BIOC 384 Exam 2
Which of the following may result from a His143 --> Ala143 mutation in adult hemoglobin? A. increased oxygen transport efficiency B. reduced affinity for 2,3-BPG C. decreased CO2 transport efficiency D. sickle cell anemia
B. reduced affinity for 2,3-BPG
Match each major class of protein with the best representative protein from each class. 1. Structural proteins 2. Genomic caretaker proteins 3. Metabolic enzymes 4. Transport proteins 5. Cell signaling proteins (Actin) (Histone) (Pepsin) (Aquaporin) (Adenylate cyclase)
1. Structural proteins (Actin) 2. Genomic caretaker proteins (Histone) 3. Metabolic enzymes (Pepsin) 4. Transport proteins (Aquaporin) 5. Cell signaling proteins (Adenylate cyclase)
Consider five proteins with the properties shown in the table above and answer the following four questions. Record your answers and choose the set of correct answers for questions a --> d. a) Which protein would elute first from a (+) charged anion exchange column in buffer at pH 4.0? b) Which protein would migrate the slowest in an SDS-PAGE gel? c) Which protein would elute last from a gel filtration chromatography column under non-denaturing conditions? d) Which protein would elute last from a (-) charged cation exchange column in buffer at pH 4.0? A, E, C, A C, E, B, A A, D, C, B E, E, C, B A, E, B, A
A, E, C, A
Choose the five correct labels for the figure to the right. "Transition State" = TS A. (1) ES (2) TS (3) EP (4) E + P (5) substrate B. (1) E + P (2) TS (3) EP (4) ES (5) enzyme C. (1) EP (2) TS (3) ES (4) E + P (5) product D. (1) ES (2) EX (3) EP (4) E + P (5) TS E. (1) ET (2) ES (3) E + P (4) TS (5) ligand
A. (1) ES (2) TS (3) EP (4) E + P (5) substrate
What is the energy requirement to transport 2 moles of K+ from the outside to inside? A. +3.7 kJ B. -26.2 kJ C. -41.2 kJ D. +1.8 kJ E. +41.2 kJ
A. +3.7 kJ
What are the THREE key assumptions of Michaelis-Menten kinetics. 1. The reaction is analyzed at a time in the reaction that negligible product is formed. 2. Product release is assumed to be a rapid step in the process. 3. The steady state condition is reached quickly under conditions where [S] >> [E]. 4. Enzymes have higher binding affinities for products than the transition state. 5. Catalysts alter the free energy of the reaction without altering the equilibrium constant. 6. Substrates and products are chemically inert until enzymes are added, catalysts = life. A. 1, 2, 3 B. 1, 2, 5 C. 2, 3, 4 D. 1, 3, 6 E. 2, 3, 5
A. 1, 2, 3
After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein? A. 3.6-fold B. None of these answers are correct. C. 0.28-fold D. 7.5-fold E. 1.3-fold
A. 3.6-fold
What distinguishes P-type transporters from ABC transporters? A. ATP hydrolysis by P-type transporters results in a phosphorylated intermediate while ATP hydrolysis causes ABC transporters to convert from an outward facing transporter to an inward facing transporter. B. P-type transporters move molecules with the chemical gradient while ABC transporters move molecules against the chemical gradient. C. None of these answers are correct. D. P-type transporters are symports while ABC transporters are antiports. E. P-type transporters are primary active transporters while ABC transporters are secondary active transporters.
A. ATP hydrolysis by P-type transporters results in a phosphorylated intermediate while ATP hydrolysis causes ABC transporters to convert from an outward facing transporter to an inward facing transporter.
Select the most correct statement regarding how catalysts increase reaction rates. A. Catalysts lower the amount of energy required to reach the transition state. B. Catalysts raise the ground state energy of the product and the reactant to lower the activation energy. C. Catalysts lower the ground state energy of the product, thereby lowering the DG of the reaction. D. Catalysts lower the ground state energy of the product and the reactant to increase the activation energy. E. Catalysts lower the DG of the reaction and the Keq of the reaction to increase reaction rates
A. Catalysts lower the amount of energy required to reach the transition state.
The solute concentration and the membrane potential each contribute to the total energy requirement for transport. Based on your DG calculations above, which direction of transport would be more energetically favorable (-DG) under the same conditions of solute concentration and membrane potential if 2 glucose molecules were transported across the membrane rather than 2 Ca2+ ions and why? A. Inside --> Outside is more favorable because solute concentration flows down the gradient. B. Outside --> Inside is more favorable because solute concentration flows down the gradient. C. Inside --> Outside is more favorable because membrane potential provides an opposite charge. D. Outside --> Inside is more favorable because membrane potential provides a similar charge. E. Transport direction from Outside --> to Inside and from Inside --> Outside are equally favorable.
A. Inside --> Outside is more favorable because solute concentration flows down the gradient.
With proteins being separated via gel electrophoresis, A. None of these answers are correct. B. for proteins of the same size, the more negative protein moves slower. C. larger proteins move faster. D. for proteins of the same size, the more positive protein moves faster. E. smaller proteins move slower.
A. None of these answers are correct.
The transition state theory states that the enzyme active site makes the most contacts with the high energy transition state, which occurs midway between ES <-> EP, than it does with either S or P. What evidence described below best supports the transition state theory? A. Transition state analogs bind tightly to enzyme active sites, for example adenosine deaminase inhibitors. B. Products of a reaction dissociate only after cleavage of enzyme intermediate in the enzyme active site. C. The activation energy of a catalyzed reaction is lower than an uncatalyzed reaction. D. Multiple substrates bind in an ordered fashion, i.e., substrate A binds before B that binds before C. E. The activation energy of a reaction is not altered by the catalytic activity of enzymes .
A. Transition state analogs bind tightly to enzyme active sites, for example adenosine deaminase inhibitors.
X-ray crystallography (XRC) and nuclear magnetic resonance (NMR) spectroscopy provide three dimensional structural information about the position of atoms in a purified protein. Name one advantage (adv) and one disadvantage (dvg) of each technique with regard to high resolution protein structures. A. XRC/adv; large proteins, XRC/dvg; requires crystals, NMR/adv; soluble protein, NMR/dvg; small proteins B. XRC/adv; small proteins, XRC/dvg; requires crystals, NMR/adv; large proteins, NMR/dvg; soluble protein C. XRC/adv; requires crystals, XRC/dvg; large protein, NMR/adv; small proteins, NMR/dvg; soluble protein D. XRC/adv; large proteins, XRC/dvg; soluble protein, NMR/adv; small protein, NMR/dvg; requires crystals E. XRC/adv; soluble protein, XRC/dvg; small proteins, NMR/adv; requires crystals, NMR/dvg; large proteins
A. XRC/adv; large proteins, XRC/dvg; requires crystals, NMR/adv; soluble protein, NMR/dvg; small proteins
This question has two parts. a) What provides the energy for a secondary active symporter to move molecules against a concentration gradient? b) Give an example of a secondary symporter protein. A. a) ATP-dependent transport of solute by a primary active transporter, b) sodium-iodide symporter B. a) ATP-dependent transport of solvent by a primary active transporter, b) lactose permease C. a) Antiporter activity of a primary active transporter, b) sarcoplasmic reticulum calcium transporter D. a) Conformational changes in an ion gated channel protein, b) serotonin symporter protein E. None of the above statements provide a correct answer for both parts (a) and (b)
A. a) ATP-dependent transport of solute by a primary active transporter, b) sodium-iodide symporter
The graph above shows three potential oxygen saturation curves for hemoglobin. If the tetrameric hemoglobin is dissociated into its subunit, the saturation curve would change as represented by a shift from... (choose ONE answer) C to B A to C A to B B to C B to A
B to A
What is the DG when transporting 2 Ca2+ from the outside of the cell to the inside of the cell? A. +5.9 kJ/mol B. -26.2 kJ/mol C. -9.5 kJ/mol D. -7.2 kJ/mol E. -13.1 kJ/mol
B. -26.2 kJ/mol
Calculate the purification of the target protein when there is a 30% decrease in activity and a 55% decrease in total protein after centrifugation. A. 0.55-fold B. 1.6-fold C. 1.8-fold D. 0.64-fold
B. 1.6-fold
The change in free energy for Solute A concentration across a gradient is calculated to be -10 kJ/mol. If Solute B is transported against its own concentration gradient using a secondary active symporter transport mechanism linked to Solute A, what is the maximum concentration ratio that can be achieved for Solute B in this system? A. 5:1 B. 50:1 C. 1:50 D. 1:5 E. 10:1
B. 50:1
Refer to the reaction coordinate diagram at right that compares catalyzed and uncatalyzed reactions. Which of the following labels are correct? "Activation energy" = AE. A. 3 = Reactant, 6 = DG, 2 = AE for the catalyzed rxn B. 6 = AE for catalyzed rxn, 5 = Product, 1 = DG C. 7 = DG, 1 = DG‡ , 4 = AE for the catalyzed rxn D. 6 = AE for uncatalyzed rxn, 3 = Substrate, 2 = DG‡ E. 3 = Substrate, 2 = AE for catalyzed rxn, 7 = DG‡‡
B. 6 = AE for catalyzed rxn, 5 = Product, 1 = DG
For this problem, assume the cell has a membrane potential of -60 mV with the interior negative with respect to the exterior, and is being kept at a constant temperature of 25 °C. The concentration of glucose outside of a given cell is 5 mM and inside the cell is 150 mM. What is the free energy change for the transport of glucose into the cell at 25 °C? A. -5.78 kJ/mol B. 8.43 kJ/mol C. -8.43 kJ/mol D. The correct answer is not given. E. 5.78 kJ/mol
B. 8.43 kJ/mol
An experiment is performed in which the kinetics of an enzyme-catalyzed reaction at different pHs is monitored. It is found that the Kmdoes not change but that the kcat increases as the pH goes above 7. Which of the following is true? Question options: A. A chemical group with a pKa of around 7 must be positively charged in order for the substrate to bind. B. A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism. C. Protons are acting as positive heterotropic allosteric effectors of this enzyme. D. A chemical group with a pKa of around 7 must be deprotonated in order for substrate to bind.
B. A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism.
Enzymes A (EnzA) and B (EnzB) have nearly identical turnover numbers (kcat) but EnzB has a lower Km. Which enzyme has the highest catalytic efficiency (specificity constant) and why? A. EnzA has the highest catalytic efficiency because it has a lower lower Km resulting in a higher kcat / Km. B. EnzB has the highest catalytic efficiency because it reaches ½ vmax at a lower substrate concentration. C. EnzB has the highest catalytic efficiency because it has a higher vmax at a lower enzyme concentration. D. EnzA has the highest catalytic efficiency because it binds the substrate with a lower affinity. E. EnzA has the highest catalytic efficiency because it reaches ½ vmax at a higher substrate concentration.
B. EnzB has the highest catalytic efficiency because it reaches ½ vmax at a lower substrate concentration.
Which of the following is true of sickle cell anemia? A. It is a dominant genetic disease. B. It is caused by a mutation in the beta-globin gene. C. It results in a hemoglobin that contains a hydrophobic amino acid D. in the interior of the protein. E. It is caused by an amino acid substitution in the F helix.
B. It is caused by a mutation in the beta-globin gene.
Which of the following is a way that an enzyme can increase the reaction rate inside a cell? A. Binding tighter to the substrate than the product. B. Orienting substrates appropriately for the reaction to occur. C. Increasing the activation energy at the transition state. D. Provide a path that forms a covalent bond to the product. E. By lowering the standard free energy change for the reaction.
B. Orienting substrates appropriately for the reaction to occur.
Enzymes increase reaction rates in the following three ways (choose the BEST answer): A. Stabilize the transition state, coenzyme-dependent redox reactions, provide optimal environment B. Provide an alternate path for product formation, stabilize the transition state, provide optimal environment C. Provide an alternate path for product formation, metabolite transformations, stabilize the transition state D. Provide an optimal environment, use catalytic functional groups, and dependent on metal ion catalysis E. The correct answer is not given.
B. Provide an alternate path for product formation, stabilize the transition state, provide optimal environment
Chymotrypsin is a serine protease requiring the formation of a covalent / noncovalent enzyme complex as a critical step in the reaction. The amino acid residue histidine has a central role in the reaction mechanism, which is described as a(n) acid-base / metal-ion catalysis mechanism. The reaction sequence results in the release of the carboxyl / amino terminal fragment first as a result of the His 57 residue abstracting / donating a proton to the substrate. The chymotrypsin reaction relies on water to generate a nucleophile / electrophile that attacks the carbonyl carbon / amide nitrogen at the cleavage site. Both the Gly 193 / Asp 102 and Serine 195 residues are essential to stabilization of the oxyanion intermediate. A. covalent, covalent, amino, abstracting, nucleophile, carbonyl carbon, Asp 102 B. covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbon, Gly 193 C. noncovalent, acid-base, carboxyl, abstracting, nucleophile, amide nitrogen, Gly 193 D. covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbon, Asp 102 E. covalent, acid-base, amino, abstracting, nucleophile, amide nitrogen, Asp 102
B. covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbon, Gly 193
Which of the experimental steps listed at the right is considered the most challenging in X-ray crystallography? A. mounting the crystal on the X-ray diffractor. B. determining the phases of the diffracted X-rays. C. dissolving the protein in the appropriate solvent. D. using the correct radio frequency for nuclear spin. E. isolating epitope-tagged proteins from bacteria.
B. determining the phases of the diffracted X-rays.
Below is a fractional saturation curve for O2 binding to adult hemoglobin. Assume that curve Y represents a system at pH 7.4 and with a normal physiological level of 2,3-BPG. Curve X represents a system that A. is at pH 7.4 with a higher than normal physiological level of 2,3-BPG. B. has a higher pH with a normal physiological level of 2,3-BPG. C. has a pH of 4.5 with a lower than normal physiological level of 2,3-BPG. D. is at pH 7.4 with a normal physiological level of 2,3-BPG but with an increased level of CO2.
B. has a higher pH with a normal physiological level of 2,3-BPG.
The K+ channel protein does not allow Na+ ions to pass through because A. Na+ ions are larger than K+ ions. B. it is unfavorable for the Na+ ions to lose their associated water molecules, which makes the solvated Na+ ions to large to fit through the channel. C. it is energetically favorable for the Na+ to interact with the amino acids in the selectivity channel. D. the Na+ ions interact too tightly with the binding sites to pass through the channel.
B. it is unfavorable for the Na+ ions to lose their associated water molecules, which makes the solvated Na+ ions to large to fit through the channel.
Place the following HMG-CoA reductase steps in the correct order: A. Reduction of aldehyde B. Breakdown of hemithioacetal C. Reduction of thioester D. Cofactor exchange Question options: A, D, C, B A, B, D, C C, D, B, A C, B, D, A
C, D, B, A
What is the energy requirement to transport 3 moles of Na+ from the inside to outside? A. +13.7 kJ B. +1.8 kJ C. +41.2 kJ D. +3.7 kJ E. -13.7 kJ
C. +41.2 kJ
Which of the THREE following statements about myosin are true? 1. The interaction between myosin and actin converts chemical energy to mechanical work. 2. Thick and thin filaments slide past each other during contraction to shorten the muscle. 3. The myosin head has a binding site for actin, titin, troponin, tropomyosin, and ATP. 4. The myosin head functions like molecular lever during the power stroke of contraction. 5. Myosin-actin reaction cycle requires hydrolysis of 1 ATP per myosin head in each cycle. 6. The A band and I band belong to the Z club and meet up at the T tubule to disco nightly. A. 2, 3, 4 B. 1, 2, 6 C. 1, 2, 5 D. 1, 3, 4 E. 2, 4, 5
C. 1, 2, 5
Both passive and active transport proteins are needed to transport __________ across membranes. A. metals and nonpolar molecules B. nonpolar molecules and ions C. polar and nonpolar molecules D. polar molecules and ions
D. polar molecules and ions
Which are critical features or properties of nearly all protein enzymes? Choose all that apply. 1. Enzymes usually display high affinity and specificity for their substrates. 2. A covalent bond forms between an enzyme and substrate following substrate binding. 3. Enzyme activity is often highly regulated to provide maximum control of catalysis. 4. Histidine is found in the enzyme active site to facilitate acid-base catalysis 5. Conformational changes, both small and large, can occur after substrate binding. 6. Enzymes alter the change in free energy without altering the rates of reactions. A. 2 and 4 B. 1, 2, 4, 5 C. 1, 3, 5 D. 2, 4, 6 E. 5 only
C. 1, 3, 5
Which of the TWO following statements about myosin are true? 1. The A band and I band belong to the Z club and meet up at the T tubule to disco nightly. 2. The myosin head has a binding site for actin, titin, troponin, tropomyosin, and ATP. 3. Thick and thin filaments slide past each other during contraction to lengthen the muscle. 4. Myosin-actin reaction cycle requires hydrolysis of 1 ATP per myosin head in each cycle. 5. The myosin head functions like molecular lever during the power stroke of contraction. 6. The interaction between myosin and actin converts chemical energy to mechanical work. A. 4 and 5 B. 1 and 3 C. 4 and 6 D. 3 and 4 E. 5 and 6
C. 4 and 6
After __________ induced changes in the structure of thin filament, myosin heads containing __________ in the nucleotide binding site will bind with high affinity to actin subunits. A. ATP; ADP + Pi B. Ca2+; ATP C. Ca2+; ADP + Pi D. ATP; Ca2+
C. Ca2+; ADP + Pi
Which separation technique exploits the density differences of biomolecules and organelles? A. Dialysis using dialysis tubing in a beaker with buffer. B. Salting out by ammonium sulfate using a beaker and stir bar. C. Centrifugation using centrifuge tubes in a rotor placed in a centrifuge. D. An ionic exchange column using a charge resin at an optimal pH. E. An affinity column using a solid matrix with a specific ligand attached.
C. Centrifugation using centrifuge tubes in a rotor placed in a centrifuge.
In one type of hemoglobin mutant the amino acid change eliminates a hydrogen bond that normally stabilizes the R state. Would you expect this mutant hemoglobin to have a higher or lower O2 affinity compared to the normal protein and why? A. Lower O2 affinity because the R-T equilibrium would be mostly shifted to the R state. B. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the R state. C. Lower O2 affinity because the R-T equilibrium would be mostly shifted to the T state. D. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the T state. E. The correct answer is not given.
C. Lower O2 affinity because the R-T equilibrium would be mostly shifted to the T state.
Which of the reactions below are examples of reversible modifications mediated by enzymes. A. Stabilization of the transition state and formation of covalent enzyme-substrate complexes. B. Isomerization reactions that do not change the molecular formula and phosphorylation of serines. C. Methylation of cytosine on nucleic acids and phosphorylation of phosphatidylinositols in the membrane. D. Condensation reactions that combine substrates and hydrolysis or dehydration using H2O in reactions. E. Methylation of phosphatidylinositols in the membrane and phosphorylation of cytosines in nucleic acid.
C. Methylation of cytosine on nucleic acids and phosphorylation of phosphatidylinositols in the membrane.
Protein-specific antibodies are useful experimental tools in biochemistry. Choose the one statement below that most correctly describes these biochemical reagents. A. Only polyclonal antibodies are used in biochemical research because they are the most specific. B. Monoclonal antibodies always bind their epitopes with higher affinity than polyclonal antibodies. C. Polyclonal antibodies are a heterogeneous mixture of antibodies that recognize epitopes on an antigen. D. Monoclonal antibodies are homogeneous and recognize multiple epitopes on a single antigen. E. Monoclonal antibodies bind to target proteins in mice but not in humans, rabbits, or goats.
C. Polyclonal antibodies are a heterogeneous mixture of antibodies that recognize epitopes on an antigen.
A mixture of enzyme and inhibitor is run through a size-exclusion chromatography column. The activity of the enzyme is assessed before and after the chromatography. The enzyme has more activity after the chromatography step. Which of the following is true? Question options: A. The enzyme was degraded by the column. B. The enzyme was not eluted fully from the column. C. The inhibitor is a reversible inhibitor. D. The enzyme was denatured during chromatography. E. The inhibitor is an irreversible inhibitor.
C. The inhibitor is a reversible inhibitor.
Look at the data in the figure below. If the sequence for the subunit was replaced with the subunit sequence from a patient with sickle cell disease, the number of A. asterisks would increase. B. asterisks would decrease. C. colons would increase. D. periods would decrease.
C. colons would increase.
Match the enzyme type with the reaction it catalyzes. Choose the correct a --> b order for (1) --> (5). A. d, b, e, a, c B. a, b, c, d, e C. d, b, c, a, e D. d, c, b, a, e E. d, b, c, e, a
C. d, b, c, a, e
Which of the following pairs correctly matches the type of interaction observed between an inhibitor and an enzyme with the type of inhibition? Question options: A. covalent; irreversible B. ionic; irreversible C. hydrogen bonding; reversible D. hydrophobic; irreversible
C. hydrogen bonding; reversible
What protein feature will cause the protein to bind to a metal in chelation affinity chromatography—specifically, a resin with immobilized Ni2+? A. proteins with antigenic affinity for divalent cations. B. proteins that have a heme that can bind divalent cation metals, such as iron or nickel. C. recombinant proteins engineered to have six histidines at the N or C terminus of the protein. D. proteins with a negative charge on the amino terminus and a positive charge on the carboxyl terminus. E. proteins that bind cadmium to form a nickel-cadmium compound similar to batteries.
C. recombinant proteins engineered to have six histidines at the N or C terminus of the protein.
Which separation technique exploits the solubility differences of proteins? A. dialysis B. ion-exchange chromatography C. centrifugation D. salting out by ammonium sulfate
D. salting out by ammonium sulfate
Choose the five correct labels for the figure to the right. "Transition State" = TS A. (1) E + P (2) TS (3) EP (4) ES (5) enzyme B. (1) ES (2) EX (3) EP (4) E + P (5) TS C. (1) EP (2) TS (3) ES (4) E + P (5) product D. (1) ES (2) TS (3) EP (4) E + P (5) substrate E. (1) ET (2) ES (3) E + P (4) TS (5) ligand
D. (1) ES (2) TS (3) EP (4) E + P (5) substrate
Although most protein sequencing is now done by mass spectrometry (MS), Edman degradation (ED) is useful if large amounts of a protein can be obtained even if from an uncharacterized species. Answer the True/False questions regarding methods used to sequence a polypeptide fragment and choose the set of all correct answers. 1. True / False - Protein sequencing by ED does not require purified protein but sequencing by MS does. 2. True / False - The N-terminal residue removed by acid treatment in ED is always a methionine. 3. True / False - Trypsin and chymotrypsin treatment often provides identical peptide fragments for ED. 4. True / False - Genomic sequences are needed to predict protein sequences by the MS method. 5. True / False - Trypsin treatment provides useful sequence information when analyzing data from MS. A. (1) False (2) True (3) True (4) False (5) False B. (1) False (2) False (3) True (4) True (5) False C. (1) True (2) False (3) False (4) True (5) True D. (1) False (2) False (3) False (4) True (5) True E. (1) True (2) True (3) False (4) False (5) True
D. (1) False (2) False (3) False (4) True (5) True
Although most protein sequencing is now done by mass spectrometry (MS), Edman degradation (ED) is useful if large amounts of a protein can be obtained even if from an uncharacterized species. Answer the True/False questions regarding methods used to sequence a polypeptide fragment: 1. True / False - The N-terminal residue removed by acid treatment in ED is always a methionine. 2. True / False - Trypsin and chymotrypsin treatment often provides identical peptide fragments for ED. 3. True / False - Genomic sequences are needed to predict protein sequences by the MS method. 4. True / False - Trypsin treatment provides useful sequence information when analyzing data from MS. 5. True / False - Protein sequencing by ED does not require purified protein but sequencing by MS does. A. (1) False (2) True (3) False (4) True (5) False B. (1) True (2) True (3) False (4) False (5) True C. (1) True (2) False (3) False (4) True (5) True D. (1) False (2) False (3) True (4) True (5) False E. (1) False (2) True (3) True (4) False (5) False
D. (1) False (2) False (3) True (4) True (5) False
Determine which major class of proteins best describes the specific representative proteins listed. Record your answer in the order of a, b, c, d, and e, by choosing the numbers 1, 2, 3, 4, and 5. A. 5, 3, 2, 1, 4 B. 3, 5, 4, 2, 3 C. 3, 4, 1, 5, 2 D. 3, 1, 4, 2, 5 E. 1, 3, 2, 4, 5
D. 3, 1, 4, 2, 5
Order the five steps in the actin-myosin reaction cycle; Which STEP is the power stroke? 1. ATP hydrolysis induces the recovery conformation. 2. ADP release empties the nucleotide binding site in myosin. 3. Ca2+ binding to troponin uncovers myosin binding sites on actin. 4. ATP binding causes myosin to dissociate from actin. 5. Pi release pulls the active filament toward the center A. 3, 5, 2, 1, 4; STEP 1 B. 1, 5, 2, 4, 3; STEP 5 C. 3, 5, 1, 4, 2; STEP 1 D. 3, 5, 2, 4, 1; STEP 5 E. None of these are correct.
D. 3, 5, 2, 4, 1; STEP 5
The cross-linked nature of the acrylamide media in SDS-PAGE can limit migration through the polymer matrix. Based on the figure to the right put the SDS-PAGE gels in the correct order of lowest to highest acrylamide concentration using A, B, and C. A. A < B < C B. C < B < A C. C < B < A D. B < C < A E. None are correct
D. B < C < A
Which statement most accurately describes the structure and function of O2 transport proteins. A. Functional myoglobin and hemoglobin both contain a heme group with a coordinated Fe3+ atom. B. Hemoglobin and myoglobin are identical in every way except the diameter of the iron heme group. C. Hemoglobin is found in all tissues except red blood cells, whereas myoglobin is only in red blood cells. D. Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG. E. None of the above statements is correct.
D. Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG.
Which statement most accurately describes the structure and function of O2 transport proteins. A. Leghemoglobin, myoglobin, and hemoglobin all have one thing in common; they bind CO2 very tightly. B. Hemoglobin and myoglobin are identical in structure with the only difference being the color of the heme. C. Myoglobin is found in skeletal muscle, red blood cells, and adipose tissue; hemoglobin is in heart muscle. D. Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG. E. None of the above statements is correct.
D. Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG.
In one type of hemoglobin mutant the amino acid change eliminates a hydrogen bond that normally stabilizes the T state. Would you expect this mutant hemoglobin to have a higher or lower O2 affinity compared to the normal protein and why? A. Lower O2 affinity because the R-T equilibrium would be mostly shifted to the R state. B. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the T state. C. Lower O2 affinity because the R-T equilibrium would be mostly shifted to the T state. D. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the R state
D. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the R state
In one type of hemoglobin mutant the amino acid change generates a strong ionic interaction stabilizing the T state conformation but only under conditions of lower pH, e.g., at pH 7.2 compared to pH 7.6. What effect would this mutation have on the amount of O2 delivered to the tissue and why? A. Less O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in lungs. B. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the R state in tissues. C. Less O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in tissues. D. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in tissues. E. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in lungs.
D. More O2 delivered to the tissue because the R-T equilibrium would be shifted to the T state in tissues.
The figure below shows the coordination of heme, O2, and two critical histidine residues in globin proteins. Which of the following steps happens first in the oxygen binding process? A. The proximal histidine moves toward heme. B. The F helix moves toward heme. C. Iron moves into the plane of heme. D. O2 binds to the iron of heme.
D. O2 binds to the iron of heme.
Which of the reactions are two examples of reversible modifications mediated by enzymes. A. Methylation of phosphatidylinositols in the membrane and phosphorylation of cytosines in nucleic acid. B. Stabilization of the transition state and formation of covalent enzyme-substrate complexes. C. Isomerization reactions that do not change the molecular formula and hydrolysis reactions. D. Phosphorylation of phosphatidylinositols in the membrane and methylation of cytosine on nucleic acids. E. Condensation reactions that combine substrates and phosphorylation of serine or threonine residues.
D. Phosphorylation of phosphatidylinositols in the membrane and methylation of cytosine on nucleic acids.
Why is the process of purifying proteins from cells considered challenging? A. There is no way to determine the structure of the protein. B. Proteins are insoluble. C. The process is expensive and time consuming. D. There are 10,000 to 100,000 proteins in one sample.
D. There are 10,000 to 100,000 proteins in one sample.
Which of the findings below provide support for the transition state theory of catalysis? A. The activation energy of a reaction is increased in the presence of enzymes. B. Products of a reaction slowly dissociate from the enzyme active site. C. Multiple substrates bind in an ordered fashion, i.e., substrate A binds before B that binds before C. D. Transition state analogs bind tightly to enzyme active sites. E. None of these finding support the transition state theory.
D. Transition state analogs bind tightly to enzyme active sites.
Which of the following curves is representative of the binding of oxygen to myoglobin? A. curve C B. curve B C. curve D D. curve A
D. curve A
One of the most difficult steps in X-ray crystallography is A. dissolving the protein in the appropriate solvent. B. using the correct radio frequency pulses to perturb the nuclear spin. C. mounting the crystal on the x-ray diffractor. D. determining the phases of diffracted X-rays. E. obtaining a large enough sample for analysis.
D. determining the phases of diffracted X-rays.
In studying a transporter, it is found that no external energy input is needed to facilitate the movement of a neutral compound through the transporter. The translocation rate of the compound reaches a plateau at high levels of compound. It is a(n) A. active transport carrier. B. active transport channel. C. passive transport channel. D. passive transport carrier.
D. passive transport carrier.
What type of transport is depicted in the figure below? A. passive transport of molecules up a concentration gradient B. active transport of molecules up a concentration gradient C. active transport of molecules down a concentration gradient D. passive transport of molecules down a concentration gradient E. membrane diffusion
D. passive transport of molecules down a concentration gradient
For reversible binding between a protein and a ligand, A. the units for Kd are M-1. B. Ka is equal to Kd. C. the larger the Kd, the higher the affinity between the protein and ligand. D. the larger the Ka, the higher the affinity between the protein and ligand. E. None of these answers are correct.
D. the larger the Ka, the higher the affinity between the protein and ligand.
Answer the following questions about the graph shown at the right. 1. The protein with the lowest dissociation constant (Kd) is protein (A or B)? 2. The protein with the highest affinity for oxygen is protein (A or B)? 3. The protein most likely to bind oxygen cooperatively is protein (A or B)? 4. The protein most likely to be an oxygen storage protein is protein (A or B)? 5. The protein most likely to be hemoglobin is protein (A or B)? 6. The protein most likely to be myoglobin is protein (A or B)? A. (1) protein A (2) protein B (3) protein B (4) protein A (5) protein B (6) protein A B. (1) protein A (2) protein A (3) protein A (4) protein B (5) protein B (6) protein A C. (1) protein B (2) protein A (3) protein B (4) protein A (5) protein B (6) protein A D. (1) protein A (2) protein A (3) protein B (4) protein A (5) protein A (6) protein B E. (1) protein A (2) protein A (3) protein B (4) protein A (5) protein B (6) protein A
E. (1) protein A (2) protein A (3) protein B (4) protein A (5) protein B (6) protein A
What is the DG when transporting 2 Ca2+ from the inside to the outside of the cell? A. +7.2 kJ/mol B. +5.9 kJ/mol C. +19.0 kJ/mol D. +9.5 kJ/mol E. +26.2 kJ/mol
E. +26.2 kJ/mol
What are the THREE key assumptions of Michaelis-Menten kinetics. 1. Substrates and products are chemically inert until enzymes are added, catalysts = life. 2. The reaction is analyzed at a time in the reaction that negligible product is formed. 3. Catalysts alter the free energy of the reaction without altering the equilibrium constant. 4. The steady state condition is reached quickly under conditions where [S] >> [E]. 5. Enzymes have higher binding affinities for products than the transition state. 6. Product release is assumed to be a rapid step in the process. A. 1, 2, 4 B. 1, 4, 5 C. 3, 4, 6 D. 1, 3, 6 E. 2, 4, 6
E. 2, 4, 6
Refer to the reaction coordinate diagram at right that compares catalyzed and uncatalyzed reactions. Which of the following labels are correct? "Activation energy" = AE. A. 3 = Substrate, 2 = AE for uncatalyzed rxn, 7 = DG‡ B. 6 = AE for catalyzed rxn, 5 = Product, 4 = DG C. 7 = DG, 1 = DG‡ , 5 = Reactant D. 6 = AE for uncatalyzed rxn, 3 = Substrate, 2 = DG‡ E. 3 = Reactant, 1 = DG, 2 = Transition state
E. 3 = Reactant, 1 = DG, 2 = Transition state
Match each representative protein with the most correct specific major protein functional class. Record your answer in the order of a, b, c, d, and e, by choosing the numbers 1, 2, 3, 4, and 5. A. 5, 4, 1, 2, 3 B. 3, 5, 4, 2, 1 C. 2, 3, 5, 1, 4 D. 4, 3, 2, 5, 1 E. 4, 1, 5, 3, 2
E. 4, 1, 5, 3, 2
If SERCA is not functioning in a myoblast, which of the processes described at the right is most likely to occur? A. The myofibrils can lengthen but not shorten. B. Actin will not be able to bind to the thin filament. C. ATP cannot be hydrolyzed to drive the power stroke D. Myosin will not be able to mediate the power stroke. E. Muscle contraction occurs but not muscle relaxation.
E. Muscle contraction occurs but not muscle relaxation.
Which of the following statements about association and dissociation constants describing the binding of Ligands X and Y to Protein Z is the most correct? A. Ligand X has a Kd = 0.2 mM, while Ligand Y has a Kd = 0.6 mM. Ligand X therefore has a lower affinity for Protein Z than does Ligand Y. B. The larger the Kd value is, the larger the Ka value will be for binding of Ligands X and Y to Protein Z. C. Ligand X has a Ka = 0.2 mM, while Ligand Y has a Kd = 0.6 mM. Ligand X therefore has a higher affinity for Protein Z than does Ligand Y. D. The smaller the Kd value is, the smaller the Ka value will be for binding of Ligands X and Y to Protein Z. E. None of these answers are correct.
E. None of these answers are correct.
Which of the following is a positive effector for oxygen binding to hemoglobin? A. H+ B. CO C. CO2 D. 2,3-bisphosphoglycerate E. O2
E. O2
If the histidine on the F helix (His F8) that coordinates the O2 that binds to the heme iron in hemoglobin is mutated to an alanine, what effect would be most likely? Choose the ONE most correct answer. A. Oxygen binding affinity would increase, since the alanine residue would form strong interaction with the oxygen molecule. B. None of these answers are correct. C. Oxygen binding would take place on the other face of the heme molecule, where the "proximal" histidine would be able to interact with the oxygen. D. Oxygen binding would cause hemoglobin polymers to form, due to the introduction of a hydrophobic patch by the addition of this alanine. E. Oxygen binding would not cause the movement of the F helix, since the alanine at F8 cannot coordinate oxygen.
E. Oxygen binding would not cause the movement of the F helix, since the alanine at F8 cannot coordinate oxygen.
Sodium dodecylsulfate (SDS) plays an important role in SDS PAGE. Select the correct description of what SDS does in denatured electrophoresis. A. Because SDS is a detergent, it supports the native state by interacting with the nonpolar portions of a protein, stabilizing the three-dimensional structure of a protein so that it can migrate based on shape. B. SDS forms hydrogen bonds with the carbonyl carbon and amide nitrogen of the polypeptide backbone. C. SDS is a charged detergent that neutralizes the protein, allowing the protein to migrate through the gel. D. SDS is a bivalent cation that can interact with two negatively charged carboxyl groups at the same time. E. SDS is an amphipathic compound that binds to the hydrophobic portion of proteins and give a negative charge derived from the polar head group such that proteins have a proportional charge to mass ratio.
E. SDS is an amphipathic compound that binds to the hydrophobic portion of proteins and give a negative charge derived from the polar head group such that proteins have a proportional charge to mass ratio.
Cofactors with organic components are called coenzymes. Which two are coenzymes? A. Biotin/Selenium B. Zinc/FADH2 C. Thymidine/Lipoamide D.NADH/Calcium E. Tetrahydrofolate/NADP+
E. Tetrahydrofolate/NADP+
What is the effect of pH on O2 binding in the lungs compared to the tissues and why? A. Decreased effect of pH in the lungs because high CO2 concentrations stabilize the R state. B. Increased effect of pH in the lungs because high O2 concentrations stabilize the R state. C. Decreased effect of pH in the lungs because low CO concentrations stabilize the T state. D. Decreased effect of pH in the lungs because high BPG levels inside lung cells stabilize the T state. E. The correct answer is not given.
E. The correct answer is not given.
For chymotrypsin, which amino acid is involved in forming the oxyanion hole, but is not part of the catalytic triad? Question options: None of these answers are correct. His 57 Asp 102 Ser 195 Gly 193
Gly 193
Assume that in the graph at the right, the curve represented by Y is normal adult hemoglobin at pH 7.4 with normal levels of 2,3-BPG. Which of the statements below is the most correct regarding curves X and Z? A. X represents O2 binding in cells with elevated 2,3-BPG, whereas Z represents O2 binding in cells with decreased 2,3-BPG. B. Z represents O2 binding in cells at a higher pH, whereas X represents O2 binding in cells with a lower pH. C. Z represents O2 binding in cells with a lower pH, whereas X represents O2 binding in cells with elevated 2,3-BPG. D. X represents O2 binding in cells at a higher pH, whereas Z represents O2 binding in cells completely lacking 2,3-BPG. E. Z represents O2 binding in cells with elevated 2,3-BPG, whereas X represents O2 binding in cells with decreased 2,3-BPG.
E. Z represents O2 binding in cells with elevated 2,3-BPG, whereas X represents O2 binding in cells with decreased 2,3-BPG.
The catalytic mechanisms of chymotrypsin, which cleaves the peptide backbone of protein substrates, is a classic example of a multistep enzymatic process. Choose the correct underlined words. Chymotrypsin is a serine / cysteine protease requiring the formation of a noncovalent / covalent enzyme intermediate as a critical step in the reaction. The amino acid residue serine / histidine has a central role in general acid-base catalysis at several steps in the reaction mechanism, which relies on water / phosphate to generate a nucleophile that attacks a carbonyl carbon. The Gly193 and Asp102 / Ser195 residues are essential to stabilization of the isotropic / oxyanion intermediate during the multistep reaction process. A. serine, covalent, serine, water, Asp102, oxyanion B. serine, covalent, histidine, phosphate, Ser195, oxyanion C. serine, noncovalent, histidine, phosphate, Ser195, oxyanion D. cysteine, covalent, serine, water, Ser195, isotropic E. serine, covalent, histidine, water, Ser195, oxyanion
E. serine, covalent, histidine, water, Ser195, oxyanion
