M1: proteins practice quiz

Chapter 3: https://quizlet.com/91815952/chapter-3-test-bank-flash-cards/

Which statement is correct with respect to the amino acid composition of proteins?

Proteins with different functions usually differ significantly in their amino acid composition

For amino acids with neutral R groups, at any pH below the pH of the amino acid, the population of amino acids in solution will have ____.

an overall net positive charge

To determine the isoelectric point of a protein, first establish that a gel:

exhibits a stable pH gradient when ampholytes become distributed in an electric field.

Select all that apply!

Which statement is NOT correct concerning cooperative binding of a ligand to a protein?

• It is usually a form of allosteric interaction

• It is usually associated with proteins with multiple subunits

• It results in a sigmoidal binding curve

• It results in a nonlinear Hill plot

Which statement comparing hemoglobin and myoglobin is NOT correct?

Hemoglobin has a stronger binding affinity for O₂ than myoglobin does

Which antibody is secreted as a cross-linked pentamer?

IgM

Select all that apply!

Permanent actin-myosin interaction defines the state of rigor mortis that we all want to avoid as long as possible. Actin-myosin interaction during our life ___.

• is interrupted when ATP binds to myosin

• is an example of protein-ligand interaction

• leaves the partipants unchanged

Which statement regarding enzyme activity is correct?

Enzymes bind the transition state better than the reaction products and reduce the activation energy required for the reaction to take place

One of the enzymes involved in glycolysis, aldolase, requires Zn²⁺ for catalysis. When the enzyme links zinc, it is referred to as the:

apoezyme

____ is an irreversible enzyme regulatory mechanism?

Activation of a zymogen

Both water and glycose include an -OH that can serve as a substrate for a reaction with the terminal phosphate of ATP catalyzed by hexokinase. Glucose, however, is about a million times more reactive as a substrate than water. The BEST explanation is that:

glucose induces a conformational change in hexokinase that brings active-site amino acids into position for catalysis.

After you mix a substrate and enzyme together, there is an initial transient period, the pre-steady state. What happens during the pre-steady state?

ES increases until it reaches a constant level

These data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics.

Collected data:

V0	Substrate added			​
(μmol/min)	(mmol/L)			​
_____________________
217	0.8		​
325	2		​
433	4		​
488	6		​
647	1,000		​

​

The K_m for this enzyme is approximately:

2 mM

V_max for an enzyme-catalyzed reaction:

is twice the initial rate observed (V_o) when [S] = K_m

The amino acid proline is unique because the R group:

is cyclical

Titration of valine by a strong base, for example NaOh, reveals two pK’s (see Table 3-1). Which is the titration reaction occuRring at pK₂ (pK₂ = 9.62)?

— NH₃⁺ + OH ^- → - NH₂ + H₂O

Which component is absolutely necessary for the purification of a protein?

a means of detecting a protein

Examine the binding curves for two proteins (A and B) that bind the same ligand. Which statement applies?

The dissociation constant for A is less than that of B

If a developing fetus made beta hemoglobin subunits instead of gamma hemoglobin subunits, what would be MOST likely to occur?

The fetus would not be able to extract O₂ from its mother’s blood as effectively

Nerve impulses control muscle contractions by releasing which ion?

Ca²⁺

Enzymes are potent catalysts because they:

Lower the activation energy for the reactions they catalyze

A protein ______ catalyzes the attachment of phosphoryl groups to specific amino acid residues including ______.

kinase; Thr and Ser

Select all that apply

Enzymes contribute to the reaction rate enhancement via entropy reduction, which may include ____.

• Constriction of the substrate in the proper orientation

• Aligning the substrates precisely on the enzyme with the help of strategically located groups

• Restriction of the relative motion of two substrates

Which statement is false about the saturation effect?

It is responsible for the linear increase of V₀ with increase in [S].

We use an enzyme at a 20nM total concentration, and its substrate at 40uM and measure V_o = 9.6 uM/s. Calculate K_m, if the catalytic rate constant (k_cat) of this enzyme is 600s^-1.

10

For enzymes in which the slowest (rate-limiting) step is the reaction

K_m becomes equivalent to:

the dissociation constant, K_d, for the ES complex

Which type of structure describes the overall three-dimensional folding of a polypeptide?

tertiary structure

Which amino acid has three pK_a values?

Cys

In an SDS-PAGE experiment, two markers of molecular weight, 11,000 g/mol and 3,000 g/mol, traveled 5 cm and 9 cm, respectively. Approximately, how far will a fragment of size 7,945 g/mol travel?

6 cm

Which statement about protein-ligand binding is correct?

The larger the K_a, the smaller the K_d (dissociation constant)

In peripheral tissues:

O₂ is released

You are working as a scientist in an antibody-design group at a biologies company. Based on your knowledge of antibodies, which region(s) on which antibody type should you target for your design efforts to develop new antigen-binding capabilities in soluble antibodies?

IgG antibodies, variable light and variable heavy chain regions

Tropomyosin and troponin prevent muscle contractions in the absence of Ca²⁺ because they:

block the myosin head binding sites on actin filaments

Which statement is false about enzyme catalysts?

They increase the equilibrium constant for a reaction, thus favoring product formation

Enzymes:

are proteins (with few exceptions).

Competitive inhibitors:

occupy the active site to exclude the substrate

An enzyme-catalyzed reaction was carried out with the substrate concentration initially a thousand times greater than the Km for that substrate. After 9 minutes, 1% of the substrate had been converted to product, and the amount of product formed in the reaction mixture was 12 μmol. If, in a separate experiment, one-third as much enzyme and twice as much substrate had been combined, how long would it take for the same amount (12 μmol) of product to be formed?

27 mins

The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the:

turnover number.

The chirality of an amino acid results from the fact that its a carbon _____

is bonded to four different chemical groups

Identify the pair of peptides that are NOT distinguished by tandem mass spectrometry.

VTSPLYANEGK and VTSPIYANEGK

Select all that apply!

When investigating ligand binding, the dissociation constant (K_d) ____.

• Equals the free ligand concentration, when half the ligand sites are occupied

• Corresponds to the reciprocal of the association constant

Which molecule is homotropic modulator of oxygen binding to hemoglobin?

oxygen

Macrophages bind to the ___ region of IgG antibodies, thereby triggering phagocytosis of an antibody-antigen complexes.

Fc

Thick filaments are made of ____.

myosin

The concept of induced fir refers to the fact that:

Substrate binding may induce a conformational change in the enzyme, which than brings catalytic groups into proper orientation

Which statement about allosteric control of enzymatic activity is false?

Heterotropic allosteric effectors compete with substrate for binding sites

Chymotryspin:

uses the oxygen of a serine side chain as a nucleophile

Which amino acid is NOT capable of using its side chain (R group) to participate in general acid-base catalysis?

Val

Phenyl-methane-sulfonyl-fluoride (PMSF) inactivates serine proteases by binding covalently to the catalytic serine residue at the active site; this enzyme-inhibitor bond is NOT cleaved by the enzyme. This is an example of what kind of inhibition?

irreversible

We use an enzyme at a 10 nM total concentration and measure V_o = 3 uM/s. We also determined that K_m = 10 uM and the catalytic rate constant (k_cat) of this enzyme is 600 s^-1. What was the [S] used in this experiment?

10

The Lineweaver-Burk plot is used to:

solve, graphically, for the rate of an enzymatic reaction at infinite substrate concentration

What are the name and abbreviations of the amino acid shown?

Asparagine; asn; N

Glutamic acid is an amino acid with pKa values of 2.19, 4.5, and 9.67, a-ketoglutarate is a bivalent organic acid. What is the approximate charge

1/2

The interactions of ligands with proteins:

are usually transient

Sickle cell anemia is caused by a single mutation in the hemoglobin protein from a Glu to a Val, which results in which alteration in the hemoglobin subunits?

fewer negative charges and formation of a hydrophobic contact point

Which statement is false?

T lymphocytes produce immunoglobulins

Which protein undergoes a conformational change upon interacting with Ca²⁺, leading to simulation of muscle contraction?

troponin

The role of an enzyme in an enzyme-catalyzed reaction is to:

Increase the rate at which substrate is converted into product

The role of the metal ion (Mg²⁺) in catalysis by enolase is to:

stabilize an intermediate during general base catalysis

Phosphorylation of enzyme:

Generally occurs on Ser, Thr, and/or Tyr side chains

The total enzyme concentration is [E_t] = ____ nM, if [S] = 6 mM, V_o = 480 nM/min, K_m = 4uM, and the catalytic rate constant (k_cat) of the enzyme is 20. min^-1

24

For the simplified representation of an enzyme-catalyzed reaction shown, the statement “ES is in steady-state” means that:

k₁[E][S] = k_-1[ES] + k₂ [ES]

Which is the dominant form of glycine at its isoelectric point?

NH₃⁺—CH₂—COO^-

The term “specific activity” differs from the term “activity” in that specific activity ___.

is the activity (enzyme units) in a milligram of protein.

What description is associated with immunoglobulin G?

More abundant immunoglobulin

During muscle contraction, hydrolysis of ATP results in a change in the:

conformation of myosin.

Which statement about enzyme-catalyzed reactions is false?

The activation energy for the catalyzed reactions is the same as for the uncatalyzed reaction, but the equillbrium constant is more favorable in th enzyme-catalyzed reaction

What is the advantage of regulatory enzymes using several regulatory mechanisms?

Cells can catalyze only the reactions that are needed at a given moment.

An enzyme that can convert glucose into fructose is a member of which class of enzymes?

isomerases

In what ways does an uncompetitive inhibitor bind to an enzyme?

It reversibly binds to the enzyme-substrate but does bind to the free enzyme

Why can only some amino acids be used to measure protein concentration based on absorption of UV light?

Only some amino acids are aromatic.

Regarding the models of cooperativity:

T state is low affinity and R state is high affinity

Select all that apply!

X-ray analysis has revealed 2 conformations of hemoglobin: the R state and the T state

• Oxygen stabilizes R state

• when oxygen binds the T state hemoglobin, then the T state hemoglobin will transition into R state

• The lack of oxygen result in the T state; thus, this is the dominant conformation in deoxyhemoglobin

Polyclonal antibodies:

are used as analytic reagents in Western blot assays

During muscle contraction, hydrolysis of ATP results in a change in the:

conformation of myosin

Enzymes are potent catalysts because they:

lower the activation energy for the reaction they catalyze

Chymotrypsin:

uses the oxygen of a serine side chain as a nucleophile

An enzyme accepts H⁺ from hydronium and transfers it to an amine group of the substrate. The result is an increase in the rate of release of the product. This is an example of:

general acid catalysts

What is the definition of K_m, the Michaelis constant?

the concentration of substrate at which the enzyme is operating at half its maximal velocity

All of the amino acids that are found in proteins, except for proline, contain a(n) _____ group.

amino

A major advance in the application of mass spectrometry to macromolecules came with the development of techniques to overcome which problem?

Mass spectrometric analysis involved molecules in the gas phase

Select all that applies!

The binding site of a protein is complementary to a specific ligand due to which characteristic of the binding site?

• its charge

• its size

• its shape

• its hydrophobicity

The Fab regions of an antibody are made of which protein chain?

both a light chain and a heavy chain containing variable and constant regions

The intestinal enzyme is produce initially as a ____, which requires ____ for activation.

zymogen; irreversible proteolytic cleavage

If a first-order reaction for the unimolar reaction S → P has a rate constant k = 0.05s^-1, how is this interpreted qualitatively?

5% of the available S will be converted to P in 1 second

In a mixture of five proteins listed, which should elute second in size-exclusion (gel-filtration) chromatography?

immunoglobulin G, M_r = 145,000

Which molecule binds MOST strongly to the heme iron?

CO

Which statement is false regarding the enolase reaction?

Two Mg²⁺ ions act as coenzymes in this reaction.

he benefit of measuring the initial rate of reaction V_o is that at the beginning of a reaction ______ as long as the substrate concentration, [S], is much higher than the enzyme concentration, [E].

changes in [S] are negligible, so [S] can be treated as a constant

For a specific enzyme/substrate system, which condition will ALWAYS result in an increase in V0 (assuming nothing else changes)?

A decrease in K_m and an increase in V_max

The following data set indicates that K_m = ____ mM and V_max = ___ uM/min.

Data set

S (mM)	Vo (μM/min)
0.0025	28
0.0040	40.
0.010	70.
0.020	95
0.040	112
0.10	128
2.0	139
10	140

0.010

70

All of the 20 common amino acids contain an R group that is attached to the:

a carbon

Which amino acid would MOST likely be found in the interior of a globular protein?

Ala

When the partial pressure of oxygen is equal to the P₅₀ of myoglobin, what is the value of Y?

0.50

Myoglobin and the subunits of hemoglobin have:

very similar tertiary structures, but different primary structures.

Which description is associated with immunoglobulin G?

most abundant immunoglobulin

In this diagram of the first step in the reaction catalyzed by the protease chymotrypsin, the process of general base catalysis is illustrated by the number ____, and the process of covalent catalysis is illustrated by the number ____.

1;2

What is the free-energy starting point for a reverse reaction designated as?

ground states

Which statement is false for enzymes where dissociation of the product (k₃) is rare-limiting?

Following the pre-steady state phase, the observed rate of product formation increases to the steady-state rate.

Which statement about a plot of V0 versus [S] for an enzyme that follows Michaelis-Menten kinetics is FALSE?

At very high [S]. the velocity curve becomes a horizontal line that intersectes the y axis at K_m