Answer key for KE0026 half time quiz 2003


WRONG1.

Amino acid substrate(s) for protein kinases:

O A.

serine

O B.

tyrosine

O C.

threonine

O D.

a and c

C E.

all of the above



WRONG2.

The dielectric constant of the interior of a protein is considerably smaller than that of water. How would you expect this to affect the strength of an electrostatic interaction between two opposite charges with the same distance between them if the charged groups were located in the interior of the protein rather than on its surface?

O A.

The strength of interaction would be stronger if the interacting charges were on thesurface of the protein.

C B.

The strength of interaction would be stronger if the interacting charges were in the interior of the protein.

O C.

The strength of interaction of the interacting charges should be independent of their location in the protein.



WRONG3.

Hemoglobin binding of oxygen is best described as a

O A.

concerted model.

O B.

Michaelis-Menten model.

O C.

sequential model.

C D.

combination of sequential and concerted models.

O E.

none of the above.



WRONG4.

What is the utility of Beer’s law and light absorbance near 280 nm in protein studies?

O A.

determining the size of proteins

O B.

determining protein purity

C C.

estimating protein concentration

O D.

estimating the amount of DNA contaminant

O E.

none of the above



WRONG5.

What determines a protein’s function?

C A.

structure

O B.

gene sequence

O C.

N-terminal amino acids

O D.

none of the above

O E.

all of the above



WRONG6.

What gives proteins such a dominant role in biochemistry?

O A.

the variation in protein sizes

O B.

the ability to act as a blueprint

O C.

their ability to self-replicate

C D.

their ability to spontaneously fold into complex three-dimensional structures

O E.

all of the above



WRONG7.

If a particular reaction has a negative DG, is it likely to occur?

O A.

Not unless energy is added to the system.

O B.

Yes, if it is coupled to another reaction.

C C.

Yes, it is spontaneous.

O D.

No, it will never occur.

O E.

Yes, if it takes place within a constrained area.



WRONG8.

The formula K' eq = 10-DG°¢/1.36 indicates the relationship between

O A.

the free energy and the equilibrium constant.

O B.

the reaction equilibrium and the isomerization rate.

C C.

the equilibrium constant and standard free energy.

O D.

all of the above.

O E.

none of the above.



WRONG9.

What is the common strategy by which catalysis occurs?

O A.

increasing the probability of product formation

O B.

shifting the reaction equilibrium

C C.

stabilization of the transition state

O D.

all of the above

O E.

none of the above



WRONG10.

What happens to nonpolar molecules in water?

O A.

They dissolve independently.

C B.

They aggregate together.

O C.

They precipitate.

O D.

All of the above.

O E.

None of the above.



WRONG11.

The use of random sequence shuffling provides a means to

C A.

estimate the statistical significance of an alignment

O B.

determine whether the gaps one introduces are in the right locations

O C.

use substitution matrices to search for distant evolutionary relationships



WRONG12.

Which of the following statements is true regarding the role an enzyme plays in catalysis?

O A.

An enzyme increases the equilibrium constant.

C B.

An enzyme decreases the activation energy by tight binding of the transition state

O C.

An enzyme increases the energy of the transition state so that it becomes more unstable and breaks down more rapidly



WRONG13.

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?

O A.

150 mM

O B.

0.15 mM

O C.

150 mM

C D.

1.5 nM

O E.

15000 pM



WRONG14.

The alteration of enzyme structure on binding of a substrate to an active site is referred to as

O A.

Enzyme denaturation

O B.

Enzyme inhibition

C C.

Induced fit



WRONG15.

Carbonic anhydrase contains water coordinated to a Zn(II) in its active site. The pH dependence of the enzyme activity has an apparent pKa near 7.0 that is attributed to the ionization of this bound water molecule. Which of the following is true?

O A.

The pKa near 7.0 indicates that there is no significant effect of the Zn(II) on the ability of the bound water molecule to gain or lose a proton

O B.

The Zn(II) activates the water, raising its pKa and making it more difficult to lose a proton

C C.

The Zn(II) activates the water, lowering its pKa and making it easier to lose a proton



WRONG16.

The allosteric properties of both ATCase and hemoglobin are reflections of

C A.

Changes in quaternary structure upon binding of small molecules

O B.

End product or feedback inhibition

O C.

Dissociation of the ATCase and hemoglobin into individual subunits



WRONG17.

Trypsin cleaves the peptide bond at

C A.

the carboxyl side of arg and lys residues.

O B.

the carboxyl side of met residues.

O C.

the amino terminus.

O D.

none of the above.

O E.

all of the above.



WRONG18.

Which of the following is true under the following conditions: The enzyme concentration is 5 nM, the substrate concentration is 5mM, and the Km is 5 mM.

C A.

The enzyme is saturated with substrate.

O B.

Most of the enzyme does not have substrate bound.

O C.

There is more enzyme than substrate.

O D.

All of the above.

O E.

None of the above.



WRONG19.

The process whereby genes or proteins are derived from a common ancestor is referred to as what kind of evolution?

O A.

Convergent

C B.

Divergent

O C.

May be either convergent or divergent - but not both at the same time



WRONG20.

Why is the peptide bond planar?

O A.

Bulky side chains prevent free rotation around the bond.

C B.

It contains partial double bond character, preventing rotation.

O C.

Hydrogen bonding between the NH and C=O groups limits movement.

O D.

None of the above.

O E.

All of the above.



WRONG21.

The Second Law of Thermodynamics states

C A.

the total entropy of a system and its surroundings always increases for a spontaneous process.

O B.

temperatures will always decrease.

O C.

the total energy of a system and its surroundings is constant.

O D.

diversity is the result of gradual evolution.

O E.

none of the above.



WRONG22.

When the Kcat /Km ratio is at its upper limit, it is referred to as

O A.

Circe limits.

O B.

Michaelis rate.

C C.

kinetic perfection.

O D.

all of the above.

O E.

none of the above.



WRONG23.

A reaction has an equilibrium constant, Keq, of 50. When performed in the presence of an appropriate enzyme, the forward rate constant is increased 20-fold. What will happen to the reverse rate constant?

O A.

It will be unaffected

C B.

It will increase 20-fold

O C.

In will decrease 20-fold



WRONG24.

2-3 Bisphosphoglycerate

O A.

binds in a pocket of the T form of hemoglobin.

O B.

preferentially binds to deoxyhemoglobin and stabilizes it.

O C.

is present in the red blood cells.

C D.

all of the above.

O E.

none of the above.



WRONG25.

How is trypsin activity turned off?

O A.

by dephosphorylation

C B.

by an inhibitor protein

O C.

by a second cleavage

O D.

all of the above

O E.

none of the above



WRONG26.

How is chymotrypsinogen activated?

O A.

cleavage between an arg and iso by chymotrypsin

O B.

cAMP binding, followed by cleavage by elastase

C C.

cleavage between an arg and iso by trypsin

O D.

all of the above

O E.

none of the above



WRONG27.

Multifunctional protein kinases

O A.

carry out phosphorylation as well as sulfation reactions.

C B.

can modify several different targets.

O C.

a and b.

O D.

all of the above.

O E.

none of the above.



WRONG28.

Common strategy(ies) for enzymatic regulation include:

O A.

multiple enzyme forms

O B.

allosteric control

O C.

reversible covalent modification

O D.

proteolytic activation

C E.

all of the above



WRONG29.

The spatial arrangement of protein subunits is called

C A.

quaternary structure.

O B.

tertiary structure.

O C.

secondary structure.

O D.

primary structure.

O E.

none of the above.



WRONG30.

In addition to the three histidyl residues involved in binding of the Zn(II), a fourth histidyl residue is also important in the function of carbonic anhydrase. The role of this fourth histidyl residue (His-64) is

O A.

To neutralize the negative charge on the hydroxide ion bound to the Zn(II)

C B.

To shuttle protons to and from the active site

O C.

To provide a fourth ligand for the Zn(II) when the hydroxide reacts with carbon dioxide to form carbonic acid



WRONG31.

How is specificity determined by chymotrypsin?

O A.

interaction of the active site amino acids with the substrate

O B.

binding of the N-terminus amino acid at the active site

O C.

covalent binding of a his residue to the substrate

O D.

conformational change upon binding of substrate

C E.

binding of the proper amino acid into a deep pocket on the enzyme



WRONG32.

An example of a conservative substitution would be

O A.

Ala to Trp.

O B.

Gly to Ser.

C C.

Asp to Glu.

O D.

all of the above.

O E.

none of the above.



WRONG33.

The most important process for direct synthesis of ATP is

O A.

transcription.

C B.

glycolysis.

O C.

replication.

O D.

all of the above.

O E.

none of the above.



WRONG34.

Which amino acids in chymotrypsin are found in the active site and take part in substrate cleavage?

C A.

his, ser, asp

O B.

his, ser

O C.

asp, lys

O D.

lys, arg

O E.

his, ser, arg



WRONG35.

The Km is

O A.

equal to the product concentration at initial reaction conditions.

C B.

equal to the substrate concentration when the reaction rate is half its maximal value.

O C.

proportional to the standard free energy.

O D.

all of the above.

O E.

none of the above.



WRONG36.

Which of the following is not true?

O A.

Enzymes force reactions to proceed in only one direction.

O B.

Enzymes alter the equilibrium of the reaction.

O C.

Enzymes alter the standard free energy of the reaction.

O D.

All of the above are true.

C E.

None of the above are true.



WRONG37.

List atoms commonly found in biological molecules that are often hydrogen bond donors.

O A.

hydrogen

O B.

oxygen

O C.

nitrogen

C D.

b and c

O E.

all of the above



WRONG38.

Reversible chemical interactions are mediated by

O A.

electrostatic interactions.

O B.

hydrogen bonds.

O C.

van der Waals interactions.

C D.

all of the above.

O E.

none of the above.



WRONG39.

The role of the Mg(II) ion in the reaction catalyzed by nucleoside monophosphate kinases is

O A.

To activate a water molecule in the active site

C B.

To form a complex with ATP which acts as the true substrate for the enzyme

O C.

To produce a conformational change in the enzyme such that ATP can bind



WRONG40.

A commonly used rule of thumb states that for proteins with more than 100 amino acids, an alignment of protein pairs with what percentage identity is not likely to the result of chance but probably indicates a homologous relationship?

O A.

> 5%

O B.

> 15%

C C.

> 25%



WRONG41.

What is the Bohr effect?

O A.

the ability of hemoglobin to retain oxygen when in competition with myoglobin

C B.

the regulation of hemoglobin binding by hydrogen ions and carbon dioxide

O C.

the alteration of hemoglobin conformation during low oxygen stress

O D.

all of the above

O E.

none of the above



WRONG42.

What is the advantage of adding SDS to gel electrophoresis?

O A.

SDS colors the proteins for visualization.

O B.

SDS reduces disulfide bonds.

C C.

SDS allows proteins to be separated on the basis of approximate mass.

O D.

None of the above.

O E.

All of the above.



WRONG43.

When enzymes are purified, the assay is often based on

O A.

light absorbance.

C B.

catalytic activity.

O C.

pH.

O D.

temperature changes.

O E.

mRNA levels.



WRONG44.

What must be true of the free energy change, DG, for a reaction to be spontaneous?

C A.

It must be negative

O B.

It must be greater than the change in entropy.

O C.

It is dominated by the enthalpy change, DH.



WRONG45.

How many N-terminii are there in an oligomeric protein with the subunit composition ab2g2?

O A.

2

O B.

3

O C.

4

C D.

5



WRONG46.

What charged group(s) are present in glycine at a pH of 7?

O A.

NH3+

O B.

COO-

O C.

NH2+

C D.

a and b

O E.

a, b, and c



WRONG47.

What is true about the side chains of residues in an a-helix?

O A.

They extend above or below the pleats

C B.

They extend redially outward from the helix axis

O C.

Hydrophobic side chains point toward the center of the helix

O D.

They hydrogen bond extensively with each other



WRONG48.

Membrane-forming molecules are said to be amphipathic. This means that

O A.

they are present in both left-handed and right-handed forms

C B.

they have both hydrophobic and hydrophilic components in the same molecule

O C.

they can adapt to different environments by interacting differently with one another in membranes.



WRONG49.

Which of the following is NOT true of peptide bonds?

O A.

They tend to be planar.

O B.

They are generally in the trans and rarely in the cis configuration

C C.

They tend to have the amide nitrogen protonated to give a positive charge



WRONG50.

Water-soluble proteins such as myoglobin tend to

C A.

fold such that hydrophobic amino acid R-groups are on the interior of the protein and hydrophilic groups are on the outside

O B.

fold such that hydrophilic amino acid R-groups are on the interior of the protein and hydrophobic groups are on the outside

O C.

fold such that all peptide bonds form hydrogen bonds



WRONG51.

Name three amino acids that are positively charged at a neutral pH.

C A.

lys, arg, and his

O B.

his, arg, and cys

O C.

cys, arg, and met

O D.

lys, arg, and pro

O E.

arg, glu, and his



WRONG52.

The definition of a homolog is

O A.

molecules related by sequence similarity.

C B.

two molecules derived from a common ancestral protein.

O C.

molecules with similar domains.

O D.

all of the above.

O E.

none of the above.



WRONG53.

Examples of cofactors include

O A.

Zn+2, Mg+2, and Ni+2.

O B.

biotin and thiamine pyrophosphate.

O C.

pyridoxal phosphate and coenzyme A.

O D.

b and c.

C E.

a, b, and c.



WRONG54.

SDS polyacrylamide electrophoresis could be used to do which of the following?

O A.

Determine the molecular weight of an oligomeric (multisubunit) protein

C B.

Determine the molecular weights of subunits of an oligomeric protein

O C.

Purify a monomeric protein serving as an enzyme in its active form



WRONG55.

Protein kinases generally regulate the activity of target proteins by transferring a phosphate group from ATP to what kind of functional group on the target protein?

O A.

carboxyl groups

O B.

hydrophobic groups

C C.

hydroxyl groups



WRONG56.

Homologous proteins (homologs)

O A.

are present in all organisms

O B.

have similar or identical functions

C C.

are derived from a common ancestor




WRONG57.

In sequencing a protein, it is necessary to break disulphide bonds within a polypeptide chain. A reagent that will accomplish this is

O A.

Guanidine hydrochloride

O B.

Iodoacetate

C C.

Mercaptoenthanol



WRONG58.

The three dimensional structure of a protein is dictated by

O A.

other proteins which assist it in folding correctly

C B.

its amino acid sequence

O C.

interaction of the newly synthesized protein with the portion of DNA which encoded it



WRONG59.

In the following peptide, which amino acid is the N-terminus?
Phe-Ala-Gly-Arg

O A.

Ala

C B.

Phe

O C.

Phe and Arg

O D.

Arg

O E.

none of the above



WRONG60.

The Second Law of Thermodynamics states that

O A.

the entropy of a system increases if a process is spontaneous.

O B.

the entropy of a system's surroundings increases if a process is spontaneous

C C.

the total entropy of a system and its surroundings increases if a process is spontaneous



WRONG61.

In consideration of a monomeric protein, which level of structure is most highly conserved?

O A.

Primary structure

O B.

Secondary structure

C C.

Tertiary structure



WRONG62.

The process of evolution has three requirements. These are

C A.

Reproduction, variation, and selective pressure

O B.

DNA, RNA, and transcription

O C.

Replication, transcription, and translation



WRONG63.

The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)?

O A.

the peptide bond only

O B.

N-Ca only

O C.

N-Ca, Ca-C, and C-N bonds

C D.

N-Ca and Ca-C bonds only



WRONG64.

The combination of two cysteine residues into disulfide is what kind of reaction?

O A.

a reduction

O B.

an addition

O C.

an alkylation

C D.

an oxidation

O E.

a solvation



WRONG65.

When is it proper to write the expression for the Gibb's free energy as
D
G = DGo + RT ln Keq ?

O A.

Always

C B.

When DG = 0

O C.

When Keq = 1



WRONG66.

Protein sequence comparisons can provide estimates of

O A.

protein function.

O B.

protein shape.

O C.

pathways of evolutionary descent.

O D.

b and c.

C E.

all of the above.



WRONG67.

The relaxed form of an allosteric enzyme has _________ affinity for the substrates.

C A.

higher

O B.

equal

O C.

lower

O D.

no

O E.

none of the above



WRONG68.

What do a-helices and b-sheets have in common?

C A.

Both are stabilized by hydrogen bonding involving the same types of groups

O B.

The same amino acids stabilize both forms of secondary structure.

O C.

The length of a 10-amino acid a-helix and b-sheet strand will be the same



WRONG69.

Vmax, the maximum velocity, of an enzyme catalyzed reaction is

C A.

the rate observed when all enzyme active sites are saturated with substrate

O B.

independent of the amount of enzyme present

O C.

the rate observed at the highest substrate concentration which can be experimentally obtained.



WRONG70.

To obtain kcat, the turnover number of an enzyme, one must

O A.

divide Vmax by 2

O B.

divide v by Vmax

C C.

divide Vmax by the total enzyme concentration



WRONG71.

The Km for a substrate is equal to the Kd (dissociation constant) for the enzyme-substrate complex only when

O A.

k-1 <<< k2

C B.

k-1 >>> k2

O C.

v = Vmax/2



WRONG72.

You have isolated a new protease that cleaves peptide bonds following Asp and Glu. Based on its inactivation by DIFP, you suspect that it may utilize a mechanism similar to chymotrypsin. The difference in specificity might be explained by

C A.

The presence of a positively charged residue in the side-chain binding pocket

O B.

The presence of a negatively charged residue in the side-chain binding pocket

O C.

Replacement of Serine-195 with a positively charged residue



WRONG73.

Which of the following is NOT true of a competitive inhibitor?

C A.

It irreversibly inhibits the enzyme by chemically modifying a group at the active site

O B.

It often resembles the substrate for the enzyme it inhibits

O C.

Its effects can be overcome by increasing the concentration of substrate.



WRONG74.

a-helices and b-sheets are often found to be amphipathic. This means that

O A.

They have positive charges on one side and negative charges on the other

O B.

They have large R-groups on one side and small R-groups on the other as small groups are easier to pack in the interior of the protein

C C.

They have one side or face that is predominately polar with the other side being predominately hydrophobic



WRONG75.

In aligning protein sequences, which of the following is NOT a major concern?

O A.

Maximizing the number of identical and conservative positions

C B.

Introduction of sufficient gaps such that the N- and C-termini of the proteins can be aligned

O C.

Minimizing the number of gaps which must be introduced



WRONG76.

Rapidly metabolizing tissues generate large amounts of protons and carbon dioxide. As a result of this

C A.

the oxygen binding curve of hemoglobin (Y vs. pO2) becomes more S-shaped

O B.

the oxygen binding curve of hemoglobin (Y vs. pO2) becomes more like that of myoglobin

O C.

the oxygen binding curve of hemoglobin (Y vs. pO2) is not affected but the amount of hemoglobin is reduced because high carbon dioxide concentrations lead to hemoglobin digestion



WRONG77.

Enzymes that are activated by specific proteolytic cleavage are called

O A.

isozymes

C B.

zymogens

O C.

allosteric



WRONG78.

Molecule(s) used for storing energy are

C A.

ATP.

O B.

vitamins.

O C.

bases.

O D.

all of the above.

O E.

none of the above.



WRONG79.

Oxygen and 2,3-bisphosphoglycerate (2,3-BPG) cannot bind to hemoglobin at the same time because

O A.

2,3-BPG is a competitive inhibitor of oxygen binding to the hemoglobin molecule

C B.

the structure of the enzyme is changed when oxygen binds such that 2,3-BPG can no longer bind

O C.

the binding of 2,3-BPG blocks a channel needed by oxygen to reach the heme



WRONG80.

Of the 20 amino acids from which proteins are made, which is most likely to be present with its R-group in a mixture of ionization states near physiological pH?

O A.

Tyr

C B.

His

O C.

Glu