5-enzymes A Flashcards
(157 cards)
1
Q
whats a ligand
A
a bound molecule
2
Q
what is the range of ligand types
A
from small molecules to other proteins
3
Q
is ligand binding covalent or non covalent
A
non covalent
4
Q
where does ligand binding occur
A
at the binding site which is complementary to ligand
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
6
Q
is ligan binding cooperative or non cooperative
A
it can be both
7
Q
is the curve like in non-cooperative ligand binding
A
it has a hyperbolic curve
8
Q
is the curve like in cooperative ligand binding and why
A
sigmoidal binding curve (allostery)
9
Q
what kind of curve for allostery
A
it is sigmoidal
10
Q
what is Kd
A
the concentration of ligand to get 50% bound
11
Q
what does a small Kd mean with affinity
A
greater the binding affinity of the ligand for its target
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
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
14
Q
what do enzymes do to kinetic rate
A
increase
15
Q
are enzymes specific
A
yes
16
Q
what are most of enzymes made from
A
protein
17
Q
what kind of conditions do most enzymes operate under
A
mild conditions (low temp and pressure)
18
Q
what are some things that some enzymes require
A
cofactors
19
Q
can enzymes be regulated
A
yes
20
Q
what does the active site provide to enzymes
A
A favorable sequestered environment for biologically important reactions to occur
21
Q
what are cofactors
A
additional chemical components that assist in enzyme function
22
Q
what are 3 examples/types of cofactors
A
metal ions, coenzymes, prosthetic groups
23
Q
what are prosthetic groups
A
metal ions or coenzymes that are tightly or covalently associated with a protein
24
Q
what is a holoenzyme
A
enzyme+prosthetic group
25
what is an apoenzyme
enzyme without a prosthetic group
26
what do enzymes do to the activation energy of a reaction
reduce
27
what do enzymes do to the dela G of the whole reaction
nothing
28
what is deltadelta G
the reduction in deltaG by a catalyst
29
what is deltadetlaG often reffered to as
Binding Energy
30
what is binding energy
deltadeltaG of the catalyzed reaction
31
can there be more than one transition state and intermediate with reactions
yes
32
what determines the overall rate of the reaction
the rate limiting step
33
what are 2 things that the rate of reaction is related to
concentration of substrates and rate constate
34
what does an increase in T do to rate
increase
35
what does a modest change in activation energy do to rate
significant change (exponential)
36
what happens to k (rate constant) when you increase activation energy
it decreases
37
what are the 7 enzyme classes
- oxidoreductases
- transferases
- hydrolases
- lyases
- isomerases
- ligases
- translocases
38
what class of enzyme is composed of reduction reaction
oxidoreductases
39
what class of enzyme is composed of oxidation reactions
oxidoreductase
40
what do oxidoreductases do
enzymes that catalyse oxido-reductions
41
what kind of enzyme is dehydrogenases
oxidoreductases
42
what kind of enzyme is oxidases
oxidoreductases
43
what kind of enzyme is reductases
oxidoreductases
44
what class of enzyme is composed of a group transfer
transferases
45
what are transferases
enzymes that transfer a group to another compound
46
what kind of enzyme class is a kinase
transferase
47
what kind of enzymes catalyse hydrolysis reactions
hydrolases
48
what do hydrolases do
catalyse hydrolysis reactions
49
which enzyme class is often named with the suffix -ase
hydrolases
50
what kind of enzyme class is a protease
hydrolases
51
what kind of enzymes cleave C-C, C-N, C-O bonds but NOT via hydrolysis or oxidation
lyases
52
what do lyases do
cleave C-C, C-N, C-O bonds but NOT via hydrolysis or oxidation
53
what enzyme class is often named the synthases
lyases
54
what are a common name for lyases
synthases
55
what is special about lyase reactions
in one direction of the reaction, there is one compound fewer
56
what kind of enzyme family catalyses elimination and addition reactions
lyases
57
what do isomerases do
catalyze structural rearrangements within a single molecule
58
which kind of enzymes catalyze structural rearrangements within a single molecule
isomerases
59
what kind of enzymatic reaction would turn a ketone into an aldehyde
isomerases
60
what do ligases do
catalyse the joining of 2 molecules or 2 parts of a molecule at the expense of a H moneluce - ATP hydrolysis
61
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
ligases
62
what is required in a ligase reaction
a high energy molecule like ATP or GTP
63
what do translocases do
catalyse the movement of ions or molecules across membranes, or their seperation within membranes
64
what kind of enzyme catalyse the movement of ions or molecules across membranes, or their seperation within membranes
translocases
65
what kind of enzyme family would the Na+K+ ATPase pump be
translocase
66
once you know these, practice with the glycolysis diagram in the notes
okie dokie
67
what are 4 ways that enzymes lower the activation energy
participate in reaction
desolvation
proximity/orientation
stabolie transition state
68
what are 3 ways that enzymes participate in reactions to increase reaction rate
(Directly or indirectly)
- general acid/base catalysis
- nucleophilic/covalent catalysis
- metal ion catalysis
69
how does proximity and orientation reduce activation energy
reduces entropy
70
what is general acid base catalysis
proton transfer/donation to/from specific side chains in the enzyme active site
71
what kind of catalysis is RNase
acid base
72
what are the 2 ways that spontaneous alkaline hydrolysis can occur
which is more common
either a 2' or 3' nucleoside monophosphate
3' is more common
73
what does His 12 and His 119 do in RNas acid base catalysis
His 12 is base His119 is acid
74
where do covalent bonds occur in non-covalent catalysis
between/within substrate molecules, not the enzyme
75
where do covalent bonds occur in covalent catalysis
enzyme becomes covalently attached to the intermediate
76
what does covalent catalysis do to the reaction pathway
alters the pathway!!
77
will the intermediates be same in a catalyzed and an uncatalyzed reaction
no
78
what are nucleophiles
anything with an appropriate lone pair
79
what are 2 examples of electrophiles
H+ and metal ions
80
what are 3 ways that metal ions can participate in catalysis
- binding/orienting of substrate
- stabilizing of transition state
- redox centers
81
what kind of catalasis happens with carbonic anhydrase
metalloenzyme --> metal ion catalysis
82
what happens to reaction rate when the two reactive groups are spatially constrained (close together)
the reaction rate increases
83
what are 2 ways to reduce entropy in a reaction
increase proximity and orientation
84
what is desolvation
substrate binding removing the water (remove water surrounding enviro so they can interaction)
85
why do you wanna do desolvation
when water forms a shell around many small molecules, you want to strip away the water so the groups can interact
86
what is induced fit and why does it happen
when enzmyes change shape upon substrate binding to bring catalytic groups into orientation
87
can induced fit be used to exclude water
yes it can
88
what kind of enzyme is hexokinase (which class and why)
transferase because it transfers a phosphate onto substrate using ATP
89
what is the hexokinase reaction a "classic example" of
induced fit
90
is induced fit with hexokinase covalent or non covalent catalysis
non-covalent
91
what does hexokinase do to the poshpate
enhances its electrophilicty
92
what do the histidines do in RNase
act as either a general base or a general acid
93
what enzyme class is RNase
hydrolase
94
does RNase do covalent cataylsis
no
95
what kind of enzyme class is carbonic anhydrase and why
lyase
| reaction is H2CO3 - H2O + CO2
96
what enzyme class is PEP carboxykinase
transferase
97
what assisnts PEP carboxykinase
metal ion cofactors
98
what is the nucleophile in the hexokinase reaction and where do they attack
O (from C6)from the OH attacks the PO4-
99
what does hexokinase provide to the reaction / act as
a general base
100
what in hexokinase acts as a general base
Asp
101
what does Mg2+ do in the hexokinase mechanism
interacts with the negative charge
102
what enhances the difference in activation energies (between catalyzed and uncatalyzed)
the strong interactions with transition state
103
does strong interactions of enzymes with transition state enhances the difference in activation energies (between catalyzed and uncatalyzed)
yes
104
does strong interactions of enzymes with substrate enhances the difference in activation energies (between catalyzed and uncatalyzed)
no, only with transition state
105
what is the enzyme class of serine proteases
hydrolases
106
what kind of catalysis is serine protease (covalent or non)
covalent
107
what kind of catalysis is hexokinase (covalent or non)
non covalent
108
what kind of catalysis is RNase (covalent or non)
non covalent
109
what does serine proteases do
breaks a polypeptide chain, generates new N and C termina
110
what do serine proteases do to transition state
stabilize
111
what is a catalytic triad and which enzyme has this
3 residues that are critical in the reaction mechanisms, in serine proteases
112
which residues are in the catalytic triad of serine proteases
His 57
Ser 195
Asp 102
113
what does His 57 do
general acid/base
114
what does Ser 195 do
nucleophile
115
what does Asp 102 do
modulates His 57 (makes sure its in the right orientation and protonation state)
116
what are zygomens
inactive precursors
117
what activates zygomens
cleavage of the peptide chain
118
what are serine proteases synthesized as
zygomens
119
how are serine proteases activated
by cleavage of peptide chain
120
how many domains in serine proteases and what are thet
2 beta barrel domains
121
where is the active site in serine protease with respect to the domains
at the junction of the 2 beta barrel domains
122
where are serine proteases located in the cell
extracellular
123
do serine proteases have disulfides and why
yes because they are extracellular
124
what is the "specificity pocket" in serine protease
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
which amino acid in chymotrypsin acts as the nucleophile
serine 195 (the OH group)
126
what kind of enzyme is chymotripsin
a serine protease (hydrolase)
127
which amino acid in chymotrypsin acts as the the general acid/base
His 57
128
which amino acid in chymotrypsin helps maintain orientation and protonation state of His 57
Asp 102
129
```
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)
```
protonated
| they will form an H bond with eachother
130
what does the oxyanion hole do (main role)
transition-state stabilization
131
what is a oxyanion hole
pocket in the active site of an enzyme that stabilizes transition state negative charge on a deprotonated oxygen
132
what kind of catalysis is chymotrypsin (covalent or non)
covalent
133
what does chymotrypsin like to cleave the most
cleave peptides after large hydrophobic residues
134
what does trypsin like to cleave the most
cleave peptides after positively charged residues
135
what does elastase like to cleave the most
cleave peptides after small non polar residues
136
is the specificity pocket part of the catalytic region of the active site
no
137
is the specificity pocket part of the active site
yes
138
which serine protease likes to cleave after large hydrophobic residues
chymotripsin
139
which serine protease likes to cleave after positively charged residues
trypsin
140
which serine protease likes to cleave after small non polar residues
elastate
141
what forms the oxyanion hole
backbone NH groups of residue 193 195
142
is the oxyanion hole partially negative or negative
positive
143
who can the oxyanion hole form hydrogen bond interactions with
negatively-charged oxygen that develops during the reaction
144
what happens in the 1st step of the chymotrypsin mechanism (2 things)
His 57 (general base) becomes protonated, ser 195 does nucleophilic attack on substrate polypeptide
145
what happens to the C=O on the substrate polypeptide after step 1 in the chymotrypsin mechanism
it becomes C-O- (negative)
146
in step one, is His 57 a general base or acid and why
general base because it becomes protonated
147
in step two, is His 57 a general base or acid and why
general acid because it loses its H+
148
what happens in the 2nd step of the chymotrypsin mechanism (3 things)
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
what happens in the 3rd step of the chymotrypsin mechanism (1 thing)
amine (first product) is released and replaced with water
150
what happens in the 4th step of the chymotrypsin mechanism (2 things)
His 57 is a general base and takes the H from H2O
| water acts as a nucleophile and attacks the carbonyl
151
in step four, is His 57 a general base or acid and why
general base because it steals the H from water
152
what happens in the 5th step of the chymotrypsin mechanism (2 things)
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
which step of the chymotripson mechanisms creats the new N-terminus
2
154
which step of the chymotripson mechanisms creats the new C-terminus
5
155
how/why does trypsin cleave after positively charged residues
it has an aspartate in the specificity pocket
156
what is the scissile bond
the bond that is gonna be cleaved
157
What role does a general base play in the mechanism of hexokinase?
It accepts a proton during nucleophilic attack of a phosphate.
