Questions and Answers of Biochemistry Concepts And Connections

How does the catalytic effectiveness of enzymes compare with that of nonenzymatic catalysts?
Are all enzymes proteins?
Catalase breaks down hydrogen peroxide about 107 times faster than the uncatalyzed reaction. If the latter required one year, how much time would be needed by the catalasecatalyzed reaction?
Give two reasons why enzyme catalysts are 103 to 105 more effective than reactions that are catalyzed by, for example, simple H+ or OH¯.
Suggest a reason why heating a solution containing an enzyme markedly decreases its activity. Why is the decrease of activity frequently much less when the solution contains high concentrations of
A model is proposed to explain the reaction catalyzed by an enzyme. Experimentally obtained rate data fit the model to within experimental error. Do these findings prove the model?
Does the presence of a catalyst alter the standard free energy change of a chemical reaction?
What effect does a catalyst have on the activation energy of a reaction?
For the hypothetical reactionthe rate was experimentally determined to beWhat is the order of the reaction with respect to A? With respect to B? What is the overall order of the reaction? Suggest how
An enzyme catalyzes the formation of ATP from ADP and phosphate ion. What is its effect on the rate of hydrolysis of ATP to ADP and phosphate ion?
Can the presence of a catalyst increase the amount of product obtained in a reaction?
The enzyme lactate dehydrogenase catalyzes the reactionNADH absorbs light at 340 nm in the near-ultraviolet region of the electromagnetic spectrum, but NAD+ does not. Suggest an experimental method
Suggest a reason for carrying out enzymatic reactions in buffer solutions.
Other things being equal, what is a potential disadvantage of an enzyme having a very high affinity for its substrate?
Amino acids that are far apart in the amino acid sequence of an enzyme can be essential for its catalytic activity.What does this suggest about its active site?
The enzyme β-methylaspartase catalyzes the deamination of β-methylaspartate[V. Williams and J. Selbin, J. Biol. Chem. 239, 1636 (1964)]. The rate of the reaction was determined by monitoring the
If only a few of the amino acid residues of an enzyme are involved in its catalytic activity, why does the enzyme need such a large number of amino acids?
Show graphically how the reaction velocity depends on the enzyme concentration. Can a reaction be saturated with enzyme?
For the Vmax obtained in Question 26, calculate the turnover number (catalytic rate constant) assuming that 1 * 10-4 mol of enzyme were used.Question 26Determine the values of KM and Vmax for the
How is the turnover number of an enzyme related to Vmax?
You do an enzyme kinetic experiment and calculate a Vmax of 100 μmol of product per minute. If each assay used 0.1 mL of an enzyme solution that had a concentration of 0.2 mg/mL, what would be the
The enzyme D-amino acid oxidase has a very high turnover number because the D-amino acids are potentially toxic. The KM for the enzyme is in the range of 1 to 2 mM for the aromatic amino acids and in
Under what conditions can we assume that KM indicates the binding affinity between substrate and enzyme?
Why does acetazolamide make beer taste flat?
How did scientists determine that carbonic anhydrase is a chemical sensor for CO2?
When does the kcat/KM value approximate the catalytic efficiency of an enzyme?
What are the three most common mechanisms for enzyme-catalyzed reactions that have two substrates?
What is the biggest difference between a ping-pong mechanism and either an ordered mechanism or random mechanism?
How do scientists determine the KM of a substrate that is part of an ordered reaction with two substrates?
If you graph the velocity of an enzymecatalyzed reaction vs. [S] for each of two substrates that are part of a random mechanism, would you expect to see the same shape curve? Why or why not?
Show graphically the dependence of reaction velocity on substrate concentration for an enzyme that follows Michaelis–Menten kinetics and for an allosteric enzyme.
Do all enzymes display kinetics that obey the Michaelis–Menten equation? Which ones do not?
How can you recognize an enzyme that does not display Michaelis–Menten kinetics?
How can competitive and pure noncompetitive inhibition be distinguished in terms of KM?
Why does a competitive inhibitor not change Vmax?
Why does a pure noncompetitive inhibitor not change the observed KM?
Can enzyme inhibition be reversed in all cases?
Why is a Lineweaver–Burk plot useful in analyzing kinetic data from enzymatic reactions?
When we compare the binding of I and of S to the enzyme in a mixed noncompetitive inhibitor, we assumed that the binding of I decreased the affinity of the enzyme for S.What would happen if the
If we made a Lineweaver–Burk plot of an irreversible inhibitor, which type of reversible inhibition would it be most likely to resemble?
How are coenzymes related to vitamins?
Crisco is made from vegetable oils, which are usually liquid. Why is Crisco a solid?
Name three proteins that are subject to the control mechanism of zymogen activation.
What are caspases?
What is apoptosis?
What diseases are linked to apoptosis?
What are the two essential amino acids in the active site of chymotrypsin?
What is the metabolic role of aspartate transcarbamoylase?
Noncompetitive inhibition is a limiting case in which the effect of binding inhibitor has no effect on the affinity for the substrate and vice versa. Suggest what a Lineweaver–Burk plot would look
You have been hired by a pharmaceutical company to work on development of drugs to treat AIDS.What information from this chapter will be useful to you?
Would you expect an irreversible inhibitor of an enzyme to be bound by covalent or by noncovalent interactions?Why?
Would you expect the structure of a noncompetitive inhibitor of a given enzyme to be similar to that of its substrate?
What part of the HIV lifecycle is disrupted by the drugs indinavir and amprenavir?
What part of the HIV lifecycle is disrupted by MK-0518?
What molecule acts as a positive effector (activator) of ATCase? What molecule acts as an inhibitor?
What is a K system?
What is a V system?
How is the cooperative behavior of allosteric enzymes reflected in a plot of reaction rate against substrate concentration?
Does the behavior of allosteric enzymes become more or less cooperative in the presence of inhibitors?
Does the behavior of allosteric enzymes become more or less cooperative in the presence of activators?
Explain what is meant by K0.5.
Which allosteric model can explain negative cooperativity?
With the concerted model, what conditions favor greater cooperativity?
With respect to the concerted model, what is the L value?What is the c value?
Is it possible to envision models for the behavior of allosteric enzymes other than the ones that we have seen in this chapter?
What has been the historical method used in drug design?
What is a main reason for side effects with traditional drugs that bind to the active site of a receptor?
Why is taking too much Valium not as dangerous as taking too much Phenobarbital?
What are two recent allosteric drugs that are currently on the market? What do they do?
What is the function of a protein kinase?
What amino acids are often phosphorylated by kinases?
What is the natural compound that eventually led to aspirin?
What is the relationship between the action of salicylate or aspirin that researchers believe accounts for some of its therapeutic effects?
List three proteases and their substrates.
Why does the enzyme reaction for chymotrypsin proceed in two phases?
Briefly describe the role of nucleophilic catalysis in the mechanism of the chymotrypsin reaction.
Explain how the pKa for histidine 57 is important to its role in the mechanism of chymotrypsin action.
An inhibitor that specifically labels chymotrypsin at histidine 57 is N-tosylamido-L-phenylethyl chloromethyl ketone. How would you modify the structure of this inhibitor to label the active site of
What properties of metal ions make them useful cofactors?
In biochemistry mechanisms, what group is often attacked by a nucleopile?
What is meant by general acid catalysis with respect to enzyme mechanisms?
Which of the two reaction mechanisms in Question 48 is likely to cause the loss of stereospecificity? Why?Question 48In biochemistry mechanisms, what group is often attacked by a nucleopile?
An experiment is performed to test a suggested mechanism for an enzyme-catalyzed reaction. The results fit the model exactly (to within experimental error). Do the results prove that the mechanism is
List three coenzymes and their functions.
What type of reaction uses vitamin B6?
What is green chemistry?
What are some of the ways that TAMLs are used?
What is a retromer?
What is the proposed role of retromers in Alzheimer’s disease.
Fighting Alzheimer’s disease by boosting the stability of retromers is based on the hypothesis that most of the APP is cleaved in the endosome to release β amyloid. What if this hypothesis is
How are researches working with extended families in Medellin, Colombia to look for methods of fighting Alzheimer’s disease?
What is the most significant difference between prion diseases and other diseases caused by amyloid-type plaques, such as Alzheimer’s disease?
What enzymes are known to be involved in Alzheimer’s disease?
What proteins are involved in the formation of the destructive plaques found in Alzheimer’s disease.
Why would doctors not want to just completely inhibit b-secretase in a patient with Alzheimer’s disease?
You have just isolated a pure lipid that contains only sphingosine and a fatty acid. To what class of lipids does it belong?
What structural features does a sphingolipid have in common with proteins? Are there functional similarities?
How does the structure of steroids differ from that of the other lipids discussed in this chapter?
What are the structural features of waxes? What are some common uses of compounds of this type?
Which is more hydrophilic, cholesterol or phospholipids? Defend your answer.

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