Test bank for biochemistry 7th edition by jeremy

http://getbooksolutions.com Link full download:https://getbooksolutions.com/download/test-bank-forbiochemistry-7th-edition-by-jeremy Test Bank for Biochemistry 7th Edition by Jeremy Sample Chapter Catalytic Strategies Matching Questions Use the following to answer questions 1-10: Choose the best answer from the list below Not all of the answers will be used a) hydrolysis b) stopped-flow c) site-directed mutagenesis d) chymotrypsin e) zinc f) P-loop g) magnesium h) two-fold rotational i) methylation j) peptide bond cleavage k) papain l) hydrogenation m) sodium n) PCR o) two-fold mirror http://getbooksolutions.com AUTONUM An enzyme that temporarily undergoes covalent catalysis as part of its mechanism Ans: d Section: Introduction and 9.1 AUTONUM The type of reaction catalyzed by proteases Ans: a Section: 9.1 AUTONUM The metal ion required by carbonic anhydrase for activity Ans: E Section: 9.2 AUTONUM The process by which chymotrypsinogen is converted into active chymotrypsin Ans: j Section: 9.1 AUTONUM A technique that requires only milliseconds to perform an enzyme-catalyzed reaction http://getbooksolutions.com Ans: b Section: 9.1 AUTONUM The process by which host DNA is protected from cleavage by the host restriction endonucleases Ans: I Section: 9.3 AUTONUM A technique that allows an investigator to test the role of individual amino acids in the determination of structure/function relationships in enzymes Ans: c Section: 9.1 AUTONUM The metal ion frequently found at active sites containing phosphate groups Ans: g Section: 9.3 AUTONUM Inverted repeats in doublestranded DNA create this type of symmetry A technique that can be used to determine mechanisms when chiral http://getbooksolutions.com molecules are involved in reactions Ans: H f Section: 9.3 Section: 9.3 AUTONUM Structures in proteins named for the fact that they interact with phosphoryl groups Ans: F Section: 9.4 Fill-in-the-Blank Questions AUTONUM Effective protease inhibitors are often _ for one enzyme Ans: specific AUTONUM Section: 9.1 The catalytic mechanism of adenylate kinase, in which the substrates are simply oriented to stabilize the transition state, is called _ Ans: catalysis by approximation Section: Introduction AUTONUM A-T base pairs are easily interrupted, as they contain only _ hydrogen bonds versus _ hydrogen bonds found in G-C base http://getbooksolutions.com pairs Ans: two, three AUTONUM The mechanism of chymotrypsin involves the formation of an unstable -shaped intermediate that is stabilized by the oxyanion hole Ans: tetrahetral AUTONUM Section: 9.3 Section: 9.1 In trypsin, the specificity pocket contains a/an residue that binds to the positive charge of the K or R residue of the substrate Ans: aspartyl, aspartic, or D AUTONUM The reaction center of most carbonic anhydrases is a zinc ion bound to water and _ residues of the enzyme Ans: histidine AUTONUM Section: 9.2 In chymotrypsin, the tetrahedral intermediate transition state is stabilized by a structural feature referred to as the “ _” hole Ans: oxyanion AUTONUM Section: 9.1 Section: 9.2 In proteases such as papain, a _ residue is activated by hydrogen-bonding to a histidine residue http://getbooksolutions.com Ans: cysteine AUTONUM Section: 9.1 Myosins hydrolyze _ in a controlled manner and use the free energy of hydrolysis to promote conformational changes within myosin itself Ans: ATP Section: 9.4 AUTONUM Kinetic studies on myosins, in the presence and absence of divalent cations, show that is the true substrate for this enzyme Ans: ATP-Mg2+ Section: 9.4 Multiple-Choice Questions AUTONUM Which amino acids in chymotrypsin are found in the active site and are participants in substrate cleavage? A) His, Ser, Asp B) His, Ser C) Asp, Lys D) Lys, Arg E) His, Ser, Arg Ans: A Section: 9.1 AUTONUM How is specificity determined by chymotrypsin? A) interaction of the active site amino acids with the substrate B) binding of the N-terminus amino acid at the active site http://getbooksolutions.com C) covalent binding of a his residue to the substrate D) large conformational change of a P-loop upon binding of substrate E) binding of the proper amino acid into a deep pocket on the enzyme Ans: E Section: 9.1 AUTONUM Where does cleavage of the scissile bond by chymotrypsin occur? A) between a his and ser amino acid B) on the N-terminal side of a Phe or Trp residue C) on the C-terminal side of a Phe or Trp residue D) at the N-terminal amino acid E) on the C-terminal side of an Arg or Lys amino acid Ans: C Section: 9.1 AUTONUM Which of the following is NOT a way in which enzymes stabilize a transition state? A) causing the temperature of the environment to increase http://getbooksolutions.com B) covalent catalysis C) using binding energy D) general acid-base catalysis E) catalysis by approximation Ans: A Section: Introduction AUTONUM What trypsin, subtilisin, and elastase have in common? A) All contain Asp in the active site B) All bind hydrophobic amino acids C) All are synthesized in the pancreas D) All contain a catalytic triad at the active site E) All contain a hydrophilic substrate-binding pocket Ans: D Section: 9.1 AUTONUM Convergent evolution is attributed to similarities found between A) trypsin and elastase D) chymotrypsin and trypsin http://getbooksolutions.com B) chymotrypsin and elastase C) chymotrypsin and subtilisin Ans: C E) trypsin and kinase Section: 9.1 AUTONUM If you carried out site-directed mutagenesis of subtilisin, changing serine 221 to isoleucine, what would you expect? A) a large change in KM D) a and c B) a small change in KM E) b and c C) a large change in kcat Ans: E AUTONUM Section: 9.1 The metal most commonly found at the active site of metalloproteases is A) zinc B) calcium C) selenium magnesium E) sodium Ans: A D) Section: 9.1 AUTONUM Carbonic anhydrases are necessary because A) spontaneous hydration and dehydration of http://getbooksolutions.com carbon dioxide occur very slowly B) spontaneous hydration and dehydration of carbon dioxide are rapid, but not at speeds necessary for biochemical processes C) hydration and dehydration of carbon dioxide are sometimes coupled to other biochemical processes D) a and c E) b and c Ans: E Section: 9.2 AUTONUM Binding of a water molecule to the zinc ion induces A) a hydronium ion to form B) a large conformation change in the binding site C) ionization of a His residue, which functions as a strong nucleophile D) a lowered pKa for water, which leads to formation of a zinc bound hydroxide ion E) an altered KM value Ans: D Section: 9.2 http://getbooksolutions.com AUTONUM Restriction endonucleases cut DNA at specific sites How many different patterns can be formed by a four-base sequence combination of any four bases? A) 64 Ans: B B) 256 C) 16 D) 1024 E) 4096 Section: 9.3 AUTONUM Type II restriction enzymes cut A) double-stranded DNA, forming a 5′ phosphoryl group and a 3′ hydroxyl group on each strand B) single-stranded DNA, forming a 5′ phosphoryl group and a 3′ hydroxyl group on the strand C) double-stranded DNA, forming a 5′ phosphoryl group and a 3′ hydroxyl group on one strand D) double-stranded DNA, forming a 3′ phosphoryl group and a 5′ hydroxyl group on each strand E) single-stranded DNA, forming two hydroxyl groups and loss of a phosphate group Ans: A AUTONUM Section: 9.3 EcoRV cleaves cognate DNA with a specificity approximately _ times that of non-cognate DNA A) 10 B) 1000 C) 10,000 D) 1,000,000 E) 100,000,000,000 http://getbooksolutions.com Ans: D Section: 9.3 AUTONUM Myosins function to A) transfer the phosphate from NTP to NDP B) couple ATP hydrolysis to large conformational changes C) couple ATP hydrolysis to glycogen oxidation D) phosphorylate NADH E) couple ATP hydrolysis to protein synthesis in muscle Ans: B Section: 9.4 AUTONUM Metal ion catalysis is facilitated by any of several mechanisms, including A) stabilizing negative charges on an intermediate B) promoting formation of nucleophiles C) metals binding directly to substrates D) a and c E) All of the above Ans: E Section: Introduction http://getbooksolutions.com Short-Answer Questions AUTONUM Complete the structure of the catalytic triad of chymotrypsin by drawing the proper structure of the missing residue side chain in the box provided Show the proper hydrogen bonding involved in this triad Ans: Section: 9.1 AUTONUM What is the challenge for a protease to facilitate hydrolysis of a peptide bond? Ans: The peptide bond contains a carbonyl that is not very reactive; therefore, the catalytic mechanism must employ a feature that promotes nucleophilic attack of this carbonyl group by a strong nucleophile so the peptide bond can be cleaved Section: 9.1 AUTONUM How can covalent modification be used to determine the mechanism of action of an enzyme? Ans: If a particular amino acid side chain is suspected of participating in a catalytic mechanism, covalent modification of the residue may alter it sufficiently that the enzyme activity is altered or inhibited However, this method is usually confirmed by other techniques, such as site-directed mutagenesis, to rule out other possible reasons for the loss of activity, such as global conformational change http://getbooksolutions.com as a result of the modification Section: 9.1 AUTONUM Why are substrate analogs often used to monitor enzyme activity? Ans: Enzyme assays must be designed so that formation of a product is rapidly and easily monitored Substrates that form a colored product are easy to observe in a quantitative manner using spectrophotometers Section: 9.1 AUTONUM What caused a “burst” of activity followed by a steady state reaction when chymotrypsin was studied by stop-flow techniques? Ans: Chymotrypsin cleaves peptide bonds in a twostep reaction, in which the first step, formation of the acyl enzyme intermediate, is faster than the second step, hydrolysis Section: 9.1 AUTONUM What supports the theory that a catalytic triad strategy is a result of convergent evolution? Ans: A number of different enzymes, including the peptidase family, some esterases, and others, have similar mechanisms of actions While the strategy is similar, the actual participating amino acids differ, suggesting a mechanism commonly employed as a result of convergent evolution http://getbooksolutions.com Section: 9.1 AUTONUM What is common strategy for cysteine, metallo, and aspartyl proteases? Ans: All employ a mechanism whereby a nucleophile is generated that attacks the carbonyl of the peptide bond Section: 9.1 AUTONUM What is the common nucleophile found in cysteine, metallo, and aspartyl proteases? Ans: The common nucleophile is water Section: 9.1 AUTONUM Designing drugs to inhibit enzymes is a large part of pharmaceutical research What are some of the enzymatic features that would be important? Ans: The enzyme could be inhibited by interaction of a potential drug at the active site or at a site that alters conformation or regulation of the enzyme The structure of natural substrates and activators, and their binding sites, would be useful features to study a new drug design The binding affinity and specificity would be important, and standard enzyme assays would be used to determine the effect of the inhibitors on Kcat, KM, and Vmax Section: 9.1 http://getbooksolutions.com AUTONUM How is the bicarbonate formed when carbonic anhydrase is present? Ans: The zinc promotes formation of a hydroxide ion, which attacks the carbon dioxide Section: 9.2 AUTONUM What features of carbonic anhydrase allow the rapid hydration of carbon dioxide? Ans: Bringing the two reactants (carbon dioxide and water) into proximity facilitates the rapid reaction rate, and the presence of a buffer system aids in proton transfer and release Section: 9.2 AUTONUM What mechanism is responsible for restriction endonuclease cleavage of DNA? Ans: An activated water molecule directly attacks the phosphorous atom in a single displacement reaction Section: 9.3 AUTONUM The sequence bp restriction cleavage site for EcoRV is GATXXX What is the complete sequence of the double-stranded restriction site? Ans: GATATC CTATAG http://getbooksolutions.com Section: 9.3 AUTONUM What is significant about the slow rate for myosin’s hydrolysis of ATP? Ans: The persitance of a conformation of myosin with ATP hydrolyzed but still bound is critical for coupling conformational changes that take place in the course of the reaction to other processes Section: 9.4 AUTONUM Describe the secondary and tertiary structures in domains that form P-loops and bind phosphoryl groups Ans: This domain structure consists of a central β sheet, surrounded on both sides by α helices Characteristically, there is a loop between the first β strand and the first helix that contains several glycine residues Section: 9.4