Chapter 6 + Quiz Questions Flashcards

1
Q

Life depends on the ability to ..?

A

Efficiently and selectively catalyze chemical reactions

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2
Q

True or False: most biomolecules are very stable with rates of uncatalyzed transformations that are too slow to permit life?

A

True

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3
Q

Enzymes provide a mechanism for 1., 2., and 3. for reactions

A
  1. Acceleration
  2. Regulation
  3. Coordination
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4
Q

The most striking feature about enzymes are their ____ ____ and ______

A

Catalytic power, specificity

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5
Q

True or False: enzymes serve only as catalysts?

A

False, they can also be information sensors

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6
Q

Define Vitalism

A

The belief that living things are fundamentally different from non-living things; that they contain some non-physical element and are governed by different principles than inanimate objects

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7
Q

Which scientist believed in vitalism?

A

Louis Pasteur

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8
Q

What as Eduard Buchner’s contribution to Biochemistry?

A

He demstrated that dead yeast still converts sugars into alcohol, indicating the reactions of life were separate from life

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9
Q

What are co-factors?

A

Inorganic ions such as Mg2+ and Fe2+

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10
Q

What are co-enzymes?

A

Complex organic molecules/vitamins

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11
Q

True or False: some enzymes require co-factors or co-enzymes for activity?

A

True

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12
Q

What is a prosthetic group?

A

A co-enzymes or co-factor that is tightly associated with the enzyme, the difference is the degree of association

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13
Q

Different enzymes that use the same co-enzyme usually perform ___ types of reactions

A

similar

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14
Q

Catalysts ___ the amount of energy required for a reaction to proceed

A

lower

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15
Q

Do catalysts speed up or slow down the attainment of equilibrium? Do they change equilibrium?

A

Speed up, and they do not influence the difference in
free energy between S and P and therefore do not influence the equilibrium

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16
Q

Catalysts are ____ by the reaction; ____ to participate in another reaction

A

unchanged, recycled

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17
Q

Which is faster: enzymes or chemical catalysts?

A

Enzymes are often much faster, some approaching catalytic perfection

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18
Q

Which of the two require extremes of temperature, pressure and pH: enzymes or chemical catalysts?

A

Chemical catalysts, enzymes function under physiological conditions

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19
Q

Which has a higher degree of specificity: enzymes or chemical catalysts?

A

Enzymes, this includes specificity for what they act upon and what they produce, and steroespecificity

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20
Q

Which of the two are responsive to the dynamic needs of the cell and organism: enzymes or chemical catalysts?

A

Enzymes

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21
Q

True or False: enzyme rates of catalysis can approach the physical limit of rates of diffusion of molecules in solution?

A

True

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22
Q

Some enzymes have ___-_____ steps that are roughly as fast as the binding of substrates to the enzymes

A

rate determining

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23
Q

Some enzymes are able to catalyze reactions ______ than predicted by diffusion-control limits

A

faster

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24
Q

What is the meaning of this relationship? E + S <-> ES <-> E + P

A

Enzymes catalyze the interconversion of substrate and product

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25
Q

What is the Active Site?

A

The portion of enzyme responsible for binding the substrate to formation of an enzyme-substrate (ES) complex

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26
Q

The active site is a 3D cleft formed from _______ parts of the _______ chain

A

different, polypeptide

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27
Q

True or False: the active site represents a large part of the enzyme?

A

False, it represents just a small part

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28
Q

Active sites are unique _______

A

microenvironments

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29
Q

Substrates are bound to enzymes by multiple ____ interactions

A

weak

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30
Q

The specificity of substrate binding depends on the ..?

A

Precisely defined arrangements of atoms in the active site. Enzymes and their active sites can be quite flexible

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31
Q

Substrate binding can cause _____ ___ or _______ ______

A

Induced fit, conformation selection

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32
Q

What is the Lock and Key model?

A

The active site is like a “lock” to which substrate fits like a “key.” The enzyme’s active site and substrate should fit like lock & key to initiate a reaction

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33
Q

What is the Hand-in-a-Glove (induced fit) model?

A

Binding of substrate induces a conformational change in the active site and both adjust their shapes to provide optimal fit

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34
Q

A reaction can only be spontaneous if ΔG ? 0

A

ΔG < 0

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35
Q

Define spontaneous

A

The reaction will proceed without the input of energy and the reaction releases energy (exergonic)

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36
Q

Define Exergonic reaction

A

The reaction releases energy

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37
Q

A reaction is non-spontaneous if ΔG ? 0

A

ΔG > 0

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38
Q

Define Endergonic reaction

A

An input of free energy is required to drive the reaction

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39
Q

In a system at equilibrium, there is no net change in the concentration of the products and reactants, and the ΔG ? 0

A

ΔG = 0

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40
Q

The ΔG of a reaction depends only on ..?

A

The free energy of the product minus the free energy of the reactants

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41
Q

True or False: the ΔG of a reaction is independent of the steps of the transformation?

A

True

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42
Q

True or False: the ΔG provides all the information about the rate of a reaction

A

False: the ΔG provides no information

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43
Q

What determines the rate at which equilibrium is reached?

A

Activation energy (ΔG‡) between S and P

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44
Q

Enzymes provide an alternate, lower-energy pathway between the substrate and product, _____ ΔG‡

A

lowering

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45
Q

The relationship between the rate of a reaction and the activation energy is _____ and _______

A

inverse, exponential

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46
Q

What determines the equilibrium of the reaction

A

Difference in free energy between S and P

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47
Q

Enzymes provide a ____-energy pathway between the substrate and product, ____ the activation energy of the transition state and ____ the rate of reaction

A

lower, decreasing, increasing

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48
Q

Catalytic capabilities of enzymes result from both _____ and ____ effects

A

chemical, binding

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49
Q

What is classified under Binding Effects?

A

Substrate Binding and Transition-state Stabilization

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50
Q

What is classified under Chemical Effects?

A

Acid/Base Catalysis and Covalent Catalysis

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51
Q

Binding of substrate in the active site provides ____ and ____ ____

A

specificity, catalytic power

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52
Q

In this relationship: E + S <-> ES <-> ETS <-> E + P, what is considered Substrate Binding and what is considered Transition State Stabilization?

A

E + S <-> ES = Substrate Binding
ES <-> ETS = Transition State Stabilization

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53
Q

What are the 5 ways Substrate Binding promotes reactions?

A
  1. Reducing entropy
  2. Alignment of reactive functional groups of the enzyme with the substrate
  3. Desolvation of the substrate to expose reactive groups
  4. Distortion of substrates
  5. Induced fit of the enzyme in response to substrate binding
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54
Q

An increased interaction of the enzyme and substrate occurs in the ____-____

A

transition-state

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55
Q

What is the essence of catalysis?

A

The stabilization of the transition state

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56
Q

The enzyme _____ the substrate, forcing it toward the transition state.

A

distorts

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57
Q

The active site is complementary to the transition-state in _____ and ______ _______

A

shape, chemical character

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58
Q

Active site must be _____ enough to substrate to ensure specificity, ____ enough to promote change

A

similar, different

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59
Q

What are Transition-state analogs (TSAs)?

A

Stable compounds that resemble unstable transition states

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60
Q

True or False: transition-state analogs have potential therapeutic applications as competitive inhibitors

A

True

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61
Q

What are Competitive Inhibitors?

A

Molecules that bind to the active site of an enzyme,
they tend to resemble the substrate molecule

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62
Q

What is the problem with competitive inhibitors and their resemblance to the substrate molecule?

A

TSAs can bind the active site of a target enzyme active site with high affinity, preventing substrate binding

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63
Q

After substrate binding, the enzyme can act upon the substrate to promote ______ of the product

A

formation

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64
Q

The active site often contains ______ ______ side chains

A

chemically reactive

65
Q

The active site often contains chemically reactive side chains.This includes polar, ionizable side chains (triprotics) such as #1, #2, #3, #4, #5, #6, #7, #8

A

Asp, Glu, His, Cys, Tyr, Lys, Arg, and Ser

66
Q

In which type of catalysis does the reaction acceleration become achieved by catalytic transfer of a proton

A

Acid-Base Catalysis

67
Q

In Acid-Base Catalysis, the side chains of some amino acids can acts as either ____(proton acceptors) or ____ (proton donors)

A

bases, acids

68
Q

In Acid-Base Catalysis, which amino acid, with a pKa near physiological pH, is often involved in acid/base catalysis?

A

Histidine

69
Q

In Acid-Base Catalysis, the pKa of a functional group is influenced by the ______ ______

A

chemical microenvironment

70
Q

In Acid-Base Catalysis, functional groups of amino acids can have ______ pKas within the active site which make them more suitable for acid/base catalysis

A

different

71
Q

In Covalent Catalysis, as a part of the reaction mechanism the substrate is covalently bound to the enzyme to form a _____ _____

A

reactive intermediate

72
Q

Covalent catalysis often involves two steps..?

A
  1. Forms a covalent linkage to the enzyme
  2. Regenerates the free enzyme
73
Q

What is the reaction of Sucrose Phosphorylase? And what are the two steps for covalent catalysis?

A

Sucrose + Pi <-> Fructose + Glucose-1-P
1. Glucosyl residue is transferred to enzyme
2. Glucose is transferred to phosphate

74
Q

Define Kinetics

A

The study of the velocity of reactions

75
Q

The velocity of a reaction is quantified as..? And what are the units?

A

V = Δ[product] ÷ Δtime. Usually mmoles/sec or moles/min

76
Q

As enzymes are proteins, any variable that influences protein structure may ..?

A

influence enzyme activity

77
Q

True or False: the activity of enzymes is temperature and pH sensitive?

A

True

78
Q

True or False: Enzymes can have different optimum temperatures and pHs?

A

True

79
Q

Enzyme velocities are also influenced by ____ and ____ concentration

A

enzyme, substrate

80
Q

As velocity is defined as the change in product concentration over time, it is necessary to measure ____ ____ before equilibrium is reached

A

product formation

81
Q

What is Initial velocity (Vo) in terms of kinetics?

A

The velocity at the beginning of an enzyme catalyzed
reaction, prior to product accumulation

82
Q

In kinetics, K1 and k-1 represent..? And K2 is ..?

A

Rapid, non-covalent interactions between enzyme and
substrate. The rate constant of formation of product from ES

83
Q

In kinetics, what is the formula for Vo that includes the concentration of ES and K2?

A

Vo = [ES]k2

84
Q

What is the steady-state assumption?

A

The rate of formation of the ES complex was equal to the rate of its breakdown

85
Q

Mathematically the steady state assumption states that:
[E][S]k1 = [ES]k-1 + [ES]k2. What is the rate of formation/breakdown of the ES complex?

A

Rate of formation of the ES complex is [E][S]k1
Rate of breakdown of the ES complex is [ES]k-1 + [ES]k2

86
Q

The Michaelis-Menten equation and plot describe the relationship between..?

A

Substrate concentration and initial velocity

87
Q

What is the equation used from the Michaelis-Menten plot, and what do the values symbolize?

A

Vo = (Vmax[S]) ÷ (Km + [S]). Km is the concentration of substrate required for the enzyme to function at
half maximal velocity. Vmax is the maximum velocity of the enzyme

88
Q

For many enzymes, Km provides an accurate approximation of the __ ____ substrate concentration

A

in vivo

89
Q

When [S] ? Km, enzymes are highly sensitive to changes in substrate concentration but have very little activity

A

[S] < Km

90
Q

When [S] ? Km, enzymes have high activity but are insensitive to changes in substrate concentration

A

[S] > Km

91
Q

When [S] ? Km, enzyme has significant activity and is responsive to changes in substrate concentration

A

[S] = Km

92
Q

What is the velocity of a reaction when substrate concentration is equal to Km?

A

Vo = 1/2 Vmax

93
Q

What is reaction velocity when substrate concentration is double Km?

A

Vo = 2/3 Vmax

94
Q

What is the reaction velocity when substrate concentration is a third of Km?

A

Vo = 1/4 Vmax

95
Q

What are Lineweaver-Burke plots and what are they used for (x4 points)?

A
  1. Describe the relationship between [S] and Vo
  2. Are a double-reciprocal plot of 1/Vo vs 1/[S]
  3. A more precise method of analysis of kinetic data
  4. Used to determine Vmax and Km
96
Q

What is the formula used from Lineweaver-Burke plots?

A

1/Vo = (Km ÷ (Vmax[S])) + 1/Vmax

97
Q

What is the Enzyme Turnover Number?

A
  1. Kcat
  2. Equals the # of molecules of substrate converted to product ÷ time under saturating conditions
  3. Calculated by Vmax / [Et]
98
Q

Reversible inhibitors bind to the enzyme by ___-_______ interactions

A

non-covalent

99
Q

What is a competitive inhibitors ..?

A

Resemble the substrate and compete with the substrate for binding the active site

100
Q

Competitive inhibitors bind only the ____ ______

A

free enzyme

101
Q

The effect of competitive inhibitors can be overcome by..?

A

An excess of substrate (washing out)

102
Q

Uncompetitive inhibitors bind only to the __ ______

A

ES complex

103
Q

Vmax is decreased by conversion of __ __ ___ which cannot form product in uncompetitive inhibitors

A

ES to ESI

104
Q

Uncompetitive inhibitors reduce __

A

[ES]

105
Q

In uncompetitive inhibitors, what causes a decrease in Km?

A

As E binds S to replenish ES this apparent increase in affinity of the E for S

106
Q

Non-competitive inhibitors binds to _ ___ __

A

E and ES

107
Q

Vmax is decreased with no change in __

A

Km

108
Q

Why is there no change in Km in non-competitive inhibitors?

A

Non-competitive inhibitors don’t influence S
binding

109
Q

Non-competitive inhibitors essentially reduces the number of active _____ _____

A

enzyme molecules

110
Q

Serine proteases serve as..?

A

Digestive enzymes that cleave peptide bonds in protein substrates

111
Q

What are some examples are serine proteases?

A

Trypsin, chymotrypsin, and elastase

112
Q

Members of this family share similar sequences and active site residues. What family is it?

A

Serine proteases

113
Q

Serine proteases are ______ and _____ in the pancreas as inactive _____ to prevent damage to _____ ______

A

synthesized, stored, zymogens, cellular proteins

114
Q

Zymogens are activated at the appropriate time by ______ ______

A

selective proteolysis

115
Q

Catalytic mechanism contains elements of both _____ and ____-____ catalysis

A

covalent, acid-base

116
Q

Serine proteases have unique _______ that reflect unique ______ _______ ________

A

specificities, substrate binding pockets

117
Q

Serine Proteases have a conserved catalytic mechanism based on a catalytic triad of residues, what is the triad?

A

Asp, His, Ser

118
Q

Each residue plays a specific role in the catalytic mechanism, what is the role of His?

A

Acts to accept and donate a proton at each of the two stages of the reaction mechanism (acid base catalysis)

119
Q

Each residue plays a specific role in the catalytic mechanism, what is the role of Asp?

A

Stabilizes the positively-charged His to facilitate serine ionization

120
Q

Each residue plays a specific role in the catalytic mechanism, what is the role of Ser?

A

Attacks the carbonyl group of the peptide bond to be cleaved (covalent catalysis)

121
Q

How many phases are in the chymotrypsin mechanism?

A

2 Phases

122
Q

Describe the three steps in Phase 1 of the Chymotrypsin mechanism

A

Step 1: (Acid/Base) Histidine acts as a base to extract proton from hydroxyl of Ser. This activates the oxygen of the hydroxyl group.
Step 2: (Covalent) Formation of a covalent linkage from the hydroxyl group of the Ser to the carbonyl carbon of the peptide bond to be cleaved in the substrate.
Step 3: (Acid/Base) Histidine acts as an acid to donate a proton to the amine group of peptide bond to be cleaved, this cuts the substrate peptide into two pieces

123
Q

Describe the three steps in Phase 2 of the Chymotrypsin mechanism

A

Step 1: (Acid/Base) Histidine acts as a base to extract a proton from a water molecule, activating the oxygen of this molecule.
Step 2: (Covalent) Activated water molecule attacks the point of covalent linkage between enzyme and substrate.
Step 3: (Acid/Base) Histidine acts as an acid to donate a proton to reform the hydroxyl group of Ser

124
Q

The activity of an enzyme can be regulated by ____________, or by _____________

A

controlling the amount of the enzyme, adjusting the activity of a constant quantity of the enzyme

125
Q

Which between these two is considered long term, and which is considered short term: controlling the amount of the enzyme, adjusting the activity of a constant quantity of the enzyme?

A

Controlling - long term, Adjusting - short term

126
Q

What does the regulation of enzyme availability entail?

A

Location, rates of synthesis and degradation

127
Q

What 2 factors entail the Regulation of enzymes activity, and what are some examples of them?

A
  1. Covalent Modification: phosphorylation, methylation
  2. Non-Covalent Modification (allosteric): allosteric regulation
128
Q

What would be the logical point to regulate a reaction pathway? (x3)

A
  1. Enzymatic pathways often controlled through negative feedback inhibition by the final product of the pathway.
  2. The final product often inhibits the enzyme catalyzing the first unique and committed step.
  3. Regulation at this step conserves material and energy and prevents the accumulation of intermediates.
129
Q

What is the ‘formula’ for regulation of enzyme activity in points of regulation, and what does each symbol mean?

A

A -> B -> C -> D -> E -> F, with an arrow going from F back to A with a negative sign. There is also an En over every arrow (E1, E2, …, E5).
F is the end product is needed in limited amounts and cannot be stored. A is valuable and showed be conserved unless F is needed. B, C, D and E and have no biological roles other except as intermediates in the production of F.

130
Q

Negative feedback in a branched pathway often occurs by..?

A

The final product of each branch acting to inhibit the enzyme catalyzing the first unique and committed step of the branch

131
Q

Describe the Regulation of enzyme Activity, and where inhibition takes place

A

Regulation when two pathways cooperate to form a single product. The final product can inhibit the first unique step of each branch. The molecules preceding the merger can inhibit the first step of their branch as well as activating the first step of the opposing branch

132
Q

____ _____ serve as information sensors to coordinate cellular metabolism

A

Allosteric enzymes

133
Q

Allosteric enzymes are regulated by _________ and by __________.

A

interaction with metabolic intermediates, allosteric modulators that bind non-covalently at sites other than the active site

134
Q

Allosteric enzymes are usually examples of _____ structure

A

quaternary

135
Q

Allosteric enzymes often catalyze ____-____ reactions

A

branch-point

136
Q

Allosteric enzymes are often ____, representing the____ _______ ____ of the pathway

A

slow, rate limiting step

137
Q

Do allosteric enzymes obey Michaelis-Menten kinetics?

A

No, they have sigmoidal curves

138
Q

Activities of allosteric regulator enzymes are changed by ____ and _____

A

inhibitors, activators (modulators)

139
Q

Allosteric modulators bind ___-______ to the enzymes that they regulate

A

non-covalently

140
Q

Regulatory enzymes often possess ______ structure

A

quaternary

141
Q

In allosteric enzymes, there is a rapid transition between the ____ and _____ conformations

A

active (R), inactive(T)

142
Q

Substrates and activators may bind only to the __ state while inhibitors may bind only to the __ state

A

R, T

143
Q

The binding of the substrate disrupts the __ to __ equilibrium in favor of __. This is the basis of the __-_____ activation of allosteric enzymes.

A

R, T, R, co-operative

144
Q

Allosteric enzymes transition from a ____ ____ ____ to a ____ ___ ___ within a narrow range of substrate concentration

A

less active state, more active state

145
Q

The activity of allosteric enzymes is more sensitive to changes in ____ ______ near the Km than Michaelis-Menten enzymes of the same Vmax

A

substrate concentration

146
Q

Describe the Threshold Effect

A

Below a certain substrate concentration there is little enzyme activity; after the threshold has been reached the enzyme activity increases rapidly

147
Q

Many enzymes are regulated through the _____ ______ of a modifying group to changes some aspect of the proteins behavior, such as activity

A

covalent linkage

148
Q

What is the most common post-translation covalent modification?

A

Through phosphorylation

149
Q

True or False: these modifications are usually reversible with one enzyme catalyzing the addition of the group and another enzyme catalyzing its removal/

A

True

150
Q

Kinases _____ phosphoryl groups, phosphatases ____ them

A

add, remove

151
Q

Production and utilization of glycogen is controlled by two enzymes:

A
  1. Glycogen Synthase (anabolic): catalyzes production of glycogen from glucose
  2. Glycogen Phosphorylase (catabolic): catalyzes the breakdown of glycogen into glucose
152
Q

In glycogen metabolism, describe the path from glycogen to glucose. (x3)

A
  1. In response to hormones that are released when you are hungry (glucagon) or scared (epinephrine) both enzymes are phosphorylated
  2. Phosphorylation activates the catabolic enzyme and inactivates the anabolic enzyme.
  3. This situation favors the breakdown of glycogen into glucose.
153
Q

In glycogen metabolism, describe the path from glucose to glycogen. (x3)

A
  1. In response to hormones released in the fed state (insulin) both enzymes are unphosphorylated
  2. When unphosphorylated the anabolic enzyme is active and the catabolic enzyme is inactive
  3. This situation favors the storage of glucose within glycogen
154
Q

In which of these situations would an enzyme have low activity but be highly sensitive to changes in substrate concentration: [S] < Km, [S] = Km, [S] > Km

A

[S] < Km

155
Q

The equilibrium between substrate and product is determined by..?

A

the difference in free energy between the substrate and product

156
Q

True or False: enzymes have equal affinities for their transition states and substrates?

A

False

157
Q

On a Michaelis-Menten plot, a sigmoidal relationship between velocity and substrate concentration indicates that..?

A

the enzyme is allosteric

158
Q

Allosteric enzymes are often the _____ enzyme in an enzymatic pathway

A

slowest

159
Q

Enzymes accelerate reactions by..?

A

providing a lower energy route between the substrate and product