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YOUR WRITE NAME AND I.D. NUMBER LEGIBLY ON EVERY PAGE PAGES WILL BE SEPARATED FOR GRADING! CHECK TO BE SURE YOU HAVE 6 PAGES, INCLUDING COVER PAGE. Signature: NAME (print): 5-digit course ID # Date: I swear/affirm that I have neither given nor received any assistance with this exam. BIOCHEMISTRY 460 THIRD HOUR EXAMINATION FORM A April 10, 2006 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 note 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) = 8.315 J mol 1 Kelvin 1 = 8.315 x 10 3 kJ mol 1 Kelvin 1 F (Faraday Constant) = 96.48 kJ V 1 mol 1 If temperature = 25 C, absolute temperature T = 298 K (Assume this temperature unless problem states otherwise.) Potentially useful equations: Energy Charge (EC): Change in Free Energy: Change in Reduction Potential: [ATP]+ 0.5[ADP] [ATP]+ [ADP]+ [AMP] G'= G '+RT ln [product]actual [substrate]actual At equilibrium (when G' = 0): E '= (E 'e- acceptor ) - (E 'e- donor) Relating G ' to E ': G '= -RT ln [product]equilibrium [substrate]equilibrium G '= -nFE ' Biochemistry 460, Exam #3 Form A April 10, 2006 NAME 5-digit course ID# 1. (5 pts) How are G Proteins inactivated (reset)? 2. (6 pts) Mutations in the protein Ras have been implicated in a number of cancers. The most common of these mutations is a glycine to valine substitution at codon 12. Why does a mutation at this position cause cancer? 3. (5 pts) Cyclic AMP (cAMP) was discussed in detail in class and in the text. What role does cAMP play in the glucagon stimulated signaling pathway and how is it made? 4. (6 pts) Define or explain the "Energy Charge" of a cell, and explain in general terms why catabolism is favored under conditions of low Energy Charge in the cell. (You do NOT need to discuss specific reactions that are regulated.) /22 p. 2 p. 3 p. 4 p. 5 p. 6 TOTAL: (22 points) (25 points) (23 points) (14 points) (16 points) (100 points) page 2 Biochemistry 460, Exam #3 Form A April 10, 2006 NAME 5-digit course ID# 5. (6 pts, 2 pts each) Which of the following statements are TRUE (T) and which are FALSE (F)? (Circle letter of correct answer for each.) T/F T/F T/F 6. Metabolic pathways exist in biological systems to maintain equilibrium with the environment. Burning 1 gram of glucose in a bomb calorimeter releases just as much energy as aerobic respiration of 15.7 g of glucose in your body. Energy input is required to increase the entropy of a biological system. (6 pts) Under certain conditions, cultures of brewers' yeast can be "made" to turn on a process that converts sugar into alcohol instead of into acetyl-CoA. A. (2 pts) What is this process called? B. (4 pts) What culture conditions are required to make this to happen? 7. (8 pts) The enzyme aldolase catalyzes the 4th step in glycolysis, the cleavage of fructose-1,6-bisphosphate into two C3 (3-carbon) molecules. A. (4 pts) What are these two C3 products? (Circle the correct answer.) 1. 3-phosphoglycerate (3-PGA) and dihydroxyacetone phosphate (DHAP) 2. 2 molecules of 3-phosphoglycerate (3-PGA) 3. glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) 4. 2 molecules of glyceraldehyde-3-phosphate (GAP) 5. 3-phosphoglycerate (3-PGA) and glyceraldehyde-3-phosphate (GAP) B. (4 pts) The G ' of this reaction in glycolysis is +23.8 kJ mol-1, but the G' is -1.3 kJ mol-1. Why is there a such a big difference in these two values? 8. (5 pts) Ferredoxin NADP+ reductase and succinate dehydrogenase both utilize a catalytic mechanism that involves a semiquinone intermediate (can carry one electron at a time). What coenzyme is required by these enzymes to be able to do this? /25 page 3 Biochemistry 460, Exam #3 Form A April 2006 10, NAME 5-digit course ID# 9. (10 pts) The enzyme, malate dehydrogenase, catalyzes the formation of the last of the three NADH molecules produced by the Citrate Cycle. Two relevant standard half reactions and their reduction potentials are written below. Write out the net reaction for this important redox conversion and calculate the change in standard free energy (G ') for the reaction. Show your work. Indicate whether this reaction is favorable or unfavorable under standard conditions. oxaloacetate2- + 2H+ + 2e- malate2NAD+ + H+ + 2e- NADH E ' = 0.166 V E ' = 0.320 V 10. (7 pts) Fill in the blanks to make the statements true about oxidative phosphorylation and photosynthesis. A. (1 pt) A minimum number of ______ photons must be absorbed during photosynthetic electron transport for every O2 that is evolved. B. (3 pts) The mathematical relationship between the energy of light and the wavelength of light is (equation or describe in words) ___________________________________________________. C. (3 pts) The _______________________ force drives the production of ATP by ATP Synthase. 11. (6 pts) Circle the correct words from each underlined pair to make the statements true: A. (3 pts) During oxidative (mitochondrial) electron transport, protons are pumped into /out of the mitochondrial matrix to generate an electrochemical gradient and then flow into /out of the matrix when ATP is produced. B. (3 pts) During photosynthetic electron transport, protons are pumped into /out of the thylakoid lumen to generate an electrochemical gradient and then flow into /out of the thylakoid lumen when ATP is produced. /23 page 4 Biochemistry 460, Exam #3 Form A April 10, 2006 NAME 5-digit course ID# 12. (14 pts) Compare mitochondrial electron transport system (ETS) and oxidative phosphorylation with the photosynthetic electron transport system and photophosphorylation, by filling in the table below from the following choices: cytosol plasma membrane chloroplast stroma chloroplast thylakoid space (thylakoid lumen) nucleus mitochondrial matrix mitochondrial intermembrane space (between inner and outer membranes) F0F1 ATP synthase succinate dehydrogenase cytochrome b6f complex photosystem I alternative oxidase complex IV ferredoxin thioredoxin Not in this system Mitochondrial ETS & Ox.Phos. Original electron donor for ETS Terminal electron acceptor for ETS Mobile protein electron carrier between protein complexes Mobile lipid electron carrier between protein complexes Where is ATP made? Protein that pumps protons Converts light energy into charge separation NADP+ NADPH NAD+ NADH -carotene chlorophyll pheophytin plastoquinone (PQ) ubiquinone (Coenzyme Q) O2 H2O ATP ADP AMP cAMP Photosynthetic ETS & Photophos. /14 page 5 Biochemistry 460, Exam #3 Form A April 10, 2006 NAME 5-digit course ID# 13. (10 points) A group of biochemists studied the Calvin Cycle enzyme, fructose-1,6-bisphosphatase (FBPase), from a plant. They analyzed activity of the enzyme under different conditions. To their surprise, they found that this enzyme was regulated in a manner similar to rubisco. They plotted their data and obtained the graph below. A A. (2pts) Where is this Calvin Cycle enzyme (FBPase) localized in the cell? B. (6 pts) What does this graph tell you about the regulation of this enzyme? In other words, what processes in the plant lead to the stimulation of the activity of this enzyme and why? B C. (2 pts) When would you expect physiological conditions around the enzyme in the plant to be similar to those of the two points indicated on the graph? Circle correct answer: Point A: Day / Night / Conditions around the enzyme are always like this in the cell. Point B: Day / Night / Conditions around the enzyme are always like this in the cell. 14. (6 pts, 3 pts each) Insert the appropriate word(s) to make the statements correct. A. C4 photosynthesis involves separation in __________________ for CO2 uptake and CO2 fixation. B. CAM photosynthesis involves separation in ________________ for CO2 uptake and CO2 fixation. /16 page 6
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lec31.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 31 GLYCOGEN METABOLISM: PATHWAYS/ALLOSTERIC CONTROL OBJECTIVES Glycogenolysis Pathway 1. general features; describe glycogen phosphorylase. 2. different fates of glucose-6-P from glycogenolysis in liver vs muscle 3. ...
exam_ans4-2.pdf
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Questions 1-8: Complete each statement by providing your response on the answer sheet. Abbreviations may be used if they are consistent with that used in the lecture notes. 1. 2. The two general groups of eicosanoid hormones that have opposite effect...
exam_ans2-2.pdf
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: [1.] Figures A and B show ribbon diagrams of 2 proteins embedded in lipid bilayers. a) For each protein identify the hydropathy plot to which it corresponds by placing the correct number on the line. (3 pts each) Protein A: _2_ Protein B:_1_ b) ...
lec22.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 22 SIGNAL TRANSDUCTION: G-PROTEINS OBJECTIVES 1. Mechanism by which glucagon/epinephrine produce cyclic AMP s via hormone-receptor complex formation, G protein, and adenylyl cyclase. 2. Mechanism by which cAMP activ...
lec37.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 DR. TISCHLER LECTURE 37 REGULATION OF ACETYL CoA PROCESSING OBJECTIVES 1. Regulation of processes in the formation of acetyl CoA: a) describe regulation of hormone-sensitive lipase by covalent modification b) mechanism by which activators...
lec13.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Lecture 13: Mechanism of Chymotrypsin Chemical Mechanism of Chymotrypsin Chymotrypsin Chymotrypsin is a digestive protease involved in breakdown of proteins and peptides so that their amino acids can be used. It is synthesized in the pancreas of ma...
lec29.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 29 OXIDATION PHOSPHORYLATION-2 OBJECTIVES 1. 1. How pH and charge gradients form across mitochondrial inner membrane Electroneutral vs electrogenic transport; significance of electrogenic transport for adenine nucleo...
lec21.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 21 METABOLISM: BASIC CONCEPTS OBJECTIVES 1. Identify the three major forms in which energy is stored and the four primary circulating fuels. 1. Distinguish between G and G, and explain the relationship between mass...
lec26.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 26 GLYCOLYSIS AND GLUCONEOGENESIS-2 OBJECTIVES Gluconeogenesis Pathway 1. Key liver gluconeogenic precursors; 4 unique rxns 1. relationship between nutritional status (i.e., fed or starved) and the amount of phosph...
lec14.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Lecture 14: Regulation of Proteins 1: Allosteric Control of ATCase Overview of Regulatory Mechanisms Description of ATCase Allosteric Properties of ATCase Biological Processes are Carefully Regulated Allosteric Control: The activity of some protein...
lec19.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Lecture 19: Membrane Proteins Architecture of Membrane Proteins Fluid Mosaic Model Protein Targeting Membrane Proteins are Responsible for Most Membrane Functions Lipid bilayers can form closed compartments. Biological membranes have specific funct...
lec36.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: <?xml version=\"1.0\" encoding=\"UTF-8\"?> <Error><Code>InternalError</Code><Message>We encountered an internal error. Please try again.</Message><RequestId>4977D0476DDA529B</RequestId><HostId>io3LzCOqfzwExCdpWvMO V1kjapIOtOqwHnBx3XmwHbXXIJHh45VbvfX8qczW...
lec27.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 27 PYRUVATE DEHYDROGENASE/ CITRIC ACID CYCLE OBJECTIVES 1. Pathways in mitochondrial matrix; role of inner membrane products for E1, E2, E3 components a) cofactors: associated...
lec17.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Lecture 17: Regulation of Proteins 4: Proteolytic Activation Examples Activation of Digestive Enzymes Blood Clotting Biological Processes are Carefully Regulated Allosteric Control: The activity of some proteins can be controlled by modulating the ...
lec15.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Lecture 15: Regulation of Proteins 2: Allosteric Control of Hemoglobin Hemoglobin and Myoglobin Allosteric Transition in Hemoglobin Physiological Role of Hemoglobin Myoglobin and Hemoglobin Myoglobin Hemoglobin Monomer Heterotetramer ( 2 2 ) Simi...
lec30.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: BIOC 460 - DR. TISCHLER LECTURE 30 PENTOSE PATHWAY & ANTIOXIDANTS OBJECTIVES 1. Pentose-phosphate pathway: a) oxidative and non-oxidative branches b) cofactor with each branch c) how oxidative branch is regulated d) three modes of the pentose phosp...
lec12.ppt
Path: Arizona >> BIOC >> 460 Summer, 2008
Description: Lecture 12: Enzyme Catalysis Catalytic Strategies Steps in a Reaction Enzymes are Classified According to the Reactions They Catalyse But while the details of the particular reaction vary from enzyme to enzyme, similar strategies are used to carry...
rasmol_tips_v2.txt
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Rasmol Tips and Tricks Overall strategy: Select something Do something to the selection Selection commands: select all select his (selects all the histidines) select 1 (selects the first residue) select 1,34,87 select 1-21 select hetero ...
SMaseD.txt
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: # smase D in ribbons with acitve site plus sulfates and waters zap load ./proteins/1XX1.pdb # Let\'s play with RASMOL! # Type \"help\" to start the help function. # Type \"help commands\" to get a list of commands. # Type \"help colors\" to get a list of c...
RASMOL466.TXT
Path: Arizona >> BIOC >> 568 Fall, 2008
Description: Sheet1 #!rasmol -script # File: RASMOL466.TXT # Creator: RasMol Version 2.6 zap background [0,0,0] load pdb \"1GLU.PDB\" set ambient 60 set specular off reset slab off rotate z -175 rotate y 38 rotate x 158 translate x 49 translate y 40 zoom 400 set bo...
shipley.pdf
Path: Arizona >> BIOC >> 585 Fall, 2008
Description: 471 Lipids Bilayers and nonbilayers: structure, forces and protein crystallization Editorial overview G Graham Shipley Address Department of Biophysics, Center for Advanced Biomedical Research, Boston University School of Medicine, Boston, MA 02118,...
landau.pdf
Path: Arizona >> BIOC >> 585 Fall, 2008
Description: Proc. Natl. Acad. Sci. USA Vol. 93, pp. 1453214535, December 1996 Biophysics Lipidic cubic phases: A novel concept for the crystallization of membrane proteins (bacteriorhodopsin structure bicontinuous phases lipidic matrices x-ray crystallography) ...
protein_structure.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Proteins: Tertiary and Quaternary Structure Reading - Chapter 6 Practice problems - Chapter 6, #5-8; Proteins extra problems Tertiary Structure Most proteins are globular, essentially spherical. They posses both secondary str...
enzyme_mechanism.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Enzyme Mechanisms Reading - Chapter 8 Practice problems - Chapter 8: (not yet assigned); Enzymes extra problems Catalytic Mechanisms General acid-base catalysis is a commonly employed mechanism in enzyme reactions, e.g., h...
secondary_structure.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Proteins: Secondary Structure and Fibrous Proteins Reading - Chapter 6, pp. 159-175 Practice problems - Chapter 6 - #1,4 (sec. struct.), #2,3 (fibrous prots); Proteins extra problems Levels of Protein Organization The function o...
Ex1AdditionalPracticeANS_06.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: BIOC 462a Additional practice problems for Exam 1 (for review in discussion sections 9/14/06) 1. Effect of polarity of the solvent and other environmental factors on the pKas of weak acids A. Consider the pKa of the -amino group of a protein. Suppose...
protEQ.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: PROTEINS - SELF STUDY QUESTIONS 1. This is the titration curve for which amino acid? 2. A Ramachandran plot shows A. The amino acid residues that have the greatest degrees of rotational freedom. B. The sterically allowed rotational angles between th...
carb_structure.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a - Carbohydrate Structure Reading - Chapter 9 Practice problems - Chapter 9: 2,4a,4b,6,9,10,13,14,15,16a,17; Carbohydrate extra problems Monosaccharides Carbohydrates (CH2O)n or saccharides are the sugars. Aldehydes or ketones...
ConceptMapThinker.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: ENZYMES Reactions are inhibited by Kinetics used to study Inhibitors Can be characterized as Mechanisms use Rates of Reactions 2 types Catalytic Tools Metal Ion Catalysis Induced Fit Acid Base Catalysis Electrostatics Reversible Mixed are aff...
hemoglobin_function.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Hemoglobin Structure and Function Reading - Chapter 7 Practice problems - Chapter 7: 1-6; Proteins extra problems Myoglobin and Hemoglobin Oxygen is required for oxidative metabolism and energy production in most cells. Ox...
nucacid_structure.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Nucleic Acid Structure Reading - Chapter 10 Practice problems - Chapter 10: #2,3,6,8,9,11; Nucleic Acids extra problems Primary Structure As is the case for proteins, nucleic acids have a primary structure -the sequence of bas...
GeneralChemRev.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: BIOC 462a General Chemistry Review: Chemical Equilibrium, Ionization of H2O, pH, pKa General Equilibrium: What are the UNITS of Keq? Example reactions: A -> B units of Keq ? A -> B + C units of Keq ? A + B -> C units of Keq ? A + B -> C + D units of...
secondary_structure.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Proteins: Secondary Structure Reading - Chapter 6 Practice problems - Chapter 6 - 1,2; Proteins extra problems Levels of Protein Organization The function of a protein can only be understood in terms of its structure. The three d...
E299.DOC
Path: Arizona >> E >> 462 Fall, 2009
Description: Exam 2 - 1999 1. (5 points) In the following table indicate by an X whether the amino acids contribute to hydrophobic, ionic and hydrogen bonding interactions in a protein at pH 7.0. Amino Acid Asp Leu Tyr Hydrophobic X X Ionic X Hydrogen bonds X X ...
E299.DOC
Path: Arizona >> E >> 99 Fall, 2009
Description: Exam 2 - 1999 1. (5 points) In the following table indicate by an X whether the amino acids contribute to hydrophobic, ionic and hydrogen bonding interactions in a protein at pH 7.0. Amino Acid Asp Leu Tyr Hydrophobic X X Ionic X Hydrogen bonds X X ...
enzyme_mechanism.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Enzyme Mechanisms Reading - Chapter 16 Practice problems - Chapter 16 - 1,2,4,5; Enzymes extra problems Catalytic Mechanisms General acid-base catalysis is a commonly employed mechanism in enzyme reactions, e.g., hydrolysis o...
WATER.DOC
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 46a Water, pH and Ionic Equilibria Reading - Chapter 2 Practice problems - Chapter 2 - 6,7,8,9,12; Physical Chemistry extra problems; buffer problems Properties of Water Unusual Properties Life as we know it could not exist without...
nucleic_acid_chemistry.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Nucleic Acid Chemistry Reading - Chapter 11 Practice problems - Chapter 11 - 3,4; Nucleic Acids extra problems Components of Nucleic Acids There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (...
nucacid_structure.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Nucleic Acid Structure Reading - Chapter 12 Practice problems - Chapter 12 - 4, 6, 7, 11; Nucleic Acids extra problems Primary Structure As is the case for proteins, nucleic acids have a primary structure -the sequence of base...
E399.DOC
Path: Arizona >> E >> 462 Fall, 2009
Description: <?xml version=\"1.0\" encoding=\"UTF-8\"?> <Error><Code>InternalError</Code><Message>We encountered an internal error. Please try again.</Message><RequestId>4FC4FDA40CEABD3F</RequestId><HostId>miucarPVnWB5JPAavAm7 PLHhtD6jg6JK5V2unsNsLT42kRoOmqROGywt/ceZ...
E399.DOC
Path: Arizona >> E >> 99 Fall, 2009
Description: <?xml version=\"1.0\" encoding=\"UTF-8\"?> <Error><Code>InternalError</Code><Message>We encountered an internal error. Please try again.</Message><RequestId>4FC4FDA40CEABD3F</RequestId><HostId>miucarPVnWB5JPAavAm7 PLHhtD6jg6JK5V2unsNsLT42kRoOmqROGywt/ceZ...
Ex1guide_02.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: <?xml version=\"1.0\" encoding=\"UTF-8\"?> <Error><Code>InternalError</Code><Message>We encountered an internal error. Please try again.</Message><RequestId>36CBC4A9FC3B38B7</RequestId><HostId>XuL6EbmuO+w+X51shse+ +gmQcCkFML7jArKhSf4X8T97zufYR356NLePDMkY...
protein_structure.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Protein: Tertiary and Quaternary Structure Reading - Chapter 6 Practice problems - Chapter 6; Proteins extra problems Tertiary Structure Most proteins are globular, essentially spherical. They posses both secondary structure ...
carb_function.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a - Carbohydrate Function Reading - Chapter 7, 9, 29.4 Practice problems - Chapter 7 - 5,6; Carbohydrate extra problems Significance and Functions of Carbohydrates Bacterial Cell Walls The cell walls of Gram-positive bacteria consist...
E298.DOC
Path: Arizona >> E >> 462 Fall, 2009
Description: Exam 2 -1988 1. (5 points) The N-terminal amino acid of the chains of oxy-hemoglobin has a pKa of 7.0. If this group plays an important role in the Bohr effect, would the pKa in deoxy-hemoglobin be higher or lower? Explain. Higher. In order for the ...
E298.DOC
Path: Arizona >> E >> 98 Fall, 2009
Description: Exam 2 -1988 1. (5 points) The N-terminal amino acid of the chains of oxy-hemoglobin has a pKa of 7.0. If this group plays an important role in the Bohr effect, would the pKa in deoxy-hemoglobin be higher or lower? Explain. Higher. In order for the ...
E398.DOC
Path: Arizona >> E >> 462 Fall, 2009
Description: Exam 3 - 1988 1. (5 points) (a) (2.5 points) What charge, if any, would a nonspecific DNA-binding protein carry at neutral pH? Why? Positive, in order to bind to the negative phosphates of the backbone. (b) (2.5 points) Why would an RNA molecule, whi...
E398.DOC
Path: Arizona >> E >> 98 Fall, 2009
Description: Exam 3 - 1988 1. (5 points) (a) (2.5 points) What charge, if any, would a nonspecific DNA-binding protein carry at neutral pH? Why? Positive, in order to bind to the negative phosphates of the backbone. (b) (2.5 points) Why would an RNA molecule, whi...
E198.DOC
Path: Arizona >> E >> 462 Fall, 2009
Description: Exam 1 -1998 1. (5 points) Which of these compounds would be the best buffer at pH 6.9? Acetic acid (pKa = 4.7), histamine (pKa = 6.5), or ethylamine (pKa = 9.0). Briefly justify your answer. Histamine. Its pKa is closest to the desired pH. 2. (8 poi...
E198.DOC
Path: Arizona >> E >> 98 Fall, 2009
Description: Exam 1 -1998 1. (5 points) Which of these compounds would be the best buffer at pH 6.9? Acetic acid (pKa = 4.7), histamine (pKa = 6.5), or ethylamine (pKa = 9.0). Briefly justify your answer. Histamine. Its pKa is closest to the desired pH. 2. (8 poi...
E199.DOC
Path: Arizona >> E >> 462 Fall, 2009
Description: Exam 1 - 1999 1. (5 points) Which of these compounds would be the best buffer at pH 4.0? Formic acid (pKa = 3.8), pyridine (pKa = 5.2), or chloroacetic acid (pKa = 2.9). Briefly justify your answer. Formic acid. Its pKa is closest to the desired pH....
E199.DOC
Path: Arizona >> E >> 99 Fall, 2009
Description: Exam 1 - 1999 1. (5 points) Which of these compounds would be the best buffer at pH 4.0? Formic acid (pKa = 3.8), pyridine (pKa = 5.2), or chloroacetic acid (pKa = 2.9). Briefly justify your answer. Formic acid. Its pKa is closest to the desired pH....
Feeder_Fermentation_handout_2009.pdf
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Lecture notes for Bioc462b lecture 5 - Feeder Pathways of Glycolysis & Fermentation Jan 26, 2009 Learning Objectives Describe the catabolism for fructose and galactose in general terms and their relationship to glycolysis. Explain the rationale behi...
compsect05_revnov15.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Biochemistry 462a Honors -Fall 2005 Computer Section Weds 12 -12:50 PM BSW 243 Updated 08/21/05 MHJC During the semester each student will develop a project using the primary biochemical literature and molecular graphics programs on the computer. The...
bioinformaticsIII_05_key.doc
Path: Arizona >> BIOC >> 462 Fall, 2008
Description: Bioinformatics III: ExPASy and PROSITE motif searching Created by: Matt Cordes 11/14/05 Lesson Date: 11/16/05 W We\'ve looked at sequence similarity searching using BLAST and structure similarity searching using VAST. Today we\'re going to do a type o...
expt4_q.pdf
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: BIOC 463A Sept. 25, 2001 In order to more fully appreciate the information gained from Experiment 4, you are strongly urged to plot the data as suggested and answer the following questions. These answers will not be collected, but you might see them ...
protein_purification.pdf
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: BIOC 463A Protein Purification Concepts General Concepts about Protein Purification Initial Considerations: Why do you want the protein (ie. what is your project all about)? How much protein do you need (ng, ug, mg, g)? How homogenous or pure? N...
tim3.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load tim3.pdb cpk off wireframe off select :A; trace on; color blue select :B; trace on; color lime select 167-177; trace 0.8 select pgh; wireframe 0.3; color red; dots on moveTo 0 -374 60 -926 176.6 125 ...
tim3.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load tim3.pdb cpk off wireframe off select :A;trace on;color trace blue select 167-177:A;trace 0.8 select :B;trace on;color trace lime select 167-177:B;trace 0.8 select pgh;cpk on;color cpk moveTo 1 -374 60 -926 176.6 125 ...
tim6.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: select pgh or 165:B wireframe 0.3 select atomno=1890 or atomno=1889 or 165:B.OE2 dots on center pgh or 12:B or 95:B or 165:B...
water4.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 1MSI.pdb.gz cpk off select 47 or 156-157 or 160 or 174 restrict selected center selected cpk 20% moveTo 0 22 -475 880 179.0 930 ...
alpha2.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 1WFB.pdb spin off cpk off restrict 12-32:B center 12-32:B wireframe 0.25 hbonds 0.15 color hbonds green restrict backbone moveTo 0 98 593 799 153.7 419 ...
actin1.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 1atn.pdb.gz restrict :a;wireframe off;cpk off select atomno=1219 center selected select :a;cartoon on;color cartoon lime select atp;wireframe on;wireframe 0.3 cpk on;cpk 0.5 select atomno= 5019; cpk on;color yellow moveTo 1 -994 -86 67 126.2 200...
sheet2.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load ./convention/1TIM.pdb.gz cpk off wireframe off restrict :A center :A cartoon on color cartoon structure select helix and :A cartoon off strands on moveTo 0 -822 -106 -559 48.0 305...
question3.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 2BRZ.pdb.gz spin off cpk off wireframe off cartoons on color white select helix color red select sheet color green select (36 or 53 or 2 or 9) and sidechain cpk color red select (15 or 27 or 3 or 6) and sidechain cpk color blue...
hk4.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 2yhx.pdb.gz cpk off wireframe off select protein;cpk on;color lime select otg spacefill on moveTo 1 -898 -227 377 169.8 ...
reset.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 2BRZ.pdb.gz spin off cpk off wireframe off cartoons on color white select helix color red select sheet color green ...
reset.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load antibeta.pdb spin off...
reset.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 1CAG.pdb.gz spin off restrict protein...
porin2.txt
Path: Arizona >> BIOC >> 463 Fall, 2008
Description: load 1prn.pdb.gz cpk off select hetero wireframe off select protein wireframe off cartoons on color magenta select sidechain and hydrophobic cpk on color lime moveTo 1 19 -103 -994 51.2 150...
