Class Note for BIOC 460 at UA 2
Class Note for BIOC 460 at UA 2
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Date Created: 02/06/15
NAME print last 4 digits of SID BIOCHEMISTRY 460 SECOND HOUR EXAMINATION June 18 2007 WRITE YOUR NAME AND ID NUMBER LEGIBLY ON EVERY PAGE CHECK TO BE SURE YOU HAVE 7 PAGES INCLUDING THE COVER PAGE I swearaf rm that I have neither given nor received any assistance with this exam Signature Date A NON PROGRAMMABLE CALCULATOR MAY BE USED ON THIS EXAM No programmable calculators are permitted and no sharing of calculators We have a couple of spare calculators to lend in an emergency SHOW YOUR WORK FOR ALL CALCULATIONS AND BE SURE TO STATE UNITS OF ANY NUMERICAL ANSWERS If the reasoning calculations or answer are shown anywhere other than in the space provided make a m in the space provided and put answer on BACK OF SAME PAGE so the grader for that page will have it USEFUL CONSTANTS R gas constant 8315 pmolloKelvinl 8315 x 103 QOmOFLKelvin 1 If temperature 25 C absolute temperature T 298 K Assume this temperature unless problem states otherwise F Faraday constant 965 kJVmol Potentially useful eg uations S max S Km MichaelisMenten Equation V C Free energy of transport AG RTln z ZFAV 1 where F is the Faraday constant 965 kJV mol z is the charge on the solute and AV is the membrane potential charge gradient across the membrane Use these generic pKa values only when no precise pKa for a speci c group is given Ionizable group in Approximate quotgenericquot pKa in peptides amp proteins from peptides and proteins Berg Tymoczko amp Stryer Biochemistry 5th ed 2001 ucarboxyl 31 side chain carboxyl 41 imidazole 60 uamino 80 thiol 83 aromatic hydroxyl 109 eamino 108 guanidino 125 BIOC 460 Exam 2 l NAME print last 4 digits of SID 1 4 pts What binds in the oxyanion hole during chymotrypsin catalysis A the imidazole group of the active site His B the nucleophilic negatively charged oxygen on the active site Ser C the negatively charged oxygen on the tetrahedral intermediate D the oxygen atom of the substrate s carbonyl CO group with the double bond to the O E the hydrophobic or aromatic R group of residue preceding the peptide bond to be cleaved F the carboxylate oxygen of the active site Asp 2 6 pts The general reaction catalyzed by protein kinases is Proteini gt Protein7 protein functional group 2nd substrate modi ed functional group 2nd product 3 3 pts Coconut oil contains only a very low proportion of unsaturated fatty acids FAs It still has a low melting point because A it contains a lot of shortchain fatty acids B it contains a lot of longchain fatty acids C it has very few hydrogen bonds per FA chain D it contains a lot of FAs with an odd number of carbon atoms 4 10 pts The Gq signal transduction pathway results in activation of a specific phospholipase C PLC which is a plasma membranebound protein A 3 pts What lipid a specific phosphoglyceride is cleaved by this enzyme B 4 pts What are the products of this PLC reaction and C 3 pts With respect to the substrate for this enzyme brie y describe the advantage for PLC to being membrane bound 23 BIOC 460 Exam 2 2 NAME print last 4 digits of SID 5 13 pts The acetylcholine receptor discussed in class is a gated ion channel in the membrane of motor nerve cell synapses that when open permits the ow of Na ions and Kl ions across the membrane in the directions dictated by their concentration gradients A 6 pts Explain the openingclosing of the acetylcholine receptor ion channel in response to acetylcholine ACh including the role of acetylcholine in the process and as much detail about the structural basis for the opening closing as you can B 3 pts Suppose that the concentration of Na ions outside the cell is 145 mM and the concen tration of Na inside the cell is 12 mM and the membrane potential AV across the plasma membrane is such that there is an excess of positive charge outside the cell When the ACh receptor channel opens the direction of ow of Na ions through the open channel will be A from inside to outside B from outside to inside C no net flow because the Na concentration gradient is exactly balanced by the charge gradient in eukaryotic cells C 4 pts Ionic or polar species have a very large thermodynamic barrier to transport DIRECTLY across a lipid membrane because in order for diffusion to occur must be lost from the ionic or polar species a thermodynamically unfavorable process Ion channels and transport proteins like the GLUT 1 glucose transporter decrease this energy barrier by presenting the molecule with 4 pts Pancreatic trypsin inhibitor and ocrantiproteinase are examples of protease inhibitors that A dramatically decrease the activation barrier for catalysis by binding tightly to the protease B bind a transition state extremely tightly show significant stabilization of the transition state C are covalent suicide inhibitors of the proteases they inhibit ie they form covalent adducts in the active sites of the target proteases D are bound so tightly as a substrate that they are only very slowly acted upon by the protease they inhibit and thus act at very low concentrations and are effective for very long time 4 pts For an enzyme whose catalytic mechanism involves a group with a pKa of 815 acting as a general acid catalyst draw the structures of two 2 di erent protein functional groups whose chemical properties would be consistent with their being able to ful ll that catalytic role Structures must be in the appropriate form to act as a general acid 1 2 21 BIOC 460 Exam 2 3 NAME print last 4 digits of SID 8 7 pts Suppose that a cell from an extraterrestrial organism has a transporter specific for a novel neutral sugar arugulose The laws of thermodynamics apply everywhere in the universe A 4 pts Ifthe extracellular concentration of arugulose is 5 mM and the intracellular concentration is 05 mM what would be the AGtransport for transporting arugulose into the cell at 25 C 2980K SHOW ALL WORK AND STATE UNITS OF THE ANSWER B 3 pts For the transport process described in part A above could the arugulose be transported into the cell by facilitated diffusion or would it require an active transport process Brie y explain your answer 9 7 pts Explain include a diagram if you wish how the activity of protein kinase A PKA is regulated by binding of cAMP Include in your explanation How the term consensus sequence RRXSTY relates to the activity of PKA where X is a small amino acid residue eg G and Y is a large hydrophobic residue eg 1 making it clear that you know how the term relates to the function and activation of PKA the term pseudosubstrate sequence where in the structure of PKA cAMP binds what happens to the structure of PKA when cAMP binds and how that relates to PKA activity 14 BIOC 460 Exam 2 4 NAME print last 4 digits of SID 10 9 pts 3 pts each question Circle the number corresponding to the best answer A The correct statement about Cpeptide is that it is also known as calmodulin 959 links the OL subunit to the 5 and Y subunits of the GS protein links the A and B chains of the insulin molecule in proinsulin binds calcium to facilitate the activation of protein kinase C PKC links the 0L and 5 subunits of the insulin receptor B A mutation in the regulatory R subunit of protein kinase A PKA that prevented the R subunits from binding cyclic AMP cAMP would cause PKA to be bP Nt active even in the presence of cAMP inactive even in the presence of cAMP active even in the absence of cAMP inactive but only at normal concentrations of cAMP C The H4 isozyme of lactate dehydrogenase 959 11 4 pts primarily is located in skeletal muscles that are used in sprinting would be impaired by a nutritional de ciency of niacin because of loss of cofactor is allosterically activated by insulin is inactivated by dephosphorylation would be impaired by a nutritional de ciency of thiamine because of loss of cofactor Epinephrine binding to the Sadrenergic receptor activates a mechanism involving protein kinase A PKA whereas insulin binding to its receptor activates a mechanism involving protein kinase B PKB Answer the questions below regarding events in these two signaling pathways Activation of adrenergic receptors Activation of insulin receptors Name the effector protein that is activated directly by the GOL subunit associated with this pathway Name the docking protein that is phosphorylated in this signaling pathway Name the second messenger signaling molecule produced by the effector protein in this pathway Name a downstream kinase other than PKB that is involved in this pathway 13 BIOC 460 Exam 2 5 NAME print last 4 digits of SID 12 22 pts 2 pts per blank Fill in each blank A Name one enzyme in a signaling pathway that is activated by calcium B The primary source what and from where of glucose in the postabsorptive state is C Name ONE of the three substances that has a greater highenergy phosphate transfer potential than does ATP z39fmore than one intermediate is given only the rst will be graded D List the three major forms in which energy is stored E Caffeine directly inhibits F Name ONE of the two enzymes that catalyzes the phosphorylation of glucose in glycolysis G The enzyme responsible for regenerating NAD to sustain glycolysis in red blood cells is H Insulin resistance will lead to the disease called BE VERY SPECIFIC I The enzyme activity associated with the Ssubunits of the insulin receptor is 22 BIOC 460 Exam 2 6 NAME print last 4 digits of SID 13 3 pts A unique toxin has been discovered that inhibits the GTPase activity of the 0L5 subunit If liver cells are exposed to this toxin the activity of pyruvate kinase in the liver cells decreases Provide a very brief reason for this effect 14 4 pts 1 pt each Glucagon stimulates the phosphatase activity of the dual function protein phosphofructokinase2 PFK2 fructose26bisphosphatase2 FBPaseZ whereas insulin stimulates the kinase activity of this same enzyme Circle the best answer in the statements below that describe regulation of the glycolytic and gluconeogenic pathways by fructose26bisphosphate F26BP Glucagon increases or decreases ux through the glycolytic pathway by increasing or decreasing the levels of F26BP in the cell Insulin increases ux through the glycolytic or gluconeogenic pathway by causing the phosphorylation or dephosphorylation of the bifunctional protein leading to a change in the concentration of F26BP in the cell 7 p 2 23 points p 3 21 points p 4 14 points p 5 13 points p 6 22 points p 7 7 points TOTAL 100 pts BIOC 460 Exam 2 7
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