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BIOCH 320 > 5-enzymes A > Flashcards

5-enzymes A Flashcards

1
Q

whats a ligand

A

a bound molecule

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2
Q

what is the range of ligand types

A

from small molecules to other proteins

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3
Q

is ligand binding covalent or non covalent

A

non covalent

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4
Q

where does ligand binding occur

A

at the binding site which is complementary to ligand

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5
Q

what causes the ligand binding site to be complementary to the ligand (4, 4 (he has two slightly diff things on two slides)

A

hydrophobic interactions, van der waals, ionic interactions, h bonds

CHARGE H-BOND POLARITY SHAPE

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6
Q

is ligan binding cooperative or non cooperative

A

it can be both

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7
Q

is the curve like in non-cooperative ligand binding

A

it has a hyperbolic curve

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8
Q

is the curve like in cooperative ligand binding and why

A

sigmoidal binding curve (allostery)

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9
Q

what kind of curve for allostery

A

it is sigmoidal

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10
Q

what is Kd

A

the concentration of ligand to get 50% bound

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11
Q

what does a small Kd mean with affinity

A

greater the binding affinity of the ligand for its target

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12
Q

what does a large Kd mean with affinity

A

the more weakly the target molecule and ligand are attracted to and bind to one another

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13
Q

In presence of 5uM ni, a nickel binding protein is found to be 25% saturated with nickel (theta = 0.25). What is the value of Kd?

A

15uM

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14
Q

what do enzymes do to kinetic rate

A

increase

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15
Q

are enzymes specific

A

yes

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16
Q

what are most of enzymes made from

A

protein

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17
Q

what kind of conditions do most enzymes operate under

A

mild conditions (low temp and pressure)

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18
Q

what are some things that some enzymes require

A

cofactors

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19
Q

can enzymes be regulated

A

yes

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20
Q

what does the active site provide to enzymes

A

A favorable sequestered environment for biologically important reactions to occur

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21
Q

what are cofactors

A

additional chemical components that assist in enzyme function

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22
Q

what are 3 examples/types of cofactors

A

metal ions, coenzymes, prosthetic groups

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23
Q

what are prosthetic groups

A

metal ions or coenzymes that are tightly or covalently associated with a protein

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24
Q

what is a holoenzyme

A

enzyme+prosthetic group

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25
Q

what is an apoenzyme

A

enzyme without a prosthetic group

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26
Q

what do enzymes do to the activation energy of a reaction

A

reduce

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27
Q

what do enzymes do to the dela G of the whole reaction

A

nothing

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28
Q

what is deltadelta G

A

the reduction in deltaG by a catalyst

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29
Q

what is deltadetlaG often reffered to as

A

Binding Energy

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30
Q

what is binding energy

A

deltadeltaG of the catalyzed reaction

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31
Q

can there be more than one transition state and intermediate with reactions

A

yes

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32
Q

what determines the overall rate of the reaction

A

the rate limiting step

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33
Q

what are 2 things that the rate of reaction is related to

A

concentration of substrates and rate constate

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34
Q

what does an increase in T do to rate

A

increase

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35
Q

what does a modest change in activation energy do to rate

A

significant change (exponential)

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36
Q

what happens to k (rate constant) when you increase activation energy

A

it decreases

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37
Q

what are the 7 enzyme classes

A
  • oxidoreductases
  • transferases
  • hydrolases
  • lyases
  • isomerases
  • ligases
  • translocases
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38
Q

what class of enzyme is composed of reduction reaction

A

oxidoreductases

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39
Q

what class of enzyme is composed of oxidation reactions

A

oxidoreductase

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40
Q

what do oxidoreductases do

A

enzymes that catalyse oxido-reductions

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41
Q

what kind of enzyme is dehydrogenases

A

oxidoreductases

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42
Q

what kind of enzyme is oxidases

A

oxidoreductases

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43
Q

what kind of enzyme is reductases

A

oxidoreductases

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44
Q

what class of enzyme is composed of a group transfer

A

transferases

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45
Q

what are transferases

A

enzymes that transfer a group to another compound

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46
Q

what kind of enzyme class is a kinase

A

transferase

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47
Q

what kind of enzymes catalyse hydrolysis reactions

A

hydrolases

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48
Q

what do hydrolases do

A

catalyse hydrolysis reactions

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49
Q

which enzyme class is often named with the suffix -ase

A

hydrolases

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50
Q

what kind of enzyme class is a protease

A

hydrolases

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51
Q

what kind of enzymes cleave C-C, C-N, C-O bonds but NOT via hydrolysis or oxidation

A

lyases

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52
Q

what do lyases do

A

cleave C-C, C-N, C-O bonds but NOT via hydrolysis or oxidation

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53
Q

what enzyme class is often named the synthases

A

lyases

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54
Q

what are a common name for lyases

A

synthases

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55
Q

what is special about lyase reactions

A

in one direction of the reaction, there is one compound fewer

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56
Q

what kind of enzyme family catalyses elimination and addition reactions

A

lyases

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57
Q

what do isomerases do

A

catalyze structural rearrangements within a single molecule

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58
Q

which kind of enzymes catalyze structural rearrangements within a single molecule

A

isomerases

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59
Q

what kind of enzymatic reaction would turn a ketone into an aldehyde

A

isomerases

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60
Q

what do ligases do

A

catalyse the joining of 2 molecules or 2 parts of a molecule at the expense of a H moneluce - ATP hydrolysis

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61
Q

what is the enzymatic reaction that catalyses the joining of 2 molecules or 2 parts of a molecule at the expense of a H moneluce - ATP hydrolysis

A

ligases

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62
Q

what is required in a ligase reaction

A

a high energy molecule like ATP or GTP

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63
Q

what do translocases do

A

catalyse the movement of ions or molecules across membranes, or their seperation within membranes

64
Q

what kind of enzyme catalyse the movement of ions or molecules across membranes, or their seperation within membranes

A

translocases

65
Q

what kind of enzyme family would the Na+K+ ATPase pump be

A

translocase

66
Q

once you know these, practice with the glycolysis diagram in the notes

A

okie dokie

67
Q

what are 4 ways that enzymes lower the activation energy

A

participate in reaction
desolvation
proximity/orientation
stabolie transition state

68
Q

what are 3 ways that enzymes participate in reactions to increase reaction rate

A

(Directly or indirectly)

  • general acid/base catalysis
  • nucleophilic/covalent catalysis
  • metal ion catalysis
69
Q

how does proximity and orientation reduce activation energy

A

reduces entropy

70
Q

what is general acid base catalysis

A

proton transfer/donation to/from specific side chains in the enzyme active site

71
Q

what kind of catalysis is RNase

A

acid base

72
Q

what are the 2 ways that spontaneous alkaline hydrolysis can occur

which is more common

A

either a 2’ or 3’ nucleoside monophosphate

3’ is more common

73
Q

what does His 12 and His 119 do in RNas acid base catalysis

A

His 12 is base His119 is acid

74
Q

where do covalent bonds occur in non-covalent catalysis

A

between/within substrate molecules, not the enzyme

75
Q

where do covalent bonds occur in covalent catalysis

A

enzyme becomes covalently attached to the intermediate

76
Q

what does covalent catalysis do to the reaction pathway

A

alters the pathway!!

77
Q

will the intermediates be same in a catalyzed and an uncatalyzed reaction

A

no

78
Q

what are nucleophiles

A

anything with an appropriate lone pair

79
Q

what are 2 examples of electrophiles

A

H+ and metal ions

80
Q

what are 3 ways that metal ions can participate in catalysis

A
  • binding/orienting of substrate
  • stabilizing of transition state
  • redox centers
81
Q

what kind of catalasis happens with carbonic anhydrase

A

metalloenzyme –> metal ion catalysis

82
Q

what happens to reaction rate when the two reactive groups are spatially constrained (close together)

A

the reaction rate increases

83
Q

what are 2 ways to reduce entropy in a reaction

A

increase proximity and orientation

84
Q

what is desolvation

A

substrate binding removing the water (remove water surrounding enviro so they can interaction)

85
Q

why do you wanna do desolvation

A

when water forms a shell around many small molecules, you want to strip away the water so the groups can interact

86
Q

what is induced fit and why does it happen

A

when enzmyes change shape upon substrate binding to bring catalytic groups into orientation

87
Q

can induced fit be used to exclude water

A

yes it can

88
Q

what kind of enzyme is hexokinase (which class and why)

A

transferase because it transfers a phosphate onto substrate using ATP

89
Q

what is the hexokinase reaction a “classic example” of

A

induced fit

90
Q

is induced fit with hexokinase covalent or non covalent catalysis

A

non-covalent

91
Q

what does hexokinase do to the poshpate

A

enhances its electrophilicty

92
Q

what do the histidines do in RNase

A

act as either a general base or a general acid

93
Q

what enzyme class is RNase

A

hydrolase

94
Q

does RNase do covalent cataylsis

A

no

95
Q

what kind of enzyme class is carbonic anhydrase and why

A

lyase

reaction is H2CO3 - H2O + CO2

96
Q

what enzyme class is PEP carboxykinase

A

transferase

97
Q

what assisnts PEP carboxykinase

A

metal ion cofactors

98
Q

what is the nucleophile in the hexokinase reaction and where do they attack

A

O (from C6)from the OH attacks the PO4-

99
Q

what does hexokinase provide to the reaction / act as

A

a general base

100
Q

what in hexokinase acts as a general base

A

Asp

101
Q

what does Mg2+ do in the hexokinase mechanism

A

interacts with the negative charge

102
Q

what enhances the difference in activation energies (between catalyzed and uncatalyzed)

A

the strong interactions with transition state

103
Q

does strong interactions of enzymes with transition state enhances the difference in activation energies (between catalyzed and uncatalyzed)

A

yes

104
Q

does strong interactions of enzymes with substrate enhances the difference in activation energies (between catalyzed and uncatalyzed)

A

no, only with transition state

105
Q

what is the enzyme class of serine proteases

A

hydrolases

106
Q

what kind of catalysis is serine protease (covalent or non)

A

covalent

107
Q

what kind of catalysis is hexokinase (covalent or non)

A

non covalent

108
Q

what kind of catalysis is RNase (covalent or non)

A

non covalent

109
Q

what does serine proteases do

A

breaks a polypeptide chain, generates new N and C termina

110
Q

what do serine proteases do to transition state

A

stabilize

111
Q

what is a catalytic triad and which enzyme has this

A

3 residues that are critical in the reaction mechanisms, in serine proteases

112
Q

which residues are in the catalytic triad of serine proteases

A

His 57
Ser 195
Asp 102

113
Q

what does His 57 do

A

general acid/base

114
Q

what does Ser 195 do

A

nucleophile

115
Q

what does Asp 102 do

A

modulates His 57 (makes sure its in the right orientation and protonation state)

116
Q

what are zygomens

A

inactive precursors

117
Q

what activates zygomens

A

cleavage of the peptide chain

118
Q

what are serine proteases synthesized as

A

zygomens

119
Q

how are serine proteases activated

A

by cleavage of peptide chain

120
Q

how many domains in serine proteases and what are thet

A

2 beta barrel domains

121
Q

where is the active site in serine protease with respect to the domains

A

at the junction of the 2 beta barrel domains

122
Q

where are serine proteases located in the cell

A

extracellular

123
Q

do serine proteases have disulfides and why

A

yes because they are extracellular

124
Q

what is the “specificity pocket” in serine protease

A

a part of the active site which interacts favourably with some aa and not others - determines substrate specificity (which ones will be cleaved) so like chymotrypsin vs. trypsin vs. elastase

125
Q

which amino acid in chymotrypsin acts as the nucleophile

A

serine 195 (the OH group)

126
Q

what kind of enzyme is chymotripsin

A

a serine protease (hydrolase)

127
Q

which amino acid in chymotrypsin acts as the the general acid/base

A

His 57

128
Q

which amino acid in chymotrypsin helps maintain orientation and protonation state of His 57

A

Asp 102

129
Q 
what protonation state do you want His 57 to be in in chymotrypsin
what happens (how do you know if it is in the right state)
A

protonated

they will form an H bond with eachother

130
Q

what does the oxyanion hole do (main role)

A

transition-state stabilization

131
Q

what is a oxyanion hole

A

pocket in the active site of an enzyme that stabilizes transition state negative charge on a deprotonated oxygen

132
Q

what kind of catalysis is chymotrypsin (covalent or non)

A

covalent

133
Q

what does chymotrypsin like to cleave the most

A

cleave peptides after large hydrophobic residues

134
Q

what does trypsin like to cleave the most

A

cleave peptides after positively charged residues

135
Q

what does elastase like to cleave the most

A

cleave peptides after small non polar residues

136
Q

is the specificity pocket part of the catalytic region of the active site

A

no

137
Q

is the specificity pocket part of the active site

A

yes

138
Q

which serine protease likes to cleave after large hydrophobic residues

A

chymotripsin

139
Q

which serine protease likes to cleave after positively charged residues

A

trypsin

140
Q

which serine protease likes to cleave after small non polar residues

A

elastate

141
Q

what forms the oxyanion hole

A

backbone NH groups of residue 193 195

142
Q

is the oxyanion hole partially negative or negative

A

positive

143
Q

who can the oxyanion hole form hydrogen bond interactions with

A

negatively-charged oxygen that develops during the reaction

144
Q

what happens in the 1st step of the chymotrypsin mechanism (2 things)

A

His 57 (general base) becomes protonated, ser 195 does nucleophilic attack on substrate polypeptide

145
Q

what happens to the C=O on the substrate polypeptide after step 1 in the chymotrypsin mechanism

A

it becomes C-O- (negative)

146
Q

in step one, is His 57 a general base or acid and why

A

general base because it becomes protonated

147
Q

in step two, is His 57 a general base or acid and why

A

general acid because it loses its H+

148
Q

what happens in the 2nd step of the chymotrypsin mechanism (3 things)

A

His57 acts as a general acid, N from peptide bond in substrate becomes protonated (thats the first product)
also ser 195 becomes an acyl intermediated

149
Q

what happens in the 3rd step of the chymotrypsin mechanism (1 thing)

A

amine (first product) is released and replaced with water

150
Q

what happens in the 4th step of the chymotrypsin mechanism (2 things)

A

His 57 is a general base and takes the H from H2O

water acts as a nucleophile and attacks the carbonyl

151
Q

in step four, is His 57 a general base or acid and why

A

general base because it steals the H from water

152
Q

what happens in the 5th step of the chymotrypsin mechanism (2 things)

A

His 57 acts as a general acid (releases its H+)

generate the 2nd product (the new C terminus) and your enzyme returns to its origional state

153
Q

which step of the chymotripson mechanisms creats the new N-terminus

A

2

154
Q

which step of the chymotripson mechanisms creats the new C-terminus

A

5

155
Q

how/why does trypsin cleave after positively charged residues

A

it has an aspartate in the specificity pocket

156
Q

what is the scissile bond

A

the bond that is gonna be cleaved

157
Q

What role does a general base play in the mechanism of hexokinase?

A

It accepts a proton during nucleophilic attack of a phosphate.

BIOCH 320 (16 decks)

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