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medical sciences
biochemistry

Questions and Answers of Biochemistry

If you had a protein X, which is a soluble enzyme found inside the peroxisome, and you wished to separate it from a similar protein Y, which is an enzyme found embedded in the mitochondrial membrane,
What is the basis for the separation of proteins by the following techniques?(a) Gel-filtration chromatography(b) Affinity chromatography(c) Ion-exchange chromatography(d) Reverse phase HPLC
What are two ways that a compound can be eluted from an affinity column? What could be the advantages or disadvantages of each?
What are two ways that a compound can be eluted from an ion-exchange column? What could be the advantages or disadvantages of each?
Why do most people elute bound proteins from an ion-exchange column by raising the salt concentration instead of changing the pH?
How can gel-filtration chromatography be used to arrive at an estimate of the molecular weight of a protein?
What is the main difference between reverse phase HPLC and standard ion-exchange or gel filtration chromatography?
How does HPLC differ from ion-exchange chromatography?
Design an experiment to purify protein X on an anion-exchange column. Protein X has an isoelectric point of 7.0.
What could be an advantage of using an anion exchange column based on a quaternary amine [i.e., resin–N+ (CH2CH3)3] as opposed to a tertiary amine [resin–NH+ (CH2CH3)2]?
You wish to separate and purify enzyme A from contaminating enzymes B and C. Enzyme A is found in the matrix of the mitochondria. Enzyme B is embedded in the mito-chondrial membrane, and enzyme C is
An amino acid mixture consisting of lysine, leucine, and glutamic acid is to be separated by ion-exchange chromatography, using a cation-exchange resin at pH 3.5, with the eluting buffer at the same
What is meant by “salting out”? How does it work?
Would you use a pH meter to monitor the progress of the reaction described in Question 14? Why or why not?
Distinguish between the lock-and-key and induced-fit models for binding of a substrate to an enzyme.
Using an energy diagram, show why the lock-and-key model could lead to an inefficient enzyme mechanism.
Define steady state, and comment on the relevance of this concept to theories of enzyme reactivity.
For an enzyme that displays Michaelis–Menten kinetics, what is the reaction velocity, V (as a percentage of Vmax), observed at the following values?(a) [S] = KM(b) [S] =
Determine the values of KM and Vmax for the de-carboxylation of a β-keto acid given the following data. Substrate Concentration (mol L–1) Velocity (mM
The kinetic data in the following table were obtained for the reaction of carbon dioxide and water to produce bicarbonate and hydrogen ion catalyzed by carbonic anhydrase: CO2 + H2O → HCO-3 +
The hydrolysis of a phenylalanine-containing peptide is catalyzed by a-chymotrypsin with the following results. Calculate KM and Vmax for the reaction.Peptide Concentration (M)Velocity (M min-1)2.5
Why is it useful to plot rate data for enzymatic reactions as a straight line rather than as a curve?
How do the KM values for glucoki-nase and hexokinase reflect their roles in sugar metabolism?
If we describe an enzyme like aspartate transcarbamoylase and say that it exhibits cooperativity, what do we mean?
For the reaction of glucose with oxygen to produce carbon dioxide and water, Glucose + 6O2 → S 6CO2 + 6H2O The DG° is 22880 kJ mol –1, a strongly exergonic reaction. However, a sample of glucose
Distinguish between the molecular mechanisms of competitive and noncompetitive inhibition.
Where do lines intersect on a Lineweaver–Burk plot showing competitive inhibition? On a Lineweaver–Burk plot showing noncompetitive inhibition?
What is the difference between pure and mixed noncompetitive inhibition?
Why can we say that having a pure non- competitive inhibitor present is similar to just having less enzyme present?
Why foes the apparent KM decrease in the presence of an uncompetitive inhibitor?
What is a suicide substrate? Why are they important?
Would nature rely on the same enzyme to catalyze a reaction either way (forward or backward) if the DG° were 20.8 kcal mol -1? If it were 25.3 kcal mol -1?
Draw Lineweaver€“Burk plots for the behavior of an enzyme for which the following experimental data are available.
For the following aspartase reaction (see Question 28) in the presence of the inhibitor hydroxymethylaspartate, determine KM and whether the inhibition is competitive or noncompetitive.
Is it good (or bad) that enzymes can be reversibly inhibited? Why?
What features distinguish enzymes that undergo allosteric control from those that obey the Michaelis–Menten equation?
Explain the experiment used to determine the structure of AT Case. What happens to the activity and regulatory activities when the subunits are separated?
Distinguish between the concerted and sequential models for the behavior of allosteric enzymes.
What are three advantages of using allosteric drugs as opposed to orthosteric ones?
How does Valium work?
What are some possible advantages to the cell in combining phosphorylation with allosteric control?
Explain how phosphorylation is involved in the function of the sodium–potassium ATPase.
Explain how glycogen phosphorylase is controlled allosterically and by covalent modification.
Explain why cleavage of the bond between arginine 15 and isoleucine 16 of chymotrypsinogen activates the zymogen.
Why is it necessary or advantageous for the body to make zymogens?
Why is it necessary or advantageous for the body to make inactive hormone precursors?
Is the term KM used with allosteric enzymes? What about competitive and noncompetitive inhibition? Explain.
Explain the function of histidine 57 in the mechanism of chymotrypsin.
Explain why the second phase of the chymotrypsin mechanism is slower than the first phase.
Explain the difference between an SN1 reaction mechanism and an SN2 reaction mechanism.
What would be the characteristics of a transition-state analog for the chymotrypsin reaction?
What is the relationship between a transition-state analog and the induced-fit model of enzyme kinetics?
Explain how a researcher makes an abzyme. What is the purpose of an abzyme?
Why can cocaine addiction not be treated with a drug that blocks the cocaine receptor?
Explain how abzymes can be used to treat cocaine addiction.
Suggest a role for coenzymes based on reaction mechanisms.
An enzyme uses NAD+ as a coenzyme. Using Figure 7.19, predict whether a radiolabeled H:– ion would tend to appear preferentially on one side of the nicotinamide ring as opposed to the other side.
What is a homotropic effect? What is a heterotropic effect?
What is the structure of ATCase?
Write an equation, with structural formulas, for the saponification of the triacylglycerol in Question 7.
Which of the following statements is (are) consistent with what is known about membranes?(a) A membrane consists of a layer of proteins sandwiched between two layers of lipids.(b) The compositions of
What structural features do a triacylglycerol and a phosphatidyl ethanolamine have in common? How do the structures of these two types of lipids differ?
In lipid bilayers, there is an order–disorder transition similar to the melting of a crystal. In a lipid bilayer in which most of the fatty acids are unsaturated, would you expect this transition
Suggest a reason why the cell membranes of bacteria grown at 20°C tend to have a higher proportion of unsaturated fatty acids than the membranes of bacteria of the same species grown at 37°C. In
Draw the structure of a phosphoacylglycerol that contains glycerol, oleic acid, stearic acid, and choline.
A membrane consists of 50% protein by weight and 50% phosphoglycerides by weight. The average molecular weight of the lipids is 800 Da, and the average molecular weight of the proteins is 50,000 Da.
Suppose that you are studying a protein involved in transporting ions in and out of cells. Would you expect to find the nonpolar residues in the interior or the exterior? Why? Would you expect to
Which statements are consistent with the fluid-mosaic model of membranes? (a) All membrane proteins are bound to the interior of the membrane. (b) Both proteins and lipids undergo transverse
What structural features do a sphingomyelin and a phosphatidylcholine have in common? How do the structures of these two types of lipids differ?
Write the structural formula for a triacylglycerol, and name the component parts.
Consider the following in light of the concept of levels of structure (primary, secondary, tertiary, quaternary) as defined for proteins.(a) What level is shown by double-stranded DNA?(b) What level
In what naturally occurring nucleic acids would you expect to find A-form helices, B-form helices, Z-form helices, nucleosomes, and circular DNA?
What are the two principal opposing views regarding the patenting of genes?
What two genes are at the heart of a current lawsuit and what is their importance?
Define supercoiling, positive supercoil, topoisomerase, and negative supercoil.
What is the difference between B-DNA and Z-DNA?
Explain, and draw a diagram to show, how acetylation or phosphorylation could change the binding affinity between DNA and histones.
Would you expect to find adenine–guanine or cytosine–thymine base pairs in DNA? Why?
What is the purpose of the Human Genome Project? Why do researchers want to know the details of the human genome?
Explain the legal and ethical considerations involved in human gene therapy.
A recent commercial for a biomedical company talked about a future in which every individual would have a card that told his or her complete genotype. What would be some advantages and disadvantages
A technology called PCR is used for replicating large quantities of DNA in forensic science (Chapter 13). With this technique, DNA is separated by heating with an automated system. Why is information
Give the name of the base, the ribonucleoside or deoxyri-bonucleoside, and the ribonucleoside triphosphate for A, G, C, T, and U.
What is the purpose of small nuclear RNA? What is an snRNP?
Why does the absorbance increase when a DNA sample unwinds?
Would you expect tRNA or mRNA to be more extensively hydrogen bonded? Why?
Would you expect mRNA or rRNA to be degraded more quickly in the cell? Why?
Which would be more harmful to a cell, a mutation in DNA or a transcription mistake that leads to an incorrect mRNA? Why?
Explain briefly what happens to eukaryotic mRNA before it can be translated to protein.
(a) Is it biologically advantageous that DNA is stable? Why or why not? (b) Is it biologically advantageous that RNA is unstable? Why or why not?
DNA synthesis always takes place from the 5' to the 3' end. The template strands have opposite directions. How does nature deal with this situation?
Is it unusual that the b-subunits of DNA polymerase III that form a sliding clamp along the DNA do not contain the active site for the polymerization reaction? Explain your answer.
Describe the discontinuous synthesis of the lagging strand in DNA replication.
What are the common features of all DNA polymerases?
Can methylation of nucleotides play a role in DNA replication? If so, what sort of role?
Why is the replication of DNA referred to as a semiconser-vative process? What is the experimental evidence for the semicon-servative nature of the process? What experimental results would you expect
How can breakdown in DNA repair play a role in the development of human cancers?
How did Messelson and Weigle demonstrate recombination?
What is the relationship between control of DNA synthesis in eukaryotes and the stages of the cell cycle?
What would be the effect on DNA synthesis if the telomerase enzyme were inactivated?

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