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MCB II Block 2 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

what is a catalyst

A

compound that increases the rate of a chemical reaction

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2
Q

what do catalysts do to activation free energy

A

lower it

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3
Q

name three characteristics (benefits) of enzymatic catalyst

A

accerlation under mild condition
high specificity
possibility for regulation

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4
Q

does a catalyst alter delta G

A

no

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5
Q

what does Delta G stand for

A

free energy

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6
Q

why are biocatalysis over inorganic catalysts?

A

greater reaction specificity: avoids side products
mider reaction conditions: conductive to condisionts in cells ph at 7 and 37 degrees celcius
higher reaction rates in context of biology
capacity for regulation: control of biological pathways

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7
Q

metabolites have many potential

A

pathways

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8
Q

what do enzymes do regarding the many potential pathways of metabolites

A

they provide direction - they tell them where to go

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9
Q

enzymes organize reactive groups into

A

close proximity and proper orientation

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10
Q

what is entropy

A

range of freedom of substrate

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11
Q

free energy has what two components

A

entropy & enthalpy

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12
Q

what is enthalpy

A

a thermodynamic quantity equivalent to the total heat content of a system. It is equal to the internal energy of the system plus the product of pressure and volume.

results in heat

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13
Q

uncatalyzed biomolecular recations are entropically unfavorable or favorable

A

unfavorable

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14
Q

uncatalyzed unimolecular reactions are entropically unfavorable or favorable

A

unfavorable

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15
Q

describe uncatalyzed biomolecular reactions

A

two free reactants single restricted transition state conversion is entropically unfavorable.
can look up more what this means

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16
Q

describe uncatalyzed unimolecular reactions

A

Flexible reactant → rigid transition state conversion is entropically unfavorable for flexible reactants.

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17
Q

when is the entropy cost paid during catalyed reaction

A

binding

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18
Q

look at how to lower delta G

A

Enzymes decrease the Gibbs free energy of activation, but they have no effect on the free energy of reaction.
Enzymes work by lowering the activation energy (Ea
or ΔG✳) for a reaction. This increases the reaction rate.

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19
Q

how do you lower delta G

A

with catalyst

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20
Q

enzymes bind what state best

A

transition state

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21
Q

enzyme active sites are _____ to the transition state of the reaction

A

complimentary

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22
Q

enzymes bind ______ _____ better than substrates

A

transition states

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23
Q

delta H stands for

A

chagne in enthalpy

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24
Q

understand the graph and slide on pg 8

A

look up in biochem book for add’l help

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25
Q

coupling reactions with ATP does what

A

makes it much lower energy - s omakes delta G much lower, and reaction s proceed more and with less energy

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26
Q

can the enzyme actually change delta G

A

no

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27
Q

acid-base catalysis

A

give and take protons

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28
Q

covalent catalysis:

A

change reaction paths

think nucleophilic catalysis

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29
Q

metal ion catalysis:

A

use redox cofactors, pKa shifters

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30
Q

what is hydroxide in water

A

10^-7

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31
Q

look up acid-base catalysis in biochem book and youtube

A

pg 10

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32
Q

in covalent catalysis what happens

A

form covalent bond b/w enzyme and substrate

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33
Q

draw the reaction pathway for uncatalyzed and catalyzed covalent catalysis

A

pg 12

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34
Q

covalent catalysis required what on the enzyme

A

nucloephile

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35
Q

what are example nucleophiles taht can be on enzye for covalent catalysis

A

can be a reactive serine, thiolate, amine, or carboxylate

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36
Q

metal ion catalysis involves a what bound to enzyme

A

metal ion

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37
Q

metal ion stabilizes

A

negative charge

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38
Q

what kind of reaction does metal ion catalysis participate in

A

oxidation reactions

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39
Q

by breaks down small peptides

A

proteases

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40
Q

what does chymotrypsin do

A

breaks peptide bonds that contain aromatic amino acids. more generally, ,it cuts peptides at specific locations on the peptide backbone

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41
Q

show what kind of bond chymotrypsin cuts

A

pg 14

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42
Q

in chymotrypsin reactions they are

A

oxidized

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43
Q

chymptrypsin uses what enzymatic mechanisms

A

most of them

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44
Q

Asp102, His57, Ser195 are referred to as

A

triad

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45
Q

what is step one of the chymotrypsin mechanism

A

substrate binding

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46
Q

how does substrate bind in first ste pof chymotrypsin mechanism

A

Hydrolytic cleavage of a peptide bond by chymotrypsin.

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47
Q

draw out or at least underestand step one of chymotrypsin mechanism

A

pg 16

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48
Q

what is the second step of chymotrypsin mechanism

A

nucleophilic attack

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49
Q

look at/draw/understand the second step of chymotrypsin mechanism

A

pg 17

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50
Q

what is step three of chymotrypsin mechanism

A

substrate cleavage

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51
Q

draw out/understand step 3 of chymotrypsin mechanism

A

pg 18

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52
Q

what is step four of chmotrypsin mechanism

A

water comes in

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53
Q

draw out/understand the fourth step of water coming in for chymotrypsin mechanism

A

pg 19

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54
Q

what is step five of chymotrypsin mechanism

A

water attacks

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55
Q

draw out/understand water attack -s tep 5 of chymotrypsin mechanism

A

pg 20

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56
Q

what is step 6 of chymotrypsin mechanism

A

break off from enzyme

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57
Q

draw out/understand the 6th step of chymotrypsin mechanism

A

pg 21

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58
Q

what is step 7 of chymotrypsin mechanism

A

product dissociates

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59
Q

draw out understand the 7th step of chymotrypsin mechanism

A

pg 22

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60
Q

list the main reaction mechanisms

A 
Most reactions fall within a few categories: 
Cleavage and formation of C–C bonds
Cleavage and formation of polar bonds
nucleophilic substitution mechanism
     addition–elimination mechanism
     hydrolysis and condensation reactions
Internal rearrangements
Eliminations (without cleavage)
Group transfers (H+, CH3+, PO32–)
Oxidations-reductions (e– transfers)
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61
Q

draw example of nucleophilic carbon-carbon bond formation

A

pg 25

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62
Q

draw example of addition-elimination reaction

A

pg 26

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63
Q

in isomerizations and eliminations there is no change in

A

oxidation state

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64
Q

draw out isomerization and elimination

A

pg 27

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65
Q

what are the two types of interaction b/w enzyme and substrate

A

Specificity: lock-and-key model

Specificity: induced fit

66
Q

what is included in complementary in lock and key model

A

size
shape
charge
hydrophobic/hydrophilic character

67
Q

describe induced fit

A

interaction induces conformational change (they do not fit together right in first interaction) and then they fit together after they have the conformational change

68
Q

in steady state, rate of formation =

A

rate of breakdown

69
Q

total enzyme concentration is

A

constant

70
Q

what is the mass balance equation for enzymes

A

Etot = [E] + [ES]

71
Q

Stot =

A

[S] + [ES]

72
Q

what does S stand for

A

substrate

73
Q

what is steady state assumption

A

concentration of substrate doesn’t change over time

74
Q

rate of formation of ES - rate of breakdown of ES =

A

0

75
Q

Kcat is?

A

constant for catalysis

76
Q

km =

A

k-1/k1

77
Q

km is important why

A

affinity of enzyme for substrate

78
Q

if Km is very high what does it mean

A

enzyme has low affinity for substrate

79
Q

if km is very low what does it mean

A

enzyme has high affinity for substrate

80
Q

write out the michaelis-menten equation

A

v = kcat [Etot][S]\Km +[S] = Vmax[S]/Km + [S]

81
Q

what is the turnover number

A

kcat

82
Q

what does Kcat stand for

A

how many substrate molecules one enzyme molecule can convert per second

83
Q

what is michaelis constant

A

km

84
Q

what does Km stand for

A

an approximate measure of a substrate’s affinity for an enzyme

85
Q

during steady state, maxium velocity occurs when?

A

all of the enzyme is in the ES complex and is dependent on the breakdown of that complex (k[ES])

86
Q

what does Vmax stand for

A

maximum velocity

87
Q

microscopic meaning of km and kcat depend on what

A

details of the mechanism

88
Q

small km for an enzyme reflects what

A

high affinity of enzyme for substrate

89
Q

large km for an enzyme reflects what

A

low affinity of enzyme for substrate

90
Q

below km the velocity of the reaction is most sensitive to what

A

changes in [S]

91
Q

if there is a mutation that reduces affinity for substrate, it does what to km?
what is needed to move reaction forward

A

increases km

higher [S] is needed to move reaction toward vmax

92
Q

does km vary with concentration of enzyme?

A

no

93
Q

describe what km means on the graph, esp in terms of velocity

A

Substrate concentration at which the initial reaction velocity is equal to ½ Vmax

94
Q

what is the linear equation that is modification of michaelis-menten

A

1/v0 = km/Vmax[S] + 1/Vmax

95
Q

why is it beneficial to have the linear graph of km vs. the hyperbolic

A

linear graph gives exact number for substrate concentrations and vmax, etc. the hyperbolic wouldn’t always give exact numbers, hard to tell when graph is curving

96
Q

what is the function of the linear modification of michaelis-menten aka what can you determine

A

km and vmax and can determine mechanism of action of enzyme inhibitors

97
Q

biotin is

A

vitamin

98
Q

avidin is

A

protein

99
Q

if you eat a lot of avidin you will have what deficiency

A

biotin (the avidin and biotin have high affinity, so they will bind and then the body can’t use the biotin)

100
Q

if you eat a lot of raw eggs you have a lot of

A

avidin

101
Q

at very high concentrations v0=

A

vmax

102
Q

at high concentrations of substrate, then concentration of substrate is much higher than

A

km

103
Q

what is zero order rxn

A

rxn doesn’t depend on concentration of substrate

104
Q

what factors affect reaction velocity

A

temperature
higher concentration of reactants
variable optimal pH

105
Q

inhibitors are compounds that do what

A

decrease enzyme’s activity

106
Q

what is irreversible inhibitors

A

one inhibitor molecule can permanently shut off one eynzyme molecule

107
Q

what are examples of irreversible inhibitors

A

powerful toxins

drugs

108
Q

what are reversible inhibitors

A

bind to enzyme and then can detatch.

often structural analogs of substrates or products

109
Q

what are examples of reversible inhibitors

A

drugs → slow down specific enzyme

110
Q

what can reversible inhibitor bind to

A

the free enzyme and prevent the binding of the substrate

the enzyme-substrate complex and prevent the reaction.

111
Q

aspirin is an

A

inhibitor

112
Q

when there is competitive inhibiton what happens to km

A

increases

113
Q

with competitive inhibition what happens to vmax

A

no change

114
Q

does competitive inhibition affect catalysis

A

no

115
Q

where does competitive inhibitor bind

A

active site - competitively binds

116
Q

draw cartoon of competitive inhibition

A

pg 40

117
Q

understand lineweaver-burk graph

A

lines intersect at y axis

pg 40

118
Q

what is affect on noncompettitive inhibition on vmax

A

decrease vmax

119
Q

what is noncompetitive inhibition affect on km

A

no affect

120
Q

what do you use to analyze noncompetitive inhibition

A

Lineweaver-Burk plot:

121
Q

draw graph of no inhibitor vs. noncompetitive inhibitior

A

pg 41

122
Q

where does non compettiive inhibitor bind

A

to active site or anther site on the enzyme

it inactivates the enzyme

123
Q

how can enzyme activity be regulated in body

A 
noncovalent modification (allosteric)
covalent modification - irreversible or reversible
124
Q

Allosteric effectors or modulators are generally

A

small chemicals

125
Q

what is an allosteric effector

A

Binding of a ligand to one site affects the binding properties of a different site on the same protein

126
Q

what are the two kinds of allosteric effects

A

homotropic

heterotropic

127
Q

what is homotropic

A

The normal ligand of the protein is the allosteric regulator.

128
Q

what is heterotropic

A

A different ligand affects binding of the normal ligand

129
Q

sigmoidal curve

A

fusion of low and high affinity

130
Q

what are zymogens

A

proteins that are invactive

131
Q

how are zymogens actiated

A

irreversible covalent modification

132
Q

What is delta G

A

the energy required to overcome the activation barrier

133
Q

enzymes catalyze reactions by lowering

A

activation barrier

134
Q

enzymes bind what better than substrates

A

transition states

135
Q

what does trypsin cleave

A

arginine & lysine

136
Q

in acute pancreatitis & cystic fibrosis there will be elevated levels of what in blood

A

trypsin & trypsinogen

137
Q

immunoreactive trypsinogen is used for screening for

A

cystic fibrosis

138
Q

what does chymotrypsin cleave

A

aromatic a.a.

leucine

139
Q

what is chymotrypsin used for medically

A

digestion

treats soft tissue injuries, sprains, sport injuries

140
Q

alpha1 antitrypsin protects lungs from

A

elastase

141
Q

what is used to treat pancreatic insufficiency

A

trypsin, chymotrypsin, carboxypeptidase

142
Q

V =

A

vmax [S]/km +S

143
Q

in equation V = vmax [S]/km +S if S is very high, what can you do

A

ignore km - it will be so low it is insignificant

144
Q

draw graph V = vmax [S]/km +S vs. Vo= Vmax

A

pg 36

145
Q

COX is responsible for

A

inflammation, pain, coagulation

146
Q

how does asprin work?

A

acetylates COX which irreversibly inactivates it

147
Q

what part of COX is acetylated

A

serine

148
Q

what does NSAID stand for

A

non-steroidal anti inflammatory drug

149
Q

HMG makes

A

cholesterol

150
Q

how does pravastatin work

A

competitive inhibitor for HMG - stops it from making cholesterol

151
Q

what is Km

A

concentration of substrate that produces half the Vmax

152
Q

competitive inhibitor vs. noncompetatitive inhibitor and how they affect km and vmax

A

competitive: no change in Vmax, increase in Km
noncompetitive: no change in Km, decrease in Vmax

153
Q

name reversible covalent modifications

A 
phosphorylation
adenylation
acetylation
myristoylation
ubiquitination
ADP-ribosylation
methylation
154
Q

draw out adenylation

A

pg 46

155
Q

draw out acetylation

A

pg 46

156
Q

draw out myristolylation

A

pg 46

157
Q

draw out uniquitination

A

pg 46

158
Q

draw out ADP-ribosylation

A

pg 46

159
Q

draw out methylation

A

pg 46

160
Q

polypeptide chains of chymotrypsin are linked by

A

disulfide bonds

161
Q

blood coagulation cascade uses irreversible

A

covalent modification

MCB II Block 2 (10 decks)

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