Module 04: Enzymes (Stoker) Flashcards

1
Q

They act as a catalyst for biochemical reactions. They can be denatured and activity is dramatically affected by alterations in pH, temperature and other protein denaturants

A

Globular Proteins (Enzymes)

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2
Q

These are exceptions and ribonucleic acids with catalytic activity.

A

Ribozymes

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3
Q

Enzymes are not consumed in the reactions; they are ______________.

A

Regenerated

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4
Q

What is the effect of enzymes on equilibrium constant (Keq) along with retention factor (Rf) and Rb values?

A

It has no effect on Keq, increase both Rf and Rb reactions at same rate. It can increase rate a 10^3 to 10^6 fold

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5
Q

What are the general characteristics of enzymes?

A

(1) Regulation (allosteric enzymes) activities of allosteric enzymes can be controlled or modulated by allosteric effectors
(2) Location: found in specific sites or organelles within the cell. Reason why enzymes are used as clinical markers for certain diseases.

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6
Q

What are the two (2) types of enzymes?

A

(1) Simple Enzymes
(2) Conjugated Enzymes

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7
Q

These are composed only of protein (amino acid chains).

A

Simple Enzyme

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8
Q

These types of enzymes has a non-protein part in addition to a protein part.

A

Conjugated Enzyme

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9
Q

This is the protein part of a conjugated enzyme (inactive).

A

Apoprotein

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10
Q

This is a nonprotein part of a conjugated enzyme.

A

Cofactor

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11
Q

These are constituted of an apoenzyme and co-factor. And is known to be the biochemically active conjugated enzyme

A

Holoenzyme (cofactor)

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12
Q

This is important for the chemically inactive enzymes and are small organic molecules or Inorganic ions

A

Cofactors

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13
Q

Cofactors are also known as ___________ or __________.

A

Coenzymes or substrates

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14
Q

Coenzymes/cosubstrates are derived from “__________.”

A

dietary vitamins

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15
Q

What are the typical metal ion cofactors?

A

Zn2+, Mg2+, Mn2+, and Fe2

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16
Q

What are the typical non metallic ion cofactors?

A

Cl-

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17
Q

Inorganic ion cofactors derived from “___________.”

A

dietary minerals

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18
Q

The nomenclature of an enzyme is based on what factors?

A

(1) Type of reaction catalyzed
(2) Identity of the substrate

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19
Q

This is the is the reactant in an enzyme-catalyzed reaction. This is the substance upon which the enzyme “acts.”

A

Substrate

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20
Q

What are the three important factors of the naming process?

A

(1) Suffix -ase identifies it as an enzymes. Exception: The suffix -in is still found in the names of some digestive enzymes, E.g. trypsin, chymotrypsin, and pepsin
(2) Type of reaction catalyzed by an enzyme is often used as a prefix
(3) Identity of substrate is often used in addition to the type of reaction

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21
Q

What are the six major classes (classification) of enzymes?

A

(1) Oxidoreductase
(2) Transferase
(3) Hydrolase
(4) Lyase
(5) Isomerase
(6) Ligase

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22
Q

What type of reaction does Oxidoreductase catalyze?

A

Oxidation-reduction

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23
Q

What type of reaction does Transferase catalyze?

A

Functional group transfer reactions

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24
Q

What type of reaction does Hydrolase catalyze?

A

Hydrolysis reaction

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25
Q

What type of reaction does Lyase catalyze?

A

Reactions involving the addition to a double bond or removal of groups forming a double bond

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26
Q

What type of reaction does Isomerase catalyze?

A

Isomerization reactions

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27
Q

What type of reaction does Ligase catalyze?

A

Reactions involving bond formation coupled with ATP hydrolysis

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28
Q

This is an enzyme catalyzes an redox reaction:

A

Oxidoreductase

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29
Q

What does Oxidoreductase require?

A

coenzyme that is either oxidized or reduced, e.g. NAD+, FAD, FMN

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30
Q

This pertains to the decrease in valence along with the gain of H or loss of O. This is undergone by oxidizing agent.

A

Reduction

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31
Q

This pertains to the increase in valence along with the loss of H or the gain of O. This is undergone by reducing agent.

A

Oxidation

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32
Q

This undergoes reduction, gain of e- or gain of H

A

Oxidizing Agent

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33
Q

This undergoes oxidation, loses e-/donor of H

A

Reducing Agent

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34
Q

This is an enzyme that catalyzes the transfer of a functional group from one molecule to another

A

transferase

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35
Q

These catalyze transfer of an amino group to a substrate, catalyze transamination reaction

A

Transaminases

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36
Q

This catalyze transfer of a phosphate group from adenosine triphosphate (ATP) to a substrate

A

Kinase

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37
Q

This is a reaction of an amino acid and a-keto acid to form a new a-keto acid and a new amino acid

A

Transamination

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38
Q

This is an enzyme that catalyzes a hydrolysis reaction

A

hydrolase

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39
Q

What does hydrolase involve?

A

The reaction involves addition of a water molecule to a bond to cause bond breakage

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40
Q

What are the three integral hydrolysis reactions in the process of digestion?

A

(1) Carbohydrase
(2) Proteases
(3) Lipases

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41
Q

These hydrolyze glyosidic bonds in oligo- and polysaccharides

A

Carbohydrase

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42
Q

These effect the breaking of peptide linkages in proteins,

A

Proteases

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43
Q

These effect the breaking of ester linkages in triacyclglycerols (TAGs) or fats.

A

Lipases

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44
Q

This is an enzyme that catalyzes the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not involve hydrolysis or oxidation

A

lyase

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45
Q

This effects the removal of the components of water forming a double bond

A

Dehydratase

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46
Q

These effects the addition of the components of water to a double bonds

A

Hydratase

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47
Q

These catalyze synthesis (joining of molecules) without use of ATP

A

Synthase

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48
Q

This is an enzyme that catalyzes the isomerization (rearrangement of atoms) reactions.

A

Isomerase

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49
Q

What does an isomerase involve?

A

Interconversion between D and L amino acid, between an aldose and a ketose or internal rearrangement.

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50
Q

This is an enzyme that catalyzes the joining of two molecules involving ATP hydrolysis as a source of energy

A

Ligase

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51
Q

What does a ligase require?

A

ATP hydrolysis is required because such reactions are energetically unfavorable (Require the simultaneous input of energy obtained by a hydrolysis of ATP to ADP.)

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52
Q

This is the relatively small part of an enzyme’s structure that is actually involved in catalysis:

A

Active Site

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53
Q

What are some of the characteristics of the active site?

A

(1) Place where substrate binds to enzyme
(2) Formed by groups from different parts of protein, brought by folding and bending of the protein.
(3) Usually a “crevice like” location in the enzyme

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54
Q

True or false: Some enzymes have more than one active site.

A

True

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55
Q

What is the formula for the Enzyme Substrate Complex?

A

S + E ————–> <—————–ES ——–> P + E

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56
Q

How do enzymes increase the rate?

A

Enzymes increase the rate by providing alternate route with lower energy of activation.

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57
Q

This is the intermediate reaction species formed when substrate binds with the active site

A

Enzyme Substrate Complex

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58
Q

What are the two models for Substrate Binding to Enzyme?

A

(1) Lock-and-Key Model
(2) Induced Fit Model

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59
Q

In this model of substrate binding, enzyme has a pre-determined shape for the active site. In this, only substrate of specific shape can bind with active site

A

Lock-and-Key Model

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60
Q

In this model of substrate binding, substrate contact with enzyme will change the shape of the active site. This allows small change in space to accommodate substrate

A

Induced Fit Model

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61
Q

What are the Forces That Determine Substrate Binding (non covalent interactions?

A

(1) H-bonding
(2) Hydrophobic interactions
(3) Electrostatic interactions

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62
Q

What kind of specificity does the Lock & key model explain?

A

absolute specificity

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63
Q

What kind of specificity does the Induced fit model explain?

A

broad specificity

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64
Q

This is the ability to discriminate between 2 competing substrate

A

Enzyme Specificity

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65
Q

This acts on only one substrate. In this, an enzyme will catalyze a particular reaction for only one substrate

A

Absolute Specificity

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66
Q

This is most restrictive of all specificities (not common)

A

Absolute Specificity

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67
Q

In this, an enzyme acts only on a particular stereoisomer. Moreover, it can distinguish between stereoisomers. For example, an L-Amino-acid oxidase - catalyzes reactions of L-amino acids but not of D-amino acids.

A

Stereochemical Specificity

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68
Q

In stereochemical specificity, this is inherent in an active site.

A

Chirality

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69
Q

This acts on structurally similar compounds that have the same functional groups.

A

Group Specificity or broad

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69
Q

This acts on 2 or more substrate containing a particular type of bond irrespective of the structural features in the vicinity of the bond

A

Linkage Specificity

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69
Q

This is considered most general of enzyme specificities

A

Linkage Specificity

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70
Q

What is the relationship between temperature and the rate of activation?

A

Higher temperature results in higher kinetic energy which causes an increase in number of reactant collisions, therefore there is higher activity.

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71
Q

This is the temperature at which the rate of enzyme catalyzed reaction is maximum

A

Optimum temperature

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72
Q

Optimum temperature for human enzymes is ______________.

A

37ºC (body temperature)

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72
Q

Increased temperature (high fever) leads to: “_________”

A

decreased enzyme activity

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73
Q

Drastic changes in pH can result in “_________________”

A

denaturation of proteins

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74
Q

pH at which enzyme has maximum activity

A

Optimum ph

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75
Q

At which pH range do enzymes have maximum activity

A

pH range of 7.0 - 7.5

76
Q

What is the optimum pH of pepsin?

A

2.0

76
Q

What is the optimum pH of trypsin?

A

8.0

77
Q

In this, Enzymes are not consumed in the reactions they catalyze

A

Enzyme Concentration

78
Q

What happens at constant substrate concentration?

A

At a constant substrate concentration, enzyme activity increases with increase in enzyme concentration. In this, the greater the enzyme concentration, the greater the reaction rate.

79
Q

What happens to the substrate concentration at constant enzyme concentration?

A

At a constant enzyme concentration, the enzyme activity increases with increased substrate concentration

80
Q

This is the concentration at which it reaches its maximum rate and all of the active sites are full

A

Substrate saturation

81
Q

This is the number of substrate molecules converted to product per second per enzyme molecule under conditions of optimum temperature and pH

A

Turnover Number

82
Q

This is the rate equation that relates the velocity of the reaction to substrate concentration

A

Michaelis-Menten Equation

82
Q

What does the Michaelis-Menten Equation yield?

A

When initial velocity, Vo is plotted against [S], a hyperbolic curve (MM plot) results, where Vmax represents the maximum reaction velocity.

83
Q

This represents the maximum reaction velocity.

A

Vmax

84
Q

What is the state of enzyme saturation at Vmax?

A

At the Vmax, all available enzyme is “saturated” with bound substrate, meaning only the ES (enzyme-substrate) complex is present.

85
Q

What happens at 1/2 Vmax?

A

At 1/2Vmax, the substrate concentration is equal to Km, the enzyme is half saturated

85
Q

What is the state of part A in the graph of the Michaelis-Menten Equation?

A

[S] < KM (Michaelis constant) only a portion of the total number of active sites are saturated by the substrate

85
Q

What is the state of part B in the graph of the Michaelis-Menten Equation?

A

[S] = Vmax/2 half of the total number of active sites are saturated

86
Q

What is the state of part C in the graph of the Michaelis-Menten Equation?

A

[S] > KM all enzymes’ active sites have bound substrate. Increasing the substrate concentration will no longer affect the rate because the enzyme is saturated.

87
Q

If Vo is set equal to 1/2 Vmax, then ______________

A

Km = [S]. Km is equal to Substrate concentration at ½ Vmax.

87
Q

What does it mean when Km is equal to Substrate concentration at ½ Vmax

A

This means that at one half of the maximal velocity, the substrate concentration needed to half saturate the enzyme to be equal to the Km

88
Q

What is the relationship between the affinity of the enzyme for the substrate and the Km (Michaelis constant)?

A

It is an inverse measure of the affinity of the enzyme for the substrate (low Km = high affinity; low S concentration to attain Vmax)

89
Q

What is the reciprocal for the Michaelis-Menten equation?

A

Lineweaver Burk Plot

89
Q

The Lineweaver Burk Plot is a ____________________.

A

Double reciprocal plot

90
Q

Why is the format of the equation a straight line?

A

x = 1/[S] and the y-intercept, b = 1/Vmax. When this relation is plotted, the result is a straight line graph

91
Q

This is an enzyme that has an additional site called regulatory site or allosteric site for the binding of a regulatory molecule.

A

allosteric enzyme

92
Q

This is a simple enzyme that has only an active site for the binding of its substrate.

A

non-allosteric enzyme

93
Q

This is a site other than the active site. Site where small molecules (effectors) bind and cause conformational changes in the enzyme. It may cause the enzyme to be more active or less active.

A

Allosteric or Regulatory Site

94
Q

The plot of allosteric enzymes contain multiple subunits; thus they do not follow the Michaelis- Menten kinetics, which results to them being ________________.

A

sigmoidal

95
Q

Allosteric enzymes display this kind of binding

A

Displays cooperative effect – binding of S to one subunit facilitates the binding of the other substrates.

96
Q

This is any molecule that acts directly on an enzyme to lower its catalytic rate or stop it. These can be cellular metabolites, or foreign substances such as drugs or toxins that have either a therapeutic or toxic (can be lethal) effect.

A

Inhibitor

97
Q

How do inhibitors inhibit?

A

It acts directly on an enzyme to lower its catalytic rate or stop it.

98
Q

What are the two types of inhibition?

A

(1) Irreversible Inhibition
(2) Reversible Inhibition
a) Competitive
b) Uncompetitive
c) Mixed/Noncompetitive

99
Q

How does an irreversible enzyme inhibitor work?

A

The inhibitor bonds strongly and increasing substrate concentration does not reverse the inhibition process . Enzyme is permanently inactivated.

99
Q

This inactivates enzymes by forming a strong covalent bond with the enzyme’s active site.

A

Irreversible Enzyme Inhibitor

100
Q

This is used as an organophosphorus insecticide.

A

diisopropylfluorophosphate

101
Q

What does the diisopropylfluorophosphate (DIFP) inhibit?

A

acetyl choline esterase

102
Q

This is a Non-steroidal anti-inflammatory drugs (NSAID) that inhibits an enzyme by acetylating a serine residue at the enzyme’s active site.

A

Aspirin

103
Q

What enzyme does aspirin inhibit?

A

cyclooxygenase

104
Q

What kind of synthesis does aspirin inhibit?

A

prostaglandin and thromboxane synthesis

105
Q

This is an irreversible inhibitor that inhibits transpeptidase?

A

penicillin

106
Q

This is the enzyme involved in bacterial cell wall synthesis

A

transpeptidase

107
Q

This inhibition competes with the substrate for the same active site, resembles normal substrate in shape and charge (thus making it bind to the active site without changing the inhibitor - no reaction).

A

Reversible Competitive Inhibition

108
Q

What is the inhibitor in Reversible Competitive Inhibition?

A

structural analog of the normal substrate

109
Q

In what kind of interactions does the enzyme inhibitor form?

A

weak interactions (hydrogen bonds, etc.).

110
Q

How is Competitive inhibition reduced?

A

Competitive inhibition can be reduced by simply increasing the concentration of the substrate

111
Q

What is the kinetic effect of competitive inhibition?

A

Vmax is unchanged and Km is increased (affinity decreased)

112
Q

How does a competitive inhibition transpire?

A

Inhibitor has close structural similarities to the normal substrate and therefore competes with the substrate for the active site. Inhibitor binds only with the free enzyme.

113
Q

This is the inhibitor of succinate dehydrogenase.

A

Malonate

114
Q

This is the normal substrate found in the Krebs Cycle.

A

Succinate

115
Q

These are competitive inhibitors of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase

A

Statins

116
Q

How do statins inhibit 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase?

A

limiting enzyme in cholesterol biosynthesis

117
Q

What are the competitive inhibitors of cyclooxygenase?

A

Ibuprofen, acetaminophen, naproxen

118
Q

This is an antidote for ethylene glycol or methyl alcohol poisoning. Competes for binding to alcohol dehydrogenase.

A

Ethanol

119
Q

This type of inhibition does not compete with the normal substrate for the active site but decreases enzyme activity by binding to a site other than the active site.

A

noncompetitive enzyme inhibitor

120
Q

What happens during reversible noncompetitive inhibition?

A

Causes a change in the structure of the enzyme and prevents enzyme activity.

121
Q

Can reversible noncompetitive inhibition be reduced?

A

No, increasing the concentration of substrate does not completely overcome inhibition.

122
Q

What is the kinetic effect of the noncompetitive inhibition?

A

Vmax is decreased and Km is unchanged but s can still bind with the enzyme

123
Q

What does the non competitive inhibition transpire?

A

Inhibitor binds at a site other than the active site (E or ES) (and free enzyme( and causes changes in the overall 3-D shape of the enzyme that leads to a decrease in activity:

124
Q

what are examples of noncompetitive inhibitors?

A

Heavy metals mercury and silver

125
Q

This is a non-competitive inhibitor of cytochrome oxidase of the ETC/ Respiratory Chain. It binds to its allosteric site.

A

Cyanide

126
Q

What does arsenate inhibit?

A

glyceraldehyde phosphate dehydrogenase

127
Q

In this, the inhibitor binds at a site other than the active site and, binds only to the ES complex.

A

Uncompetitive Inhibition

128
Q

What is the kinetic effect of Uncompetitive Inhibition?

A

Both Km and Vmax are decreased.

129
Q

This is a rarer phenomenon in uncompetitive inhibition

A

Uncompetitive inhibition of single-substrate enzyme-catalyzed reactions is a rare phenomenon,

130
Q

What does hydrazine inhibit?

A

aryl sulphatase

131
Q

What does phenylalanine inhibit?

A

intestinal alkaline phosphatase

132
Q

What are the general mechanisms involved in regulation? (APCOFEEN)

A

Allosteric regulation
Proteolytic enzymes and zymogens
covalent modification of enzymes
Feedback control regulation
Enzyme concentration

133
Q

What kind of structures do allosteric enzymes have?

A

All allosteric enzymes have quaternary structure (Composed of two or more protein chains/ subunits)

134
Q

What are the two binding sites of allosteric enzymes

A

Substrate (active site) and regulator binding site (allosteric site), wherein the active and regulatory binding sites are located independently and the shapes of the sites (electronic geometry) are different

135
Q

what happens to the binding in regulatory sites?

A

Binding of molecules at the regulatory site causes changes in the overall three dimensional structure of the enzyme:
Change in three dimensional structure of the enzyme leads to change in enzyme activity

136
Q

These regulators increase are enzyme activity

A

Activators

137
Q

These regulators decrease are enzyme activity

A

Inhibitor

138
Q

This is the binding of an allosteric modulator that changes activity of the active site.

A

Allosteric Modification

139
Q

A process in which activation or inhibition of the first reaction in a reaction sequence is controlled by a product of the reaction sequence.

A

Feedback Control

140
Q

Regulators of a particular allosteric enzyme may be:

A

(1) Products of entirely different pathways of reaction within the cell
(2) hormones compounds produced outside the cell

141
Q

In this form of inhibition, the product of the reaction inhibits its own formation by inhibiting an early enzyme in the pathway.

A

Feedback Inhibition

142
Q

Feedback Inhibition is also known as “_________”

A

End product Inhibition

143
Q

This is another mechanism of regulating enzyme activity wherein the productions of enzymes are in inactive forms and are turned on at the specific time or place.

A

Proteolytic Enzymes and Zymogens

144
Q

They hydrolyze peptide bonds in proteins and are generated in an inactive form then converted to their active form.

A

proteolytic enzymes

145
Q

What are examples of proteolytic enzymes?

A

digestive and clotting enzymes

146
Q

These are called inactive forms.

A

zymogens

147
Q

The zymogens are activated by _______

A

proteolytic cleavage

148
Q

This is a process in which enzyme activity is altered by covalently modifying the structure of the enzyme. This involves adding or removing a group from an enzyme

A

Covalent Modification

149
Q

This is the most common form of covalent modification and is often derived from an ATP molecule

A

Phosphate group

150
Q

This pertains to the addition of a phosphate group

A

phosphorylation

151
Q

What catalyzes phosphorylation?

A

Kinase

152
Q

This pertains to the removal of a phosphate group

A

dephosphorylation

152
Q

What catalyzes phosphorylation?

A

phosphatase enzyme

153
Q

What happens in phosphorylation?

A

Phosphate group is added to (or removed) from the R group of a serine, tyrosine, or threonine amino acid residue in the enzyme regulated.

154
Q

This is the is the major regulatory enzyme in glycogen breakdown (glycogenolysis).

A

Glycogen phosphorylase

155
Q

Glycogen phosphorylase is activated by what

A

activated by phosphorylation

156
Q

This is the major regulatory enzyme in the synthesis of glycogen from glucose. This is inhibited Phosphorylation.

A

Glycogen synthase

157
Q

What activates Glycogen synthase?

A

activated by dephosphorylation

158
Q

In the regulation of glycogen synthesis and degradation to maintain glucose levels, this is where the glycogen synthesis is activated

A

Well fed state

159
Q

In the regulation of glycogen synthesis and degradation to maintain glucose levels, this is where the glycogen degradation is accelerated

A

Fasting

160
Q

In the skeletal system, degradation is activated during

A

exercise

161
Q

In the skeletal system, glycogen accumulation is activated during

A

rest

162
Q

How are glycogen synthase and phosphorylase regulated?

A

allosterically and hormonally regulated

163
Q

This regulatory enzyme in glycogen synthesis is activated by dephosphorylation

A

Glycogen synthetase

164
Q

This regulatory enzyme in glycogen breakdown is activated by phosphorylation

A

Glycogen phosphorylase

165
Q

What happens in induction or repression of enzyme synthesis during a well fed state?

A

When the level of insulin increases, the synthesis of key enzymes involved in glucose degradation are activated

166
Q

What happens in induction or repression of enzyme synthesis during a starvation state?

A

When the level of glucagon increases, the synthesis of key enzymes involved in glucose synthesis are activated

167
Q

This is used to treat high blood pressure as well as other heart conditions.

A

angiotensin converting enzyme inhibitors

168
Q

This is an octapeptide hormone involved in BP regulation, it increases BP by narrowing blood vessels.

A

Angiotensin

169
Q

What are examples of angiotensin?

A

lisinopril, enalapril and captopril.

170
Q

This is a substance that kills bacteria or inhibits their growth

A

antibiotic

171
Q

What are the two families of antibiotics?

A

(1) sulfa drugs
(2) Penicillin

172
Q

These are derivatives of sulfanilamide which exhibit antibiotic activities

A

Sulfa drugs

173
Q

Why are humans not affected of sulfa drugs?

A

Sulfa drugs don’t affect humans because we absorb folic acid from our diet

173
Q

Where is sulfanilamide structurally?

A

PABA (p-aminobenzoic acid)

173
Q

Why is sulfanilamide a competitive inhibitor?

A

Sulfanilamide is a competitive inhibitor of enzymes responsible for converting PABA to folic acid in bacteria

173
Q

What is the coenzyme of PABA (p-aminobenzoic acid?

A

Folic acid

173
Q

This retards bacterial growth and that eventually kills them

A

Folic acid deficiency

174
Q

Who accidentally discovered penicillin?

A

Accidently discovered by Alexander Fleming in 1928

175
Q

What structures do penicillin have?

A

All have structures containing a four-membered Beta-lactam ring fused with a five-membered thiazolidine ring

176
Q

What does penicillin inhibit?

A

Selectively inhibits transpeptidase by covalent modification of serine residue

177
Q

This catalyzes the formation of peptide cross links between polysaccharides strands in bacterial cell walls,

A

Transpeptidase

178
Q

How does penicillin inhibit transpeptidase?

A

It weakens it and so it easily undergo lysis

179
Q
A