Biochem exam 3

What will happen to the rates of the forward and reverse reactions when a catalyst is added?

both forward and reverse rates increase

In _______, the inhibitor competes with substrate for binding to the active site, but does not covalently modify the active site. View Available Hint(s)

competetive inhibition

The steady-state kinetics of an enzyme are studied in the absence and presence of an inhibitor BB (two different concentrations of BB were used). The initial rate is given as a function of substrate concentration in the following table: What kind of inhibitor is inhibitor BB?

competitive

What kind of inhibitor is inhibitor BB?

competitive

Indicate whether each of the following disaccharides is a reducing or nonreducing sugar by the criterion of reaction with Fehling's solution. Drag the appropriate items to their respective bins.

reducing Galβ�(1 →→ 4)Glc Glcβ�(1 →→ 6)Glc Glcα�(1 →→ 4)Glc nonreducing Glcα�(1 →→ 2)Frucβ� Glcα�(1 →→ 1)Glcα�

Enzymes work by _____.

reducing EA

Look at the graph of reaction rate versus substrate concentration for an enzyme. (Figure 1) In which region does the reaction rate remain constant?

region C

Refer again to the graph. (Figure 1) In which region is the enzyme saturated with substrate?

region C

Refer again to the graph. (Figure 1) In which region is the enzyme saturated with substrate? View Available Hint(s)

region C

ook at the graph of reaction rate versus substrate concentration for an enzyme. In which region does the reaction rate remain constant?

region C

In the following Fischer projection, the hydroxyl group on the chiral carbon furthest from the carbonyl group points _____, meaning that this is the _____ isomer of tagatose.

right / D

Elastase is closely related to chymotrypsin. Suggest two kinds of amino acid residues you might expect to find in or near the active site. Check all that apply.

serine, histidine

The enzyme urease catalyzes the breakdown of urea in the body. Urease breaks urea down to 2NH3+CO22NH3+CO2. This is an example of a hydrolysis reaction (urea plus water). For each equivalent of carbon dioxide (CO2CO2), two equivalents of ammonia (NH3NH3) are produced. Label the enzyme, substrate, enzyme-substrate complex, enzyme-product complex, and product in the enzymatic reaction for the breakdown of urea by urease using the induced-fit model. Drag the appropriate labels to their respective targets.

starting at the blue and going in a circle to the right: urease, urea, urease-urea, urease-2NH3+CO2 complex, 2NH3 + CO2

An enzyme _____.

is an oragnic catalyst

As a result of its involvement in a reaction, an enzyme _____.

is unchanged

The Lineweaver-Burk plot is a double reciprocal plot of 1/v versus 1/[S]. The slope reveals what kind of information?

kM/vmax

Calculate kcat/KM�cat/�� for the enzyme reaction.

kcat/KM�cat/�M = 8.5×107 M−1s−1M−1s−1

Calculate kcat/KM�cat/�� for the enzyme reaction. Express your answer to two significant figures.

kcat/KM�cat/�M = 8.5×107 M−1s−1M−1s−1 SubmitPrevious Answers

Consider the enzyme-catalyzed reaction with Vmax=164�max=164 (μmol/L)min−1(�mol/L)min−1 and KM=32�M=32 μmol/L�mol/L. If the total enzyme concentration was 1 nmol/Lnmol/L, how many molecules of substrate can a molecule of enzyme process in each minute?

kcat�cat = 1.64×105 min−1min−1

If the total enzyme concentration was 1 nmol/Lnmol/L, how many molecules of substrate can a molecule of enzyme process in each minute? Express your answer to three significant figures.

kcat�cat = 1.64×105 min−1min−1

What name is given to the reactants in an enzymatically catalyzed reaction?

substrate

The steady-state assumption proposes ...(Please assume that steady state has already been reached.)

that the concentration of enzyme-substrate complex [ES] remains nearly constant through much of the reaction.

The Haber process is typically carried out at a temperature of approximately 500∘C∘C. What would happen to the rate of the forward reaction if the temperature were lowered to 100∘C∘C?

the reaction rate would decrease

What would happen to the rate of the forward reaction if the concentration of nitrogen were decreased?

the reaction rate would decrease

Consider the electron flow shown. Describe the errors associated with the product of this proposed mechanism.

there is a pentavalent carbon atom, which is not possible. the carbon atom participating in the double bond needs a formal charge of 1−− added.

Pancreatic zymogens are converted to fully active enzymes by irreversible proteolytic cleavage. The enzyme enteropeptidase cleaves which zymogen?

trypsinogen

Which mode of enzyme inhibition decreases both the apparent KM and apparent Vmax?

uncompetitive inhibiton

Determine the apparent KM�M at each inhibitor concentration. Enter your answers separated by commas in requested order.

without inhibitor, 3 mMm�, 5 mMm� 2.48,3.88,5.15 mmol/Lmmol/L

Determine the apparent Vmax�max at each inhibitor concentration.

without inhibitor, 3 mMm�, 5 mMm� 5.13,5.13,5.11 (mmol/L)min−1(mmol/L)min−1

Determine the apparent Vmax�max at each inhibitor concentration. Enter your answers separated by commas in requested order.

without inhibitor, 3 mMm�, 5 mMm� 5.13,5.13,5.11 (mmol/L)min−1(mmol/L)min−1

Which statement about a biological catalyst is true.

Catalysts increase the velocity of chemical reactions.

Identify which of the following molecules are chiral and which are achiral. Drag each item to the appropriate bin.

Chiral 2-bromobutane 2-butanol Achiral butane 2-propanol 1-bromobutane

The reagent periodate (IO4−)(IO4−) oxidatively cleaves the carbon-carbon bonds between two adjacent carbons carrying hydroxyl groups. Explain how periodate oxidation might be used to distinguish between methyl glycosides of glucose in the pyranose and furanose forms. Match the words in the left column to the appropriate blanks in the sentences on the right.

Cleavage of the pyranose form will occur twice, producing formic acid. Cleavage of the furanose form will occur twice (between C2C2 and C3C3 and between C5C5 and C6C6), but formaldehyde will be produced from C6C6.

Indicate whether the structures shown are R� or S� in the absolute system. Drag the appropriate labels to their respective targets.

S = left structure R = right structure

An enzyme is irreversibly inhibited by diisopropylfluorophosphate (DFP). What does this show?

Serine is likely an important residue in the active site

Is the effect of the N155TN155T mutation what you would expect for a residue that makes up part of the oxyanion hole? How do the reported values of kcat�cat and KM�M support your answer? Check all that apply.

kcat�cat should be reduced due to the loss of enthalpic stabilization of the transition state.For a mutation of a residue that only interacts with the oxyanion intermediate, one would not expect KM�M to change significantly.The oxyanion is formed after SS binds.

Synthesis of sugar polymers is enzyme catalyzed and requires activated monomers like ________ in lactose biosynthesis.

UDP-Galactose

Classify the carbohydrate tagatose by both the carbonyl group and the number of carbon atoms. Enter the classification (e.g., aldotriose

ketohexose

In general, enzymes are what kinds of molecules?

proteins

Describe the function of uridine triphosphate (UTP) in carbohydrate metabolism. Match the words in the left column to the appropriate blanks in the sentences on the right.

UTP is a precursor to uridine diphosphate glucose, an activated intermediate in the biosynthesis of glucose-containing oligosaccharides and polysaccharides.

Which might be most useful for determining the amino acid residues in an enzyme's active site?

Use an irreversible inhibitor that reacts with the side chains of specific amino acids.

When two different substrates react to form two different products, the rate constants for each separate substrate can be determined by ________.

Varying one substrate at a time, keeping the other in excess

Describe the profile you would expect for a biological catalyst. Complete the sentences to explain why an enzyme is different than an inorganic catalyst. Match the words in the left column to the appropriate blanks in the sentences on the right.

When looking at the plot of GG versus reaction coordinate, the profile for a biological catalyst (e.g., an enzyme) will have multiple transition state(s), with an overall activation energy that is low in comparison to the uncatalyzed reaction. Enzymes have a high molecular weight and are organic compounds, while inorganic catalysts often have a low molecular weight and are inorganic compounds. When comparing rates, enzymes are typically several times faster than inorganic catalysts.

Protein kinases are ATP-dependent enzymes that facilitate which covalent modification to a protein?

phosphorylation

You have a racemic mixture of d-2-butanol and l-2-butanol. The d isomer rotates polarized light by +13.5∘+13.5∘. What is the rotation of the polarization of light of your mixture? Express your answer in degrees.

0 degrees

Which statements about nicotinamide adenine dinucleotide (NAD+) are true? The cofactor is derived from the vitamin niacin Nicotinaminde adenine dinucleotide phosphate (NADP+) has a phosphoryl group at the 2' position of the ribose attached to the adenine base NAD+ acts as an oxidizing agent in the conversion of alcohols to aldehydes or ketones In the conversion from NAD+ to NADH a proton is transferred

1, 2, and 3

Which statements about allosteric enzymes are true?exhibit cooperativity in substrate binding (homoallostery)exhibit regulation of their activity by other, effector molecules (heteroallostery)there is no difference in the binding curve for a cooperative binding versus noncooperative binding enzymeare frequently multisubunit proteins, with multiple active sites View Available Hint(s)

1,2, and 4

Complete this vocabulary exercise relating to the three types of enzyme inhibitors. Drag the words on the left to the appropriate blanks in the sentences on the right. Each word is used only once.

1. A (n)competitive inhibitor has a structure that is so similar to the substrate that it can bond to the enzyme just like the substrate. 2. A (n)noncompetitive inhibitor binds to a site on the enzyme that is not the active site. 3. Usually, a(n) irreversible inhibitor forms a covalent bond with an amino acid side group within the active site, which prevents the substrate from entering the active site or prevents catalytic activity.target 3 of 6 4. The competitive inhibitor competes with the substrate for the active site on the enzyme.target 4 of 6 5. When the noncompetitive inhibitor is bonded to the enzyme, the shape of the enzyme is distorted.target 5 of 6 6. Enzyme inhibitors disrupt normal interactions between an enzyme and its substrate.

Complete the following sentences. Match the words in the left-hand column with the appropriate blank in the sentences in the right-hand column.

1. A monosaccharide is a(n) aldose if the carbonyl group is on the end of the carbon chain.target 1 of 6 2. The most common carbohydrate, glucose, has six carbon atoms.target 2 of 6 3. Glyceraldehyde is an example of a(n) aldotriose, because it has three carbon atoms.target 3 of 6 4. With the carbonyl group on the end of a six-carbon chain, the carbohydrate would be classified as a(n) aldohexose.target 4 of 6 5. Any carbohydrate with the carbonyl group on the second carbon is a(n) ketose.target 5 of 6 6. If a carbohydrate, like xylulose, has five carbon atoms and a carbonyl group on the second carbon, it is called a(n) ketopentose.

Complete the following sentences about carbohydrates. Match the words in the left-hand column with the appropriate blank in the sentences in the right-hand column.

1. A simple sugar is composed of equal parts carbon and water, which gave rise to the general name of any sugar as a carbohydrate .target 1 of 4 2. A carbohydrate that yields many monosaccharides when hydrolyzed is a polysaccharide .target 2 of 4 3. Lactose, the sugar in milk, is a disaccharide, because it can be split into two monosaccharides.target 3 of 4 4. A monosaccharide cannot be hydrolyzed any further.

Complete this vocabulary exercise relating to enzymes. Match the words in the left-hand column to the appropriate blank in the sentences in the right-hand column.

1. An enzyme is denaturedwhen it loses its native conformation and its biological activity.target 1 of 7 2. An enzyme is considered a catalystbecause it speeds up chemical reactions without being used up.target 2 of 7 3. An enzyme is considered specificbecause of its ability to recognize the shape of a particular molecule.target 3 of 7 4. A cofactor, such as a vitamin, binds to an enzyme and plays a role in catalysis.target 4 of 7 5. When properly aligned, the enzyme and substrate form an enzyme-substrate (ES)complex.target 5 of 7 6. A substrate binds to an enzyme at the active site, where the reaction occurs.target 6 of 7 7. In a catalyzed reaction a reactant is often called a substrate.

In an enzyme-catalyzed reaction, the reactant species to which the enzyme binds is called the substrate. The substrate is then converted into products by a series of steps. The lock-and-key model explains the steps involved in an enzyme-catalyzed reaction. Label the following diagram that illustrates the lock-and-key model of enzyme activity. Drag the appropriate labels to their respective targets.

1. active site 2. enzyme-substrate complex 3. (top) products (bottom) enzyme

Estimate Vmax�max from a direct graph of v� versus [S][S] using the plot you created in part A. Express your answer using two significant figures.

1.5×102 (μmol/L)min−1(�mol/L)min−1

An enzyme contains an active site aspartic acid with a pKa=5.0p�a=5.0, which acts as a general acid catalyst. Choose the curve of enzyme activity (reaction rate) versus pHpH for the enzyme (assume the protein is stably folded between pHpH 2−−12 and that the active site AspAsp is the only ionizable residue involved in catalysis).

100 to 11

By what factor does increasing the temperature of a reaction from T1�1 = 273 KK to T2�2 = 283 KK increase the rate of reaction? Assume the activation energy (Ea�a) of this reaction is 164,500 JJ and that the pre-exponential constant (A�) is 2.1×109 s−12.1×109 s−1.

13

Use the equation from part E to estimate Vmax�max. Express your answer using three significant figures.

164 (μmol/L)min−1(�mol/L)min−1

Match each term with its definition. 1) Reaction coordinateA) represents the additional free energy that molecules must have to attain the transition state2) ΔG°B) a generalizedmeasure of the progress of the reaction through intermediate states3) ΔG°‡C) free energy of the reaction

1:B; 2:C; 3:A

Match each of the following terms from the Michaelis-Menten equation to its correct definition.1) V maxA) numerically equal to the substrate concentration at 0.5 V max2) k catB) rate of a reaction when enzyme is saturated with substrate3) k cat/K MC) enzyme efficiency4) K MD) number of substrate molecules turned over by enzyme

1:B; 2:D; 3:C; 4:A

Match each function with the correct enzyme class.1) transfer functional groups between moleculesA) oxidoreductases2) catalyze intramolecular rearrangementsB) transferases3) catalyze redox chemistryC) hydrolases4) catalyze the joining of two molecules togetherD) lyasesE) isomerasesF) ligases

1:B; 2:E; 3:A; 4:F

Please match each cofactor with its function.1) thiamine pyrophosphateA) CO2 activation/transfer2) coenzyme AB) oxidation/reduction3) biotinC) activation of aldehydes4) NAD+D) acyl group transfer

1:C; 2:D; 3:A; 4:B

Which of the following statements about the oxyanion hole in serine proteases are true?This preformed loop is properly positioned to stabilize the negatively charged tetrahedral intermediate involved in amide bond hydrolysis.The backbone NH bonds of S195 and G193 create H-bonding interactions with the developing negative charge as S195 attacks the scissile carbon bond.It represents an enthalpic interaction that helps stabilize the transition state.It represents an electrostatic interaction that leads to a lower energy state.

2, 3, and 4

Determine KM�M in the absence of inhibitor. Express your answer using three significant figures.

2.48 mmol/Lmmol/L

Determine KM�M in the presence of inhibitor. Express your answer using three significant figures.

2.63 mmol/Lmmol/L

Determine KM�M in the presence of inhibitor. Express your answer using three significant figures.

2.67 mmol/Lmmol/L

Determine Vmax�max in the presence of inhibitor. Express your answer using three significant figures.

2.90 (mmol/L)min−1(mmol/L)min−1

Assuming that the T155T155 side chain cannot HH-bond to the oxyanion intermediate, by how much (in kJ/molkJ/mol) does N155N155 appear to stabilize the transition state at 37 ∘C∘C? Express your answer to two significant figures and include the appropriate units.

20 kJ/mol

Estimate KM�M from a direct graph of v� versus [S][S] using the plot you created in part A. Express your answer using two significant figures.

25 μmol/L�mol/L

Determine Vmax�max in the presence of inhibitor. Express your answer using three significant figures.

3.14 (mmol/L)min−1(mmol/L)min−1

Use the equation from part E to estimate KM�M. Express your answer using two significant figures.

32

A rate enhancement of 106106 requires that the enzyme bind its transition state complex with higher affinity than its substrate. Using the Arrhenius equation, shown before this part, find ΔΔG‡catΔΔ�cat‡ for a rate enhancement of 106106 at 298 KK. Express ΔΔG‡catΔΔ�cat‡ in kJ/molkJ/mol to three significant figures.

34.2 kJ/mol

How many chiral carbon atoms does the monosaccharide glucose have?

4

How many hemiacetal rings with a different connectivity between atoms (ignoring stereoisomers) can be made from glucose, assuming that rings that would generate ring strain (fewer than four atoms or greater than six atoms) are not favored? Enter your answer as an integer.

4

Arrange the events for the hydrolysis of amide bonds by chymotrypsin in their correct order.attack by Ser 195 to give a tetrahedral intermediateprotonation by His 57 and release of the free C-terminus of the hydrolyzed bondprotonation by His 57 and release of the free N-terminus of the hydrolyzed bondattack by water, leading to formation of a tetrahedral intermediatebinding of substrate to properly position the scissile bond for cleavage

5,1,2,4,3

A ribopyranose contains ________ carbon atoms while a ribofuranose has ________ carbon atoms.

5,5

Estimate KI�I from these data.

5.08 mMm�

Determine Vmax�max in the absence of inhibitor. Express your answer using three significant figures.

5.13 (mmol/L)min−1(mmol/L)min−1

How many tripeptides can be formed from one molecule of each amino acid? Express your answer as an integer.

6

How many tripeptides can be formed from one molecule of each amino acid? Express your answer as an integer.

6 tripeptides

Enzymes achieve rate enhancement through which of the following mechanisms?

All of the listed choices describe mechanisms used by enzymes to achieve their rate enhancement of reactions.

On the basis of these data, suggest what features of amino acid sequence dictate the specificity of proteolytic cleavage by elastase. Match the words in the left column to the appropriate blanks in the sentences on the right. Make certain each sentence is complete before submitting your answer.

A hydrophobic residue seems to be favored at the position CC-terminal to the site of bond cleavage. Elastase always requires a small residue (like Ala) to the NN-terminal side.

Explain why it is important to animals for the major carbohydrate storage polymer, glycogen, to be branched rather than unbranched. Match the words in the left column to the appropriate blanks in the sentences on the right.

A(n) branched polymer has far more terminal glucose residues than a(n) unbranched polymer of equivalent molecular weight, thereby allowing a larger number of terminal glucose residues to be mobilized in the face of an energy demand.target 1 of 4target 2 of 4target 3 of 4 It seems likely that the enzyme and the polymer coevolved to meet the potential need for rapid mobilization.

In E. coli ________ is an activator and ________ is a negative allosteric modulator of the enzyme phosphofructokinase-1.

ADP; phosphoenolpyruvate

Proteins can be glycosylated (have sugar molecules added to them) through the formation of either acetals/ketals or Schiff bases. Which amino acids have side chains that can be used as reactants to form acetals/ketals or Schiff bases? Drag the appropriate amino acids to their respective bins.

Acetal/ketal Tyr Ser Thr Schiff base Lys Arg Neither His Val Pro Gly Trp

You have an enzymatic reaction proceeding at the optimum pH and optimum temperature. You add a competitive inhibitor to the reaction and notice that the reaction slows down. What can you do to speed the reaction up again?

Add more substrate; it will outcompete the inhibitor and increase the reaction rate.

Select the statement that is incorrect.

All carbohydrates have the general formula Cn(H2O)nC�(H2O)�.

Non-classical competitive inhibition involves ________.

Binding of either the substrate to the active site or the inhibitor to its own binding site thus preventing the other from binding

The bacterial cell wall is sensitive to penicillin because it ________.

Binds to an enzyme which recognizes D-alanine-D-alanine dipeptide

Naturally occurring glycosides have roles in cells which include all EXCEPT ________.

Building blocks of lipids

The disaccharide α�,β�-trehalose differs from the α�,α� structure in the figure below by having an (α1→β1�1→�1) linkage. Complete its structure as a Haworth projection. α�,α�-Trehaloseα�-D-glucopyranosyl(1 →→ 1)α�-D-glucopyranose

Correct answer = Oxygen connected to a U shape to the structure, on the ring structure there is an "OH" sticking out from the bottom left corner towards the inside

Complete the sentence to explain whether allose and altrose are epimers. (Consider only D-sugars.) Match the words in the left column to the appropriate blanks in the sentences on the right.

D-allose and D-altrose differ in configuration only at C2C2 and hence are epimers.

Complete the sentence to explain whether gulose and talose are epimers. (Consider only D-sugars.) Match the words in the left column to the appropriate blanks in the sentences on the right.

D-gulose and D-talose differ in configuration at both C2C2 and C3C3 and hence are not epimers.

Are mannose and galactose, allose and altrose, gulose and talose, and ribose and arabinose diastereoisomers? Consider only D-sugars. Match the words in the left column to the appropriate blanks in the sentences on the right.

D-mannose and D-galactose are diastereomers because they are not mirror images. They differ in configuration about two asymmetric carbon atoms. D-allose and D-altrose are diastereomers because they are not mirror images. They differ in configuration about one asymmetric carbon atom. D-gulose and D-talose are diastereomers because they are not mirror images. They differ in configuration about two asymmetric carbon atoms. D-ribose and D-arabinose are diastereomers because they are not mirror images. They differ in configuration about one asymmetric carbon atom.

Are mannose and galactose, allose and altrose, gulose and talose, and ribose and arabinose diastereoisomers? Consider only D-sugars. Match the words in the left column to the appropriate blanks in the sentences on the right.

D-mannose and D-galactose are diastereomers because they are not mirror images. They differ in configuration about two asymmetric carbon atoms. D-allose and D-altrose are diastereomers because they are not mirror images. They differ in configuration about one asymmetric carbon atom. D-gulose and D-talose are diastereomers because they are not mirror images. They differ in configuration about two asymmetric carbon atoms. D-ribose and D-arabinose are diastereomers because they are not mirror images. They differ in configuration about one asymmetric carbon atom.target 1 of 12target 2 of 12target 3 of 12target 4 of 12target 5 of 12target 6 of 12target 7 of 12target 8 of 12target 9 of 12target 10 of 12target 11 of 12target 12 of 12

Complete the sentence to explain whether mannose and galactose are epimers. (Consider only D-sugars.) Match the words in the left column to the appropriate blanks in the sentences on the right.

D-mannose and D-galactose differ in configuration at both C2C2 and C4C4 and hence are not epimers.

Complete the sentence to explain whether ribose and arabinose are epimers. (Consider only D-sugars.) Match the words in the left column to the appropriate blanks in the sentences on the right.

D-ribose and D-arabinose differ in configuration only at C2C2 and hence are epimers.

Enzymes that oxidize NADH can best be measured by the ________.

Decrease in absorbance at 340 nm

Consider the dextran sucrase reaction. Why do you suppose there is not an ATPATP requirement to energetically drive the creation of glycosidic bonds in the dextran product? Match the words in the left column to the appropriate blanks in the sentences on the right.

Dextran sucrase uses the bond energy stored in the glycosidic linkbetween glucose and fructose to drive formation of the glucose-glucose bond.

Define what is meant by the following species. Match the species in the left column to the appropriate blanks in the sentences on the right.

E+S is the state where the enzyme and substrate are first mixed together. ES is the enzyme-substrate complex.target 2 of 3 ES‡ is the transition state of the enzyme-substrate complex as it is reacting to form the enzyme-product complex.

Enalapril is administered in pill form, but enalaprilat must be administered intravenously. Why do you suppose enalapril works as a pill, but enalaprilat does not?

Enalaprilat is too polar to cross membranes, whereas enalapril can cross membranes to get from the gut to circulation.

Which of the following statements are true with respect to enzyme activity? Check all that apply.

Enzymes affect the reaction pathway by forming an enzyme-substrate complex. Enzymes speed up the reaction rate. Enzymes are regenerated when the reaction is completed.

Complete the sentences to explain why is it important that ESES is not too much more stable than E+SE+S. Determine how this is related to the lock and key versus induced fit models of enzyme function. Match the words in the left column to the appropriate blanks in the sentences on the right.

Enzymes catalyze reaction by stabilizing the transition state. If the enzyme binds to the substrate too well, the activation energy for the catalyzed reaction increases. Thus, the enzyme binds best to the transition state, and the activation energy decreases. In the lock and key model, the enzyme binds to the substrate most efficiently. In the induced fit model, both the enzyme and substrate change their structure upon binding in a way that favors the formation of the transition state. Thus, when comparing the models, the induced fit model lowers the energy of the transition state more.

Now consider three sugars−−glucose, glucuronic acid, and NN-acetylglucosamine. Use shorthand (e.g., Glcα(1→4)GlcUAβ(1→4)GlcNAcGlc�(1→4)GlcUA�(1→4)GlcNAc) to represent trisaccharides with the sequence Glc−GlcUA−GlcNAcGlc−GlcUA−GlcNAc. Select all that apply.

Glcα(1→2)GlcUAα(1→3)GlcNAc Glcβ(1→4)GlcUAβ(1→4)GlcNAc Glcα(1→2)GlcUAβ(1→4)GlcNAc

Now consider three sugars−−glucose, glucuronic acid, and NN-acetylglucosamine. Use shorthand (e.g., Glcα(1→4)GlcUAβ(1→4)GlcNAcGlc�(1→4)GlcUA�(1→4)GlcNAc) to represent trisaccharides with the sequence Glc−GlcUA−GlcNAcGlc−GlcUA−GlcNAc.

Glcα(1→4)GlcUAβ(1→3)GlcNAc Glcβ(1→4)GlcUAβ(1→4)GlcNAcGlc Glcα(1→2)GlcUAα(1→3)GlcNAc

If glucose supplies the anomeric carbon atom in a glycosidic link, the resulting compound is classified as a ________.

Glucoside

Which is a general term indicating a carbohydrate polymer?

Glycan

What is the natural polysaccharide whose repeating structure can be symbolized by GlcUAβ(1→3)GlcNAcGlcUA�(1→3)GlcNAc, with these units connected by β(1→4)�(1→4) links?

Hyaluronic acid

Most of the known enzymes are ________.

Hydrolases

Below is the Fischer projection of D-galactose. Which is the proper Haworth projection of β-D-galactopyranose?

I

For enzyme-catalyzed reactions, as temperature is increased, an increase in rate is observed to a point, and then the rate decreases dramatically. Propose a reason for this effect. Match the words in the left column to the appropriate blanks in the sentence on the right.

If the temperature of an enzyme-catalyzed reaction is too high, the enzyme will be denatured, rendering it inactive and thus reducing the rate of reaction.

Provide an explanation for the fact that α�-D-mannose is more stable than β�-D-mannose, whereas the opposite is true for glucose. Match the words in the left column to the appropriate blanks in the sentences on the right.

In the chair form there is less steric clash between the 2-OHOH and the 1-OHOH in the β� form of glucose and in the α� form of mannose.

Consider a situation in which the enzyme is operating at optimum temperature and pHpH, and has been saturated with substrate. What is your best option for increasing the rate of the reaction?

Increase the enzyme concentration.

Enalaprilat is a competitive inhibitor of the angiotensin-converting enzyme (ACEACE), which cleaves the blood-pressure regulating peptide angiotensin I. ACEACE has a KM=52�M=52 μM�� for angiotensin I, which is present in plasma at a concentration of 75 μM��. When enalaprilat is present at 2.8 nMn�, the activity of ACE in plasma is 15 %% of its uninhibited activity. What is the value of KI�I for enalaprilat?

KI�I = 2.0×10−10 MM

Indicate whether the structures shown are R� or S� in the absolute system.

Left molecule = S Right Molecule = R

Given the two plots in parts A and D and the analysis methods available within each part, which is better to estimate Vmax�max and KM�M?

Lineweaver-Burk plot

Classify each of the characteristics as lock-and-key model or induced-fit model or both. Drag the appropriate items to their respective bins.

Lock-and-key modeldroppable Active site is rigid Induced-fit modeldroppable Active site-substrate interaction induces an optimal fit for catalysis Substrate shape is modified Active site is flexible Bothdroppable Enzyme is substrate specific Enzyme returns to its initial state after catalysis

If a mixture of these three substrates was presented to elastase with the concentration of each peptide equal to 0.5 mMm�, which would be digested most rapidly? Which most slowly? (Assume enzyme is present in excess.) Rank from most rapidly to most slowly. To rank items as equivalent, overlap them.

Most rapidly PAPAPAPA↓↓FF middle PAPAPAPA↓↓AA least rapid PAPAPAPA↓↓GG

Much of organic chemistry and inorganic chemistry is concerned with covalent, ionic, and metallic bonding, whereas non-covalent bonding is often given cursory treatment. Which of the following statements are TRUE about the importance of non-covalent interactions?

Non-covalent interactions are readily reversible. Non-covalent interactions include hydrogen bonding, dipole-induced dipole interactions, and London dispersion forces. Non-covalent interactions are relatively weak forces.

Analyze the data and complete the following sentences. Match the words in the left column to the appropriate blanks in the sentences on the right. Make certain each sentence is complete before submitting your answer.

Of the two enzymes studied, when plotting concentration versus reaction rate, enzyme AA produces a plot with no defined shape and enzyme BB produces a plot with a hyperbolic shape.target 1 of 7target 2 of 7 The reaction rate of enzyme AAshows no trend as the concentration of substrate increases to its saturation point, and the reaction rate of enzyme BBincreases uniformly over the same set of conditions.target 3 of 7target 4 of 7 Given this data, enzyme B obeys the Michaelis-Menten equation. Analyzing the shape of this plot, the estimated value of Vmax�max is 16mmol/smmol/s and KM�M is 8×10−38×10−3mmol/Lmmol/L.

Which of the following rate-enhancing features does lysozyme use to increase the rate of the hydrolysis reaction it catalyzes? general acid-base catalysis electrostatic catalysis distortion of substrate covalent catalysis

Only choices 1, 3, and 4 are correct.

Consider the following reaction:A → BWhich of the following statements about this reaction are correct?If you double the concentration of reagent A, you will double the rate.The reaction rate (or velocity) is dependent only on the concentration of A.The units for the first-order rate constant are M s-1.A plot of the log[A] versus time yields an inverse hyperbola.

Only statements 1 and 2 are correct.

Which of the following statements is most likely to be true in the case of the feedback-regulated enzymatic pathway shown?

P4 binds E1 and deactivates it.

Enzyme reactions with multiple substrates fall into different classes of substrate binding mechanisms. Which mechanism is best described by the following order: one substrate is bound, one product is released, a second substrate comes in, and a second product is released.

Ping-Pong mechanism

In a certain enzyme-catalyzed reaction the following steps occur:1. A phosphate group on substrate A is transferred to a side chain of an active site residue of the enzyme.2. The dephosphorylated form of substrate A dissociates from the enzyme.3. Substrate B enters the active site and is phosphorylated with simultaneous regeneration of the enzyme in its original form.What kind of kinetic mechanism is described?

Ping-pong

Ribozymes are ...

RNA molecules that can catalyze specific biochemical reactions in the same way protein enzymes do.

A reducing sugar will undergo the Fehling reaction, which requires a (potential) free aldehyde group. Which of the disaccharides shown in the figure below are reducing and which are nonreducing?

Reducing: Lactose Cellobiose Maltose Gentiobiose Nonreducing: Sucrose Trehalose

Subtilisin does have a problem in that it becomes inactivated by oxidation of a methionine close to the active site. Suggest a way to make a better subtilisin. Match the words in the left column to the appropriate blanks in the sentences on the right. Make certain each sentence is complete before submitting your answer.

Replace the methionine, by site-directed mutagenesis, with another residue. Because methionine is quite hydrophobic, a hydrophobic replacement would seem appropriate. A single base change in the MetMet codon could yield ThrThr, LysLys, ArgArg, LeuLeu, IleIle, or ValVal.

The five principal means of enzyme regulation introduce a variety of terms and concepts. In this vocabulary exercise, find the word or concept that best completes each sentence.

Reversible inhibition relies on non-covalent interactions, the low binding energies of which allow for the rapid binding and release of small molecules. Allosteric regulation is a term for when the binding of one molecule induces a conformational change in the enzyme such that a second binding site is also altered. Phosphorlyation is a reversible covalent modification in which a phosphate group is attached to an enzyme to regulate its activity. This modification is typically at an alcohol, such as that found on serine, threonine, or tyrosine. Oftentimes, a pathway with multiple enzymes is regulated at its first step by the binding of a downstream product. In this scenario, termed feedback regulation, the downstream product may look very different from the substrate for the first enzyme in the pathway (that which is regulated). In proteolytic cleavage, the precursor molecule - called a(n) zymogen (or proenzyme) - is activated through its cleavage by a proteolytic enzyme. Product inhibition occurs when the product of an enzymatic reaction can bind to - and inhibit - the activity of the enzyme that produced it.

Protein kinase C (PKC) is a central signaling molecule for many pathways. The typical protein kinase C is made up of three domains and a pseudosubstrate The kinase domain (blue) is the catalytic subunit. Responsible for transferring phosphate to substrates, the kinase domain itself is phosphorylated at three sites.These phosphorylation events activate the kinase domain. Even when phosphorylated, however, the kinase domain is inhibited by the presence of two regulatory domains (the C1 and C2 domains) and a pseudosubstrate. The pseudosubstrate (violet) is an internal sequence of amino acids that looks just like a kinase substrate. This pseudosubstrate, then, binds the active site, thereby inhibiting the kinase until the proper activation signals are provided.

Reversible inhibition: A pseudosubstrate occupiesthe active site via non-covalentinteractions to render PKCinactive in unstimulated cells Allosteric control: Binding of calcium to theC2 domain causes aconformational change toallow the C1 domains to searchfor their specific lipid ligands Binding of lipids to theC1 domain causes aconformational change to openup the active site of PKC Covalent modification: Phosphorylation activatesthe kinase domain Proteolytic cleavage: The protease-sensitive "hinge"region can be cleaved by aprotease to liberate the catalyticdomain from the regulatorydomains, thereby creating aconstitutively active (unregulated)kinase domain

As laid out in the Foundation Figure, there are five principal means by which the cell can regulate the activity of its enzymes and proteins. Match each scenario below with the type of regulation it exemplifies.

Reversible inhibition: Naproxen, a pain reliever,works by binding to theenzyme cyclooxygenase (COX)to prevent the enzyme fromproduce pro-inflammatorymolecules. Naproxen binds toCOX through multiplenon-covalent bonding. Irreversible inhibition: Aspirin is a typical"suicide inhibitor": whenacted upon by its targetenzyme (COX-1), aspirinbecomes covalently boundto the active site, renderingCOX-1 inactive. Allosteric control: Protein kinase A (PKA) hastwo types of subunits: thecatalytic and regulatorysubunits. The binding ofcyclic AMP (cAMP) to theregulatory subunits of PKAinduces a conformationalchange in regulatory subunits,thereby releasing- andactivating - the kinase. Covalent modification: The phosphorylation of aserine residue on proteinkinase C results in aconformational change thatrenders the kinasecatalytically active. Proteolytic cleavage: The inactive precursor proteinprothrombin is cleaved byFactor X (a serine protease)to generate thrombin as partof the proteolytic cascadeinvolved in blood coagulation.

Monosaccharide derivatives in which an amino group replaces one of the hydroxyl groups may have important roles in _______

Sialic acid

Explain how oseltamivir (Tamiflu) interferes with influenza virus replication. Match the words in the left column to the appropriate blanks in the sentences on the right.

Tamiflu is a structural analog of neuraminic acid. Tamiflu inhibits the neuraminidase enzyme that is carried on the surface of the influenza virus particle. Action of this enzyme is necessary for breakdown of the plasma membrane of an infected cell so that virus can be released to infect more cells.

Which of the following statements about the proposed mechanisms of action for hen egg white lysozyme does NOT support either model?

The active site aspartic acid changes between being protonated and deprotonated.

The elasticity and resistance to compression of connective tissue is due to ________.

The carboxyl and sulfated groups in the glycosaminoglycans

The value you calculated in part D represents the strength of the HH-bond between N155N155 and the oxyanion in the transition state. This value is higher than typical HH-bonds in water. How might this observation be rationalized? Hint: Consider the Coulomb's Law. Match the words in the left column to the appropriate blanks in the sentences on the right. Make certain each sentence is complete before submitting your answer.

The dielectric constant, ε�, is lower in the enzyme active site than it is in water; thus, Coulomb,s law predicts a stronger interaction between the HH-bond donor and acceptor.

You have added an irreversible inhibitor to a sample of enzyme and substrate. At this point, the reaction has stopped completely. What can you do to regain the activity of the enzyme?

The enzyme is inactive at this point. New enzyme must be added to regain enzyme activity.

Subtilisin is used in some laundry detergents to help remove protein-type stains. What unusual kind of stability does this suggest for subtilisin?

The enzyme must be stable both to the presence of detergents and to moderately high temperatures.

Why do you suppose that the influenza virus protein that binds the virus to an infected cell is called hemagglutinin? Hemagglutination is the clumping together of red blood cells. Match the words in the left column to the appropriate blanks in the sentences on the right.

The influenza hemagglutinin on the virus particle binds to the surface of any cell that contains sialic acid. When it binds to the surface of erythrocytes, this causes the cells to agglutinate, or to aggregate, or clump.

What distinguishes an aldonic acid from an alduronic acid?

The oxidation of the aldehyde group in an aldonic acid and the oxidation of the highest numbered carbon in the alduronic acid.

α�-D-Galactopyranose rotates the plane of polarized light, but the product of its reduction with sodium borohydride (galactitol) does not. Explain the difference. Match the words in the left column to the appropriate blanks in the sentences on the right.

The product of the reaction is galactitol, which has a plane of symmetry between CC-4 and CC-3.

Complete the sentences comparing the reaction rate for each condition in Parts A and C. Match the words in the left column to the appropriate blanks in the sentences on the right.

The reaction order for histidine-catalyzed hydrolysis is the same as that for trypsin-catalyzed hydrolysis at low concentrations. The reaction order for trypsin-catalyzed hydrolysis at low concentrations is different from that for trypsin-catalyzed hydrolysis at high concentrations. The shape of the curve for trypsin-catalyzed hydrolysis at high concentrations is most likely due to saturation of the enzyme. This means that the ratio rate/concentration reached its maximum approaching high concentrations.

Determine the rate order for the hydrolysis of pNPA at low (1 mMm� and lower) and high (10 mMm� and higher) concentrations when trypsin is the catalyst using the enlarged portions of your plot shown. Match the words in the left column to the appropriate blanks in the sentences on the right.

The reaction order for the hydrolysis of pNPA by trypsin at low concentrations is first order. The reaction order for the hydrolysis of pNPA by trypsin at high concentrations is zero order.

Below is a table of common intermolecular forces found in the active sites of enzymes: kJ/molkJ/molHydrogen bonds10 to 40Dipole-dipole interactions5 to 25Dispersion forces0.5 to 40 Using your value from the previous question, determine how many H bonds or dipole interactions would be required to achieve a rate enhancement of 106106. Match the values in the left column to the appropriate blanks in the sentences on the right.

To achieve a rate enhancement of 106106, a total of 0.86 to 3.42 hydrogen bonds or 1.37 to 6.84 dipole interactions would be required.

Consider the proposed mechanism of an acid catalyzed aldol reaction. Mark with the green check to indicate that the given direction of electron flow using curved arrow notation is correct and with the red X label to indicate it is incorrect for this specific mechanism. Drag the appropriate labels to their respective targets.

Top: X check check Bottom: X check X

Why is a person with type AB blood able to receive a blood transfusion from a donor with any of the major blood types (A, B, AB, and O) but is able to donate blood only to another type AB individual? Match the words in the left column to the appropriate blanks in the sentences on the right.

Transfusion of type AB blood would introduce both A and B tetrasaccharides, which would be recognize(d) as foreign and trigger an immune reaction in recipients lacking either the A saccharide (type B) or B (type A) or both (type O). The type AB blood would contain both A and B and would not recognize(d) those tetrasaccharides as foreign.

Why is a person with type AB blood able to receive a blood transfusion from a donor with any of the major blood types (A, B, AB, and O) but is able to donate blood only to another type AB individual? Match the words in the left column to the appropriate blanks in the sentences on the right. ResetHelp

Transfusion of type AB blood would introduce both A and B tetrasaccharides, which would be recognize(d) as foreign and trigger an immune reaction in recipients lacking either the A saccharide (type B) or B (type A) or both (type O). The type AB blood would contain both A and B and would not recognize(d) those tetrasaccharides as foreign.

Is this a fairly efficient enzyme? (See table below)

Yes, this is a very efficient enzyme.

The expression: Vmax = k2[E]total applies to ________.

Zero order kinetics of an enzyme-catalyzed reaction

The cofactor NAD+ is ________.

an oxidant

What is the correct label for "A"?

energy of activation

Which are possible conformations of a furanose molecule?

enevlope and twist

Identify the rate order for the hydrolysis of pNPA when histidine is the catalyst.

first order

Below is an energy profile for the reaction of carbon dioxide and water to form carbonic acid in the presence and absence of a catalyst, catalase. Label the energy values associated with the profile, including the enthalpy of reaction (ΔHrxnΔ�rxn), uncatalyzed activation energy (Ea,uncat�a,uncat), and catalyzed activation energy (Ea,cat�a,cat). Drag the appropriate labels to their respective targets. Not all targets will be filled.

from left to right: delta H rxn, Ea uncat, blank, Ea cat

The Michaelis-Menten parameters, kcat�cat and KM�M, for selected enzymes are given in the table below. Use these parameters to determine the catalytic efficiency of each enzyme. Based on your calculations arrange the enzymes in increasing order of their efficiencies.

from lowest to highest: urease, trioesphosphate i, catalase, acteylcholin, crotonase

Activation energy is the energy that a reaction must overcome to convert a substrate to the product. Enzymes lower the activation energy of a chemical reaction just as all catalysts lower activation energy. This means that less energy is required to convert reactant molecules to products. Enzymes also increase the rate of a biological reaction compared to the rate of the uncatalyzed reaction. Label the energy reaction graph for the following reaction showing the energy profile for a catalyzed and an uncatalyzed reaction. Drag the appropriate labels to their respective targets.

from top to bottom: activation energy, reaction not catalyzed by an enzyme, reaction catalyzed by an enzyme, energy released by the reaction

Consider a situation in which the enzyme is operating at optimum temperature and pHpH, and has been saturated with substrate. What is your best option for increasing the rate of the reaction?

increase the enzyme concentration

Which of the following would increase the rate of the reverse reaction?

increasing the concentration of ammonia

In the following Fischer projection, the hydroxyl group on the chiral carbon furthest from the carbonyl group points _____, meaning that this is the _____ isomer of mannose.

left / L

Label the missing components on the diagram below. Drag the appropriate labels to their respective targets.

left to right Ea, E+S binding; Ea uncatalyzed; blank; ES +-; Ea catalysis, Ea release of P

The steady-state kinetics of an enzyme are studied in the absence and presence of an inhibitor (inhibitor A). The initial rate is given as a function of substrate concentration in the following table: What kind of inhibition (competitive, uncompetitive, or mixed) is involved?

mixed

What kind of inhibition (competitive, uncompetitive, or mixed) is involved?

mixed

The graph presents three activation energy profiles for a chemical reaction (the hydrolysis of sucrose): an uncatalyzed reaction, and the same reaction catalyzed by two different enzymes. Rank these by reaction rate, as measured by the rate of product formation (from the most product formed to the least product formed). To rank items as equivalent, overlap them.

most product formed reaction catalyzed by enzyme B middle reaction catalyzed by enzyme A least product formed uncatalyzed reaction

Which myoglobin is more thermodynamically stable, the mutant or the wild-type?

mutant myoglobin

Is your list exhaustive?

no

Choose the equation of the line.

y=0.196x+0.0061

Is this a fairly efficient enzyme? (See table below)

yes

The main reasons that glycoproteins are so diverse when compared to other proteoglycans are ________.

β or α-glycosidic linkages may join various carbon atoms in the sugars