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BIOCHEM > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Why biocatalysts over inorganic catalysts

A

greater reaction specificity, milder conditions, greater regulation, faster reaction rates

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2
Q

The — of enzymes are essential to their catalytic
activity

A

structure

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3
Q

What are some common inorganic co-factors?

A

Fe,Mg,Mn,Zn, complex organic/metalloorganic molecules

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4
Q

why are co-factors important?

A

Bind to enzyme to form catalytically active enzyme

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5
Q

what reaction do oxidoreductases catalyze?

A

Oxidation reduction reactions (movement of electrons)

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6
Q

What reactions do transferases catalyze?

A

transfer of functional groups

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7
Q

What reactions do hydrolases catalyze?

A

Hydrolysis (transfer of functional groups to water)

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8
Q

What reactions do lyases catalyze?

A

cleavage of c-c,c-o,c-n & other bonds by elimination resulting in double bond

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9
Q

What reactions do isomerases catalyze?

A

Transfer of atom group within the molecule to yield isomers

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10
Q

What reactions do Ligases catalyze?

A

Formation of c-c,c-s,c-o, and c-n bonds by condensation

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11
Q

Each enzyme has a — number classification

A

4 part

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12
Q

What is the first number of the enzyme classification?

A

the class name

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13
Q

What is number two of enzyme classification?

A

subclass

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14
Q

What are the 3rd and 4th number of the enzyme classification?

A

provide more information about the reaction

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15
Q

A specific substrate interacts with a specific group of —– in the enzyme at the active site

A

amino acid residues

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16
Q

The substrate binds to an enzyme to produce?

A

The products

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17
Q

Active site

A

location on enzyme in which the enzyme catalyzed reaction occurs

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18
Q

Substrate

A

molecule which binds to the enzyme active site and is acted upon by the enzyme

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19
Q

Enzymes Affect

A

reaction rates no the equilibria

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20
Q

——– change in gibbs free energy is favored

A

negative

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21
Q

A higher activation energy means

A

slower reaction

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22
Q

Catalysts increase
reaction rates by

A

lowering change in gibbs free energy

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23
Q

Rate-limiting step

A

Step in enzymatic reaction which has the largest activation energy barrier. Thus, dictates overall rate of reaction

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24
Q

What is the reaction rate is determined by

A

the concentration of reactant and a rate constant k

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25
Q

Equation for Keq

A

keq=[products]/[reactants]

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26
Q

If ΔG° < 0, then

A

Keq>1 and products are favored at equilibrium

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27
Q

If ΔG° > 0, then

A

Keq<1 and reactants are favored at equilibrium

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28
Q

What helps to lower activation energies?

A

Weak non-covalent interactions between the substrate and enzyme

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29
Q

What are the weak Interactions between E and S in ES complex?

A

Hydrogen bonding, hydrophobic interactions, and ionic interactions

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30
Q

Some of the weak interactions in the ES complex occur during the reaction
transition state and

A

stabilize the transition state

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31
Q

binding energy, ΔGB

A

energy concerning enzyme and substrate interactions

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32
Q

The binding energy can be used to lower substrate entropy or
to cause a

A

conformational change in the enzyme (induced fit)

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33
Q

Enzymes binds to the —– better than the —–

A

transition states, substrates

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34
Q

Stronger/additional interactions ———–
compared to the ground state lowers the activation barrier

A

between the enzyme and transition state

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35
Q

Why are enzymes large?

A

maximizes number of weak interactions between enzyme and transition states

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36
Q

Specificity

A

enzyme is selective for a particular substrate or group of substrates

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37
Q

induced fit

A

enzyme undergoes conformational change upon binding to substrate. Caused by weak interactions between substrate and enzyme

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38
Q

Binding energy holds substrates in the proper orientation to react resulting in

A

entropy reduction

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39
Q

Enzyme-substrate interactions replace all

A

hydrogen bonding between substrate and water

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40
Q

Catalytic residues

A

functional groups directly involved in a catalytic reaction

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41
Q

When there is no catalyst present, unstable, charged
intermediates formed in many biochemical reactions tend

A

to break down into the reactants with zero product formation

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42
Q

These charged intermediates can be stabilized by

A

proton transfers and be broken down into products

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43
Q

Specific acid-base catalysis

A

only utilizes the H+ or OH- ions present in water

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44
Q

General acid-base catalysis

A

proton transfer facilitated by other molecules

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45
Q

In an enzyme’s active site, amino acid side-chains can act as

A

proton acceptors or donors

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46
Q

Glu, Asp general proton donor form

A

R-COOH

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47
Q

Glu,Asp general proton acceptor form

A

R-COO(-)

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48
Q

Lys,Arg general proton donor form

A

R-NH3(+)

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49
Q

Lys, Arg general proton acceptor form

A

R-NH2

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50
Q

Cys genral proton donor form

A

R-SH

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51
Q

Cys general proton acceptor form

A

R-S(-)

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52
Q

Ser general donor form

A

R-OH

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53
Q

Ser general proton acceptor

A

R-O(-)

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54
Q

What is the purpose of catalysis?

A

Stabilize the charged intermediate to promote the formation of a product

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55
Q

What are the two major steps of covalent catalysis?

A

1) covalent bonding between amino acid residues in active site of enzyme and substrate
2) Cleavage of covalent bond between substrate and enzyme to return enzyme to original state

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56
Q

Covalent catalysis requires a — and —

A

nucleophile and electrophile

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57
Q

In covalent catalysis, the —- attacks the —-

A

nucleophile attacks the electrophile

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58
Q

In covalent catalysis, the nucleophile may be

A

a reactive serine, amine, thiolate, carboxylate

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59
Q

Metal Ion Catalysis involves

A

ionic interaction between enzyme with metal cofactor and a substrate

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60
Q

Ionic interactions between an enzyme-bound metal and a
substrate can

A

orient the substrate into the correct position for reaction, or stabilize the transition state

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61
Q

enzyme bound metal participate in —- reactions

A

redox

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62
Q

chymotrypsin uses – and — catalysis

A

covalent and general acid base catalysis

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63
Q

enzyme kinetics

A

study of how enzyme catalyzed reaction rate responds to changes in experimental parameters

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64
Q

the Michaelis-Menten
equation

A

V0=Vmax[S]/[S]+Km

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65
Q

Km equation

A

Km=[E][S]/[ES]

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66
Q

What is the definition of Km?

A

When the substrate concentration is equal to 1/2 of max rate. Thus, 50% of substrate is bound to enzyme

67
Q

Which step is the fast step in enzyme action?

A

The binding of the substrate to the enzyme to form complex

68
Q

Which step is the slow step(rate limiting) in enzyme action ?

A

Enzyme-substrate complex breaks down to generate free enzyme and product

69
Q

The overall reaction rate must be
proportional to

A

The concentration of enzyme-substrate complex

70
Q

The saturation effect

A

A plateau in velocity at high [S]

71
Q

At low [S], KM» [S], most of the
enzyme is in the free form. Thus, —

A

change in velocity is linear and dependent on [S]

72
Q

At high [S], KM&laquo_space;[S]the enzyme is
saturated with substrate; almost all
enzymes are in the combined form. Thus,

A

change in velocity is not linear or dependent on [S]

73
Q

steady state

A

[ES] and other intermediates remain approximately constant over time

74
Q

what does steady state imply about [ES] formation and breakdown

A

[ES] formation = [ES] breakdown

75
Q

The Michaelis-Menten equation can be algebraically
transformed into a more useful form in plotting
experimental data, simply by

A

taking the reciprocal of both sides to yield a linear equation

76
Q

What is the slope of the Lineweaver-Burk equation

A

Km/Vmax

77
Q

What is the y-intercept of the Lineweaver-Burk equation?

A

1/Vmax

78
Q

Lineweaver-Burk equation

A

1/V=(Km/Vmax)+(1/Vmax)

79
Q

Why is Lineweaver-Burk equation preferred over the the Michaelis-Menten
equation?

A

It provides a more accurate measure of Vmax

80
Q

For a reaction with two steps, Km

A

Km=(K2+K(-1))/k1

81
Q

What is the mathematical measure of Kd?

A

Kd=(k-1)/K1

82
Q

What is Kd an indicator of?

A

Affinity between the substrate and enzyme

83
Q

When is Km equal to Kd the dissociation constant?

A

When K2<K-1

84
Q

if product release is rate-limiting, then most of the enzyme
is present in the — form at saturation

A

EP

85
Q

What is Kcat the rate constant for?

A

The rate limiting step

86
Q

when product release is the rate limiting step what does v max equal

A

Vmax=Kcat[Etotal]

87
Q

kcat is also known as

A

the turnover number

88
Q

What is the turnover number?

A

number of substrate molecules converted to product in a given period of time

89
Q

the overall rate constant for conversion of E+S ➔ E+P

A

kcat/km and measures how efficiently an enzyme turns a substrate into product

90
Q

Enzymes with two substrates usually involve a transfer of

A

an atom or functional group from one substrate to another

91
Q

Enzyme inhibitors

A

interfere with catalysis to slow or halt enzyme catalyzed reactions

92
Q

Reversible Inhibition

A

noncovalent binding of inhibitor to enzyme . can be reversed by removal of inhibitor

93
Q

What are the three kinds of reversible inhibition?

A

Competitive, noncompetitive, mixed inhibition

94
Q

Irreversible Inhibition

A

covalently binds to enzyme and destroys essential functional group or portion of enzyme

95
Q

A competitive inhibitor molecule competes with the substrate molecule
for

A

the active site of an enzyme

96
Q

Usually, a competitive inhibitor is very similar to

A

the substrate

97
Q

Formation of an EI complex consumes [E] thus

A

decreases formation of ES complex

98
Q

In the presence of a competitive inhibitor, how does the km change

A

it increases and is now αKm

99
Q

Due to reversibility of competitive inhibition, the ES complex is favored
over EI

A

at high [S] thus v max stays the same

100
Q

Why does km increase in the presence of a competitive inhibitor?

A

a larger [S] is required to reach 1/2 v max

101
Q

An uncompetitive inhibitor binds at a

A

site distinct from the active site

102
Q

How does uncompetitive inhibition impact the V max and Km

A

it decreases them by a factor of alpha’

103
Q

A mixed inhibitor binds at

A

a site distinct from the active site but may bind to enzyme of ES

104
Q

When α=α’
, it is known as

A

noncompetitive inhibition and Km is not affected

105
Q

Suicide inactivators are a special type of

A

irreversible inhibitor

106
Q

Suicide inhibitors are inactive until

A

they covalently bind to the active site of a particular enzyme

107
Q

Chymotrypsin catalyzes

A

the hydrolytic cleavage of peptide bonds adjacent to large aromatic amino acid residues

108
Q

What amino acids does chymotrypsin cleave at?

A

Trp, Phe, Tyr and on the c side

109
Q

What is the substrate of chymotrypsin?

A

a protein or peptide with Trp,Phe, and Tyr residues

110
Q

What is the Acylation phase of the chymotrypsin mechanism

A

Cleavage of peptide bond to establish formation of ester linkage between carbonyl carbon of amino acid residue and enzyme

111
Q

What us the deacylation phase of the chymotrypsin mechanism?

A

Hydrolysis of the ester linkage and regeneration on non acylated enzyme

112
Q

Where is the active site of chymotrypsin?

A

A hydrophobic pocket next to the catalytic triad

113
Q

What amino acid residues compose the catalytic triad of chymotrypsin?

A

His57,Asp102,Ser195

114
Q

What family does chymotrypsin belong to?

A

The Serine protease family

115
Q

What position is the gly residue located at in chymotrypsin?

A

G193

116
Q

The acylation and deacylation of the chymotrypsin involves which enzyme?

A

The Serine residue

117
Q

Which step is faster acylation or deacylation?

A

acylation

118
Q

What is the rate determining step of the chymotrypsin mechanism?

A

The deacylation

119
Q

During acylation, —- as a general acid and — as a general base facilitate the
nucleophilic attack of —–

A

Asp102,His57,Ser195

120
Q

During acylation,—— acts as a general base, which can remove the proton from the ——

A

His57,Ser 195

121
Q

Why is the catalytic triad important?

A

Aids in the stabilization of intermediates formed during the acylation and deacylation steps. Thus, lowering energy of activation

122
Q

An optical rate of chymotrypin is observed at a pH of

A

8

123
Q

Why is chymotrypsin reaction rate not ideal at low pH?

A

The His57 residue is pronated and unable to remove the proton from the Ser195 residue

124
Q

Why does reaction rate decrease after pH of 8?

A

Deprotonation of N-terminus in one of three polypeptide chains. Hydrophobic pocket at active site closes and substrate binding decreases

125
Q

What is the first step of Chymotrypsin mechanism?

A

Enzyme substrate binding

126
Q

What is the second step of chymotrypsin mechanism?

A

Nucleophilic attack by ser 195 to carbonyl of substrate. Forming a tetrahedral intermediate

127
Q

How does His 57 make Ser195 a better nucleophile?

A

Removing the proton from Ser residue’s hydroxyl group

128
Q

What is the third step of chymotrypsin mechanism?

A

The re-instatement of the carbonyl double bond resulting in cleavage of peptide bond in substrate.

129
Q

What is step four of the chymotrypsin mechanism?

A

A water molecule is deprotonated by His 57 to generate a nucleophilic -OH molecules

130
Q

What is the fifth step in chymotrypsin mechanism?

A

The OH nucleophile attacks the acyl enzyme ester linkage to form a second tetrahedral intermediate

131
Q

What is the fifth step in chymotrypsin mechanism?

A

The OH nucleophile attacks the acyl enzyme ester linkage to form a second tetrahedral intermediate

132
Q

What is step six of the chymotrypsin mechanism?

A

The tetrahedral intermediate collapses to form carboxylate anion. Ser 195 is displaced in collapse of intermediate

133
Q

What is the final step of the chymotrypsin mechanism?

A

The final product diffuses away from the enzyme’s active site to produce a free enzyme

134
Q

How does inhibition of chymotrypsin occur?

A

Metal ion binding to the His 57

135
Q

What serves to inhibit enzyme activity of papain

A

Metal ion binding to the Cys25 residue whichi is similar to the -oH group of the Ser 195 in chymotrypsin

136
Q

Di-isopropylfluorophosphate
(DIFP) is an —
for chymotrypsin

A

irreversible inhibitor

137
Q

What amino acid reside does the DIFP inhibitor bind to in chymotrypsin?

A

Forms covalent bond to the Ser195

138
Q

Transition-state analogs are molecules
that resemble

A

transition states

139
Q

Binding to an allosteric regulatory enzyme affects the – and – structure of a protein

A

tertiary and quatenary

140
Q

How does an allosteric enzyme bind to a substrate? What does the binding result in

A

Reversible non-covalent bonds resulting in conformational change. Conformational change results in change of activity

141
Q

the regulatory enzyme is homotropic when

A

the enzyme and substrate are similar

142
Q

ATCase is an alloesteric enzyme that catalyzes the formation of

A

N-carbamoylaspartate from carbamoyla phosphate and aspartate

143
Q

What is the quaternary structure of ATcase?

A

6 catalytic subunits and 6 regulatory subunits

144
Q

– is an inhibitor of ATCase

A

CTP

145
Q

Do allosteric enzymes follow Michaelis-Menten kinetics?

A

No

146
Q

UMP can be converted to

A

UTP by ATP

147
Q

UTP can be reacted with — to give –

A

Glutamine, CTP

148
Q

ATP and CTP are — of ATCase

A

heterotropic regulators

149
Q

n feedback
inhibition, a —— in a sequence
of reactions inhibits
the synthesis of ———-

A

final product, additional product

150
Q

The attachment of phosphoryl
groups (-PO3
2-
) to specific amino
acid residues of a protein is
catalyzed by

A

protein kinases

151
Q

removal of a phosphoryl
group is catalyzed by

A

protein phosphotases

152
Q

——- the most common type of regulatory modification

A

phosphorylation

153
Q

The phosphoryl group comes from

A

Atp

154
Q

An oxygen atom from the phosphoryl group may form a —– with one or multiple groups of the protein

A

hydrogen bond repeling charged amino acid residues. This disrupts protein tertiary structure

155
Q

To become an active enzyme —–must occur in chymotrypsinogen and trypsinogen

A

proteolytic cleavage

156
Q

Hydrolysis of the peptide bond between — and —

A

Arg15 and Ile16

157
Q

hydrolysis is followed by — to produce three active chymotrypsin peptide chains

A

Lys6, Ile7

158
Q

Hexokinase reaction

A

ATP + D-glucose ➔ADP + D-glucose-6-phosphate

159
Q

In the hexokinase reaction, what must ATP be bound to?

A

Mg2+

160
Q

Hexokinase undergo — upon binding of
glucose, which allows correct positioning of active site residues for catalysis

A

Induced fit

161
Q

Enolase is a glycolytic enzyme (dimer,
Mr 93,316). It catalyzes reversible
dehydration of 2-

A

2-phosphoglycerate to phosphoenolpyruvate

162
Q

In the enolase reaction, —- as as the base catalyst by removing a proton at C-2

A

Lys345

163
Q

In the enolase reaction, — acts as a acid catalyst by donating a proton to the -OH leaving group

A

Glu211

BIOCHEM (3 decks)

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