from branch points Phosphorylase binds the cofactor Pyridoxal5 phosphate a vitamin BG derivative covalently linked to the enzyme via a Schiff base formed between its aldehyde group and the 8 amino group of Lys 680 In phosphorylase only the phosphate group participates in catalysis Phosphorolysis of glycogen proceeds by a random mechanism Glycogen phosphorylase undergoes conformational changes between the active R and inactive T conformations The Tstate enzyme has a buried active site and hence a low affinity for its substrates whereas the Rstate enzyme has an accessible catalytic site and a high affinity phosphate binding site AMP promotes phosphorylase s T 9 R shift by binding to the R state of the enzyme at its allosteric effector site increasing access to the active site by disordering a loop of residues that otherwise block it The conformational change also causes the Arg 569 side chain which is located in the active site to rotate in a way that increases the enzyme s binding affinity ATP also binds to the allosteric effector site but in the T state so that it inhibits not promotes the T R conformational shift Glycogen Debranching Enzyme AC1 as a Glucosyltransferase Phosphorolysis proceeds along a glycogen branch until it approaches to within four or five residues of an 01 16 branch point Glycogen debranching enzyme acts as an 01 14 transglycosylase by transferring an 01 14 linked trisaccharide unit from a limit branch of glycogen to the nonreducing end of another branch This reaction forms a new 01 14 linkage with three more units available for phosphorylase catalyzed phosphorolysis Debranching enzyme has separate active sites for the transferase and the Cl6 glucosidase reactions The maximal rate of the glycogen phosphorylase reaction is much greater than that ofthe glycogen debranching reaction Glycogen degradation beyond this point requires debranching and hence occurs more slowly Phosphoglucomutase interconverls G1P and G6P Phosphorylase converts the glucosyl units of glycogen to GlP which is converted by phosphoglucomutase to GGP Similar to the reaction in glycolysis catalyzed by phosphoglycerate mutase A phosphoryl group is transferred from the active phosphoenzyme to GlP forming Gl6P which then rephosphorylates the enzyme to yield GGP An important difference between this enzyme and PGM is that the phosphoryl group in PGM is covalently bound to a Ser hydroxyl group rather than to a His imidazole nitrogen The GGP produced by glycogen breakdown can continue along the glycolytic pathway or the pentose phosphate pathway Since the glucose is already phosphorylated the ATPconsuming hexokinase step can be bypassed In the liver this GGP is also made available for use by other tissues Because GGP cannot pass through the cell membrane it is first hydrolyzed by GGPase Although GGP is produced in the cytosol GGPase resides in the endoplasmic reticulum membrane Consequently GGP must be imported into the ER by a GGP translocase before it can be hydrolyzed The resulting glucose and phosphate are then returned to the cytosol via specific transport proteins A defect in any of the components of this GGP hydrolysis results in type glycogen storage disease Glycose leaves the liver via a specific glucose transporter named GLUTZ and is carried by the blood to ther tissues GGPase and therefore retain their GGP Muscles and other tissues lack GGPase and therefore retain their GGP