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Sample Questions

 

Chapter 4 Protein Three-Dimensional Structure

                                                                                                    

 

Matching Questions

Use the following to answer questions 1–10:

 

Choose the correct answer from the list below. Not all of the answers will be used.

1.   a) amino

2.   b) water

3.   c) protons

4.   d) DNA

5.   e) secondary structure

6.   f) tertiary structure

7.   g) Ramachandran

8.   h) RNA

9.   i) domain

10.                j) cystine

11.                k) proline

12.                l) Sanger

13.                m) d amino acids

14.                n) cysteine

 

1.	When a peptide bond is formed between two amino acids, a(n) ____________molecule is lost.
	Ans:	b
	Section: 4.1

 

2.	____________: Codes for the sequence of amino acids.
	Ans:	d
	Section: Introduction

 

3.	According to convention, ____________ is the terminus drawn on the left side of a peptide.
	Ans:	a
	Section: 4.1

 

4.	Two amino acids undergo oxidation to form a dimer called ____________.
	Ans:	j
	Section: 4.1

 

5.	Changes in ____________ create amyloid fibers, which are insoluble and are the source of mad cow disease, Alzheimer disease, and Parkinson disease.
	Ans:	e
	Section: 4.5

 

6.	____________: Compact regions that may be connected by a flexible segment of polypeptide chain.
	Ans:	i
	Section: 4.3

 

7.	____________: This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.
	Ans:	k
	Section: 4.2

 

8.	The plot that allows one to investigate the likely orientation of certain amino acid pairs is called the ____________.
	Ans:	g
	Section: 4.1

 

9.	____________: The type of structure to which α helices, β sheets, and turns are referred.
	Ans:	e
	Section: 4.2

 

10.	The overall 3D-structure of a single polypeptide chain is referred to as ____________.
	Ans:	f
	Section: 4.3

 

 

Fill-in-the-Blank Questions

 

11.	The       of a disulfide bridge results in a separation of two protein chains.
	Ans: oxidation                         Section 4.1

 

12.	The peptide bond is also known as a(n)     .
	Ans: amide bond                     Section 4.1

 

13.	Peptides differ from proteins in      .
	Ans: the number of amino acid residues                      Section 4.1

 

14.	Due to the side chain steric clash, almost all peptide bonds are      in their configuration.
	Ans: trans                                Section 4.1

 

15.	The secondary structure that is stabilized by CO and NH hydrogen bonding within the peptide chain is the      .
	Ans: alpha helix                       Section 4.2

 

16.	The      indicates the left- or right-handedness of an α helix.
	Ans: screw sense                     Section 4.2

 

17.	is a fibrous protein and is the primary component of wool and hair.
	Ans: α-keratin                          Section 4.2

 

18.	Every third residue in the protein collagen is      .
	Ans: glycine                             Section 4.2

 

19.	Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as      .
	Ans: β-mecaptoethanol                        Section 4.3

 

20.	The      β-sheet structure occurs when the two strands are oriented in opposite directions (N → C).
	Ans: antiparallel                       Section 4.3

 

21.	A protein whose peptide backbone is mostly extended and hydrogen bonded to different strands of the protein is composed mostly of the      secondary structure.
	Ans: β-sheet                 Section 4.3

 

22.	A protein is considered to be      when it is converted into a randomly coiled structure without its normal activity.
	Ans: denatured                                    Section 4.4

 

23.	is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.
	Ans: Collagen                          Section 4.3

 

24.	Collagen contains      , a modified amino acid.
	Ans: hydroxyproline                Section 4.3

 

25.	Compact, globular proteins are typically water      and consist mostly of       secondary structure.
	Ans: soluble; an alpha helical  Section 4.3

 

26.	refers to the spatial arrangement of subunits and the nature of their interactions.
	Ans: Quaternary structure        Section 4.3

 

Multiple-Choice Questions

 

27.	What determines a protein’s function?
	A) its structure
	B) its gene sequence
	C) N-terminal amino acids
	D) None of the above.
	E) All of the above.
	Ans: A             Section: Introduction

 

28.	What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other protein modifications.)
	A) 20,000
	B) 11,000
	C) 22,000
	D) 222,000
	E) None of the above.
	Ans: C             Section: 4.1

 

29.	Key properties of proteins include:
	A) a wide range of functional groups.
	B) an ability to possess either rigid or flexible structures as dictated by functional requirements.
	C) the ability to interact with other proteins.
	D) A and B.
	E) All of the above.
	Ans: E              Section: 4.1

 

30.	Why is the peptide bond planar?
	A) Bulky side chains prevent free rotation around the bond.
	B) It exhibits partial double-bond character, preventing rotation.
	C) Hydrogen bonding between the NH and C=O groups limits movement.
	D) None of the above.
	E) All of the above.
	Ans: B             Section: 4.1

 

31.	The configuration of most α-carbon atoms of amino acids linked in a peptide bond is:
	A) cis.
	B) circular.
	C) parallel.
	D) trans.
	E) perpendicular.
	Ans: D             Section: 4.1

 

32.	What structure(s) did Pauling and Corey predict in 1951?
	A) α helix
	B) β sheet
	C) β turn
	D) A, B, and C
	E) A and B
	Ans: E              Section: 4.2

 

33.	Which of the following protein(s) contain examples of α-helical character?
	A) keratin
	B) ferritin
	C) myosin
	D) tropomyosin
	E) All of the above.
	Ans: E              Section: 4.2

 

34.	Which of the following amino acid residues would most likely be buried in the interior of a water-soluble, globular protein?
	A) aspartate
	B) serine
	C) phenylalanine
	D) lysine
	E) glutamine
	Ans: C             Section 4.3

 

35.	Where are β turns and loops often found?
	A) in a hydrophobic pocket
	B) on the interior cleft
	C) at the protein interface with ligand
	D) on the surface of proteins
	E) None of the above.
	Ans: D             Section: 4.3

 

36.	The folding of a protein into its native shape can best be described as:
	A) a random event.
	B) a random event catalyzed by ribosome proteins to maintain a low energy structure.
	C) a series of controlled folds with a few random-shaped structures.
	D) a series of repeatable random events where the lowest energy structure is maintained.
	E) an event where the highest possible energy state is stabilized with discrete folding intermediates.
	Ans: D             Section: 4.5

 

37.	Your study group is trying to identify differences in the four levels of protein structure. Which of the following would you say is true of important stabilizing forces in secondary structure but not tertiary structure?
	A) The structure is stabilized by ionic attractions between oppositely charged side chains.
	B) The structure is stabilized by H-bonding between polar side chains.
	C) The structure is stabilized by hydrophobic interactions between nonpolar side chains.
	D) The structure is stabilized by H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine.
	E) None of these differentiate between secondary and tertiary structure.
	Ans: D             Sections: 4.2 and 4.3

 

38.	A clinician friend comes to you and tells you she has a patient that she thinks has some sort of defect in the collagen structure. She wants to know what kinds of structural differences there might be. Which of the following is NOT true for defects leading to scurvy or brittle bone disease?
	A) Proline residues are not hydroxylated.
	B) Glycine is replaced by other amino acids.
	C) Proyloyl hydroxylase activity is deficient.
	D) Accumulation of defective collagen causes cell death.
	E) All of the above are true.
	Ans: E              Section: 4.2

 

39.	All of the following would disrupt quaternary structure except:
	A) increase the temperature.
	B) decrease the pH.
	C) add 8 m Urea.
	D) treat with ascorbic acid (vitamin C).
	E) treat with β-mercaptoethanol.
	Ans: D             Section: 4.4

 

40.	Which of the following secondary structures would you expect to find on the surface of a globular protein?
	A) α helix
	B) β sheet
	C) loops between two α-helices
	D) none of the above because water would disrupt the hydrogen bonding that stabilizes these structures
	E) A, B, and C as long as the polar and charged amino acid side chains face the surface of the protein
	Ans: E              Section: 4.2

 

41.	The metamorphic protein lymphotactin undergoes changes in _____what_______ structure in order to carry out its full biochemical activity?
	A) primary and therefore also tertiary
	B) primary, secondary, and tertiary
	C) quaternary (subunits separate and carry out individual activities)
	D) secondary and tertiary
	E) primary, secondary, tertiary, and quaternary
	Ans: D             Section: 4.5

 

 

Short-Answer Questions

 

42.	How does a protein’s amino acid sequence influence the tertiary structure?
	Ans:	A protein will spontaneously fold into a three-dimensional structure determined by the amino acid sequence.
	Section: Introduction

 

43.	What is the advantage of protein interaction and assembly with other proteins?
	Ans:	When proteins interact or assemble, new functions and specificity become available. Protein interactions allow new binding sites at the assembly interface, and provide multifunctional activity and specificity, such as that found in polymerases and signal transduction.
	Section: Introduction

 

44.	How does the protein backbone add to structural stability?
	Ans:	The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.
	Section: 4.2

 

45.	Why are all the theoretical combinations of phi and psi not possible?
	Ans:	Steric hindrances of the side chains make certain combinations and angles impossible.
	Section: 4.2

 

46.	Describe some of the features of an α helix.
	Ans:	The α helix is a coil stabilized by intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away. There are 3.6 amino acids per turn. The hydrogen bonds are between amino acid residues that have two intervening residues. Thus, these amino acid residues are found on the same side of the coil. The helix is almost always right-handed, although left-handed helices are, in theory, possible.
	Section: 4.2

 

47.	What is the “hydrophobic effect” as it relates to protein structure?
	Ans:	The three-dimensional structure of a water-soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule.
	Section: 4.3

 

48.	What are the key characteristics that make the peptide bond important to protein folding/structure?
	Ans:	The resonance of the amide bond creates a planar, rigid region of the peptide backbone with the R groups on opposite sides of the peptide bond. This results in a limit to the types and angles of conformation, allowing a predictable folding pattern.
	Section: 4.1

 

49.	What are prions?
	Ans:	Prions are proteins that can assume (after infection or by other causes) a new protein structure that is self-propagating. Prion diseases have several variants, at least one of which is fatal to humans.
	Section: 4.5

 

50.	In the ribonuclease experiments performed by Anfinsen, what was the significance of the presence of the reducing agent β-mercaptoethanol?
	Ans:	The reducing agent reduced incorrectly paired disulfide bonds, allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.
	Section: 4.5

 

51.	What is the advantage of having certain regions of partially correct folded regions?
	Ans:	If some regions interact preferentially, lending stability to certain conformations as the protein folds, they can impact the overall structure of the protein.
	Section: 4.3

 

52.	A primary sequence of a protein contains a run of reasonably small amino acids, containing few branched amino acids or serines. This sequence ends in a proline. What can you deduce from this information?
	Ans:	The sequence is likely an α helix. The smaller amino acids do not sterically hinder the side groups on the outside of the helix and the absence of amino acids that would interfere with the helix are all evidence for this secondary structure. The proline is likely to be the end of the sequence.
	Section: 4.2

 

53.	What is the sequence of amino acids found in collagen? What is the significance of the sequence and what is the complication of scurvy?
	Ans:	Gly-Pro-Pro. The small side group of the glycine allows for a tight screw turn for this atypical helix. The prolines are important to stabilize tight three-amino-acid helices. In addition, the prolines are also hydroxylated by an enzyme that requires ascorbic acid to maintain activity. Without the hydroxylation of collagen by prolylhydroxylase, the collagen superstructure is less stable and results in adverse flexibility of the connective tissues (scurvy).
	Section: 4.2

 

54.	Prion diseases are often latent; that is, those with prion diseases are asymptomatic for many years after their initial infection. What causes this latency?
	Ans:	Prion diseases are protein based; more specifically, protein-structure based. Because it takes time to convert the prion protein from the soluble, mostly helical form to the beta-strand, insoluble form, there is lag time before enough proteins are converted to the polymer, which causes cell injury This characteristic of prion diseases makes it difficult to diagnose before it is too late.
	Section: 4.5

Chapter 7 Kinetics and Regulation

 

 

Matching Questions

Use the following to answer questions 1-10:

 

Choose the correct answer from the list below. Not all of the answers will be used.

1.   a) first-order reaction

2.   b) second-order reaction

3.   c) metabolism

4.   d) ensemble

5.   e) biomolecular

6.   f) turnover number

7.   g) Michaelis

8.   h) equilibrium

9.   i) sequential

10.                j) kinetics

11.                k) initial reaction velocity

12.                l) allosteric

13.                m) ping-pong

 

1.	____________is a complex array of enzyme catalyzed reactions organized in multiple pathways.
	Ans:	c
	Section:  Introduction

 

2.	_______________ is the study of rates of chemical reactions.
	Ans:	j
	Section:  7.1

 

3.	A reaction that is directly proportional to the concentration of reactant is a ____________.
	Ans:	a
	Section:  7.1

 

4.	A reaction with two substrates is considered a ____________ reaction.
	Ans:	e
	Section7.1

 

5.	At ____________ there will be no net change in the concentration of substrate or product.
	Ans:	h
	Section:  7.2

 

6.	The value Vo is called the ____________.
	Ans:	k
	Section:  7.2

 

7.	The kcat is often referred to as the ____________.
	Ans:	f
	Section:  7.2

 

8.	The property that describes the enzyme-substrate interaction is measured by what constant?
	Ans:	g
	Section:  7.2

 

9.	____________ Enzymes that do not obey Michaelis–Menten kinetics.
	Ans:	l
	Section:  7.3

 

10.	____________ Experiments that determine the kinetics of a population of enzyme molecules.
	Ans:	d
	Section:  7.4

 

 

Fill-in-the-Blank Questions

 

11.	One way to measure the rate of an enzymatic reaction is to measure the loss of       over time.
	Ans: substrate    Section:  7.1

 

12.	Reactions that have more than two reactants or substrates are considered       reactions.
	Ans: second-order     Section:  7.1

 

13.	The      rule states that all subunits in an allosteric enzyme must be in either the R or the R state; no hybrids.
	Ans: symmetry      Section:  7.3

 

14.	The Michaelis–Menten model assumes that       is the rate constant ignored because P has not accumulated.
	Ans: k–2     Section:  Appendix

 

15.	is directly dependent on enzyme concentration.
	Ans: Vmax    Section:  7.2

 

16.	An enzyme will be most sensitive to changes in cellular substrate concentration when the concentration is     .
	Ans: near the KM   Section:  7.2

 

17.	The type of inhibition where the  product of one enzyme inhibits another enzyme that acts earlier in a metabolic pathway is considered a(an)       inhibitor.
	Ans:  feedback     Section:  7.3

 

18.	Allosteric enzymes can be identified because the plot of initial velocity, V0, versus substrate concentration, S, is not hyperbolic but      -shaped.
	Ans:  sigmoidal     Section:  7.3

 

19.	Negative allosteric      stabilize the T-state of the enzyme.
	Ans:  effectors     Section:  7.3

 

20.	The straight-line kinetic plot of 1/ V0 versus 1/S is called a      .
	Ans:  Lineweaver–Burk plot, or double-reciprocal plot     Section:  7.2

 

 

Multiple-Choice Questions

 

21.	A critical feature of the Michaelis–Menten model of enzyme catalysis is
	A)	increasing the probability of product formation.
	B)	shifting the reaction equilibrium.
	C)	formation of an ES complex.
	D)	All of the above.
	E)	None of the above.
	Ans:  C     Section:  7.2

 

22.	What value of [S], as a fraction of KM is required to obtain 20% Vmax? [S] =
	A)	0.2 KM
	B)	0.25 KM
	C)	0.5 KM
	D)	0.75 KM
	E)	0.8 KM
	Ans:  B     Section:  7.2

 

23.	Allosteric proteins:
	A)	contain distinct regulatory sites and have multiple functional sites.
	B)	display cooperativity.
	C)	always consist of several identical subunits.
	D)	A and B.
	E)	A, B, and C.
	Ans:  D     Section:  7.3

 

 

24.	Allosteric effectors alter the equilibria between:
	A)	the ES state.
	B)	the R and T forms of a protein.
	C)	the forward and reverse reaction rate.
	D)	the formation of product and it’s reverse reaction.
	E)	All of the above.
	Ans:   B   Section:  7.3

 

25.	The formula V0 = Vmax           [S]   , indicates the relationship between [S] + KM
	A)	the enzyme activity and the equilibrium constant.
	B)	the rate of a catalyzed reaction and the equilibrium constant.
	C)	enzyme activity as a function of substrate concentration.
	D)	All of the above.
	E)	None of the above.
	Ans:  C     Section:  7.2

 

26.	The model describing allosteric regulation that requires all subunits to be in the same state is called the ________.
	A)	concerted model
	B)	syncopated model
	C)	cooperative model
	D)	equilibrium model
	E)	None of the above.
	Ans:    A   Section:  7.3

 

27.	Loss of allosteric regulation in the production of purine nucleotides results in ___________.
	A)	excess nucleotides for DNA
	B)	loss of RNA due to ribose phosphate synthetase
	C)	decreased urate degradation
	D)	loss in urate concentration
	E)	None of the above.
	Ans:   E    Section:  7.3

 

28.	The KM is:
	A)	equal to the product concentration at initial reaction conditions.
	B)	equal to the substrate concentration when the reaction rate is half its maximal value.
	C)	proportional to the standard free energy.
	D)	All of the above.
	E)	None of the above.
	Ans:  B     Section:  7.2

 

29.	Given are five KM values for the binding of substrates to a particular enzyme. Which has the strongest affinity when k–1 is greater than k2?
	A) 150 mM     B) 0.15 mM     C) 150 mM     D) 1.5 nM     E) 15,000 pM
	Ans:  D     Section:  7.2

 

30.	When substrate concentration is much greater than KM, the rate of catalysis is almost equal to
	A) Kd.     B) kcat.     C) Vmax.     D) All of the above.     E) None of the above.
	Ans:  C     Section:  7.2

 

31.	Which of the following is true under the following conditions: The enzyme concentration is 5 nM, the substrate concentration is 5 mM, and the KM is 5 mM.
	A)	The enzyme is saturated with substrate.
	B)	Most of the enzyme does not have substrate bound.
	C)	There is more enzyme than substrate.
	D)	All of the above.
	E)	None of the above.
	Ans:  A     Section:  7.2

 

32.	Homotrophic effects of allosteric enzymes:
	A)	are due to the effects of substrates.	D)	shift the kinetics curve to the right.
	B)	are due to the effects of allosteric activators.	E)	None of the above.
	C)	shift the kinetics curve to the left.
	Ans:  A     Section:  7.3

 

33.	Multiple substrate enzyme reactions are divided into two classes:
	A)	sequential reactions and double displacement reactions.
	B)	double displacement reactions and concerted reactions.
	C)	sequential reactions and concerted reactions.
	D)	A and C.
	E)	None of the above.
	Ans:  A     Section:  7.2

 

34.	When [S] << KM, the enzymatic velocity depends on__________.
	A)	the values of kcat/KM, [S], and [E]t
	B)	the Vmax of the reaction
	C)	the affinity of the substrate for the catalytic site
	D)	kcat
	E)	the formation of the ES complex
	Ans:   A    Section:  7.2

 

35.	Allosteric effectors:
	A)	can cause large changes in enzymatic activity.
	B)	can lead to a decrease in the availability of a protein.
	C)	do not alter the sensitivity of a metabolic pathway.
	D)	decrease the sensitivity of the enzyme at nearly all concentrations of substrate.
	E)	alter enzyme activity by binding to the active site of an enzyme.
	Ans:  A      Section:  7.3

 

36.	For decades, enzymes have been studied using ensemble methods, but technology now allows them to be studied in singulo. Which of the statements below states one of the significant outcomes of this new technology?
	A)	New methods better demonstrate cooperativity of allosteric enzymes.
	B)	New methods allow for better determination of kcat.
	C)	New methods reveal a distribution of enzyme characteristics.
	D)	New methods validate the steady-state assumption of Michaelis–Menten kinetics.
	E)	New methods provide understanding of average enzyme kinetic data.
	Ans:  C      Section:  7.4

 

37.	When reaction conditions are such that the amount of substrate is far greater than the amount of enzyme present, then the following conditions are also met.
	A)	The [substrate] is much less than KM.
	B)	The V0 is half Vmax.
	C)	The enzyme is displaying second-order kinetics.
	D)	The enzyme is displaying first-order kinetics.
	E)	The enzyme is displaying zero-order kinetics.
	Ans:  E     Sections:  7.1 and 7.2

 

38.	During the early stages of an enzyme purification protocol, when cells have been lysed but cytosolic components have not been separated, the reaction velocity versus substrate concentration is sigmoidal. As you continue to purify the enzyme, the curve shifts to the right. Explain your results.
	A)	This is an enzyme that displays Michaelis–Menten kinetics, and you purify away a homotrophic inhibitor.
	B)	This is an enzyme that displays Michaelis–Menten kinetics, but you must use a Lineweaver–Burk plot to determine KM and Vmax correctly.
	C)	This is an allosteric enzyme, but you must use a Lineweaver–Burk plot to determine KM and Vmax correctly.
	D)	This is an allosteric enzyme, and during purification you purify away a heterotrophic activator.
	E)	This is an allosteric enzyme displaying a double-displacement mechanism, and during purification you purify away one of the substrates.
	Ans: D     Sections:  7.2 and 7.3

 

39.	After purifying the enzyme in the previous question, you determine the Mr to be 75,000. By assaying 5 μg of the enzyme under saturating [S] concentrations, you determine the Vmax to be 1.68 μmol/sec. Calculate the turnover number for this enzyme.
	A)	2.25 ´ 106 sec-1
	B)	1.50 ´ 105 sec-1
	C)	2.50 ´ 104 sec-1
	D)	1.79 ´ 105 sec-1
	E)	You need to also know the KM for this enzyme to calculate turnover number.
	Ans: D     Section:  7.2

 

 

Short-Answer Questions

 

40.	In many enzyme assays, the natural substrate and product are not used. Why?
	Ans:	Many products are difficult to measure accurately. Some are simply difficult to measure, while others are difficult to discern against the background of other molecules present in the reaction. Instead, substrates are chosen that the enzyme can still process but that result in products that can be easily measured. For example, substrates are chosen that result in products that are colored and can be detected spectrophotometrically.
	Section:  7.1

 

41.	A protease hydrolyzes the peptide backbone.  What is the substrate(s) and product for this reaction?  Assuming that the concentration of water is so high (~55M) that it does not appreciably change, to what kind of reaction order would one assign this reaction?
	Ans:	The reaction would be Protein + H2O ® peptide-1 + peptide-2.  As water doesn’t significantly change it’s concentration in an aqueous reaction, the concentration change is zero and can be ignored, thus the rate of the reaction is directly proportionate to the concentration of the protein and is a first-order reaction.
	Section:  7.1

 

 

42.	The rate of a reaction is dependent on [ES].  Using an enzyme catalyzed reaction scheme, (6), describe the kinetic model for [ES].
	Ans:	The concentration of an ES complex is described as the enzyme binding to substrate and can be measured as one kinetic rate constant forming the ES complex.  Loss of the ES can be described as the separation of the two components without reacting (k-1) and the resulting reaction where ES ® EP ® E + P (k2­­).
	Section:  7.2

 

43.	Figure 7.8 is a simplified version of a common set of converging metabolic pathways.  Describe the type of regulation necessary if each of the reactions was reversed and a product, A or G, were preferred.
	Ans:	A feed-forward inhibition where a product, G or H, inhibits e1, e2, e3, or e5. Another possibility is that one or more of the products A through F inhibits e10 or e11.
	Section:  7.3

 

44.	Draw a Cleland notation for a sequential reaction and for a double-displacement reaction.
	Ans:	See Figures 7.6 A and 7.6B.
	Section:  7.2

 

45.	What is the Michaelis–Menten equation? Define all parameters.
	Ans:	V0 = Vmax(S/(S + KM))   Initial velocity V0   Maximum velocity Vmax   Substrate concentration S   Michaelis constant KM
	Section:  7.2

 

46.	What does Vmax indicate?
	Ans:	The maximum velocity or rate of reaction as catalyzed by a specific amount of enzyme when it is saturated with substrate.
	Section:  7.2

 

47.	What is the upper limit of kcat / KM?
	Ans:	The diffusion-controlled interaction of the substrate and enzyme determines the upper limit of the rate. The upper limit is 108 – 109 s-1M-1.
	Section:  7.2

 

48.	How do the intermediate steps in multi-substrate enzyme mechanisms differ?
	Ans:	In a sequential displacement reaction, both substrates bind and a ternary complex of all three is formed. In a double displacement (ping-pong), one or more products are released prior to binding of all substrates. Thus, a substituted enzyme intermediate is formed.
	Section:  7.2

 

49.	Describe the difference between the concerted and the sequential model of allosteric regulation.
	Ans:	The concerted model describes where a multi-subunit enzyme can only assume an R or T conformation, whereas the sequential model assumes that the subunits can assume its conformation different from the neighboring subunits.  In the former, substrate influences the equilibria between each subunit’s R-T conformation and in the latter, substrate can have an intermediate impact on affinity and conformation.
	Section:  7.3

 

50.	Would you expect the order of substrate binding to be critical for enzyme catalysis?
	Ans:	Yes, in some cases. For example, in ping-pong reactions, the proper substrate would have to bind to form the right substituted enzyme intermediate form. In sequential displacement, both conditions are observed. Substrates may need to bind in a particular order (lactate dehydrogenase) or the enzyme may bind substrates and release products in random order (creatine kinase).
	Section:  7.2

 

51.	What is the turnover number for an enzyme and what does this value tell us about the enzyme?
	Ans:	The rate of reaction and dissociation of the ES complex to E + P is k2.  That is the rate at which an enzyme saturated with substrate converts substrate to product.  This is basically the measure of the reaction without an impact on substrate binding and is dependent on the concentration of enzyme and describes the relative speed of a reaction.
	Section:  7.2

 

52.	When designing a drug to inhibit the formation of a product, which requires several enzymes in a metabolic pathway, what should be the first piece of information a biochemist needs in order to develop the drug?
	Ans:	Find the committed step.  In a metabolic pathway there will be a rate-limiting, committed enzyme step that is often the target of physiological regulation.  This protein would be the best target for a new drug.
	Section:  7.2

 

53.	How does the sequential model differ from the concerted model for allosteric enzymes?
	Ans:	The concerted model does not allow for anything other than an “all-or-none” complete tense- or relaxed-form protein. In contrast, the sequential model allows for a mixed type of protein, containing some tense and some relaxed subunits. The form is in response to the ligand binding by a particular subunit.
	Section:  7.3
54.	Draw a sketch of a Michaelis–Menten plot and a Lineweaver–Burk plot. Identify how you would determine KM and Vmax from each of these plots. Explain why the Michaelis–Menten is used more widely than the Lineweaver–Burk plot even though, in general, straight-line plots are easier to interpret.
	Ans:	Sketches should look like Fig 7.3 and 7.5 in the textbook.  KM and Vmax should be identified on the plots. The reason why Lineweaver–Burk plots are rarely used in enzyme studies is because the data points at high and low concentrations are weighted differently, making them sensitive to errors. In addition, computer software has advanced to the point where hyperbolic plots like Michaelis–Menten plots are much more readily analyzed by computers than they were originally.
	Section:  7.2