Enzymes Flashcards
(161 cards)
1
Q
what is a catalyst
A
compound that increases the rate of a chemical reaction
2
Q
what do catalysts do to activation free energy
A
lower it
3
Q
name three characteristics (benefits) of enzymatic catalyst
A
accerlation under mild condition
high specificity
possibility for regulation
4
Q
does a catalyst alter delta G
A
no
5
Q
what does Delta G stand for
A
free energy
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
7
Q
metabolites have many potential
A
pathways
8
Q
what do enzymes do regarding the many potential pathways of metabolites
A
they provide direction - they tell them where to go
9
Q
enzymes organize reactive groups into
A
close proximity and proper orientation
10
Q
what is entropy
A
range of freedom of substrate
11
Q
free energy has what two components
A
entropy & enthalpy
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
13
Q
uncatalyzed biomolecular recations are entropically unfavorable or favorable
A
unfavorable
14
Q
uncatalyzed unimolecular reactions are entropically unfavorable or favorable
A
unfavorable
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
16
Q
describe uncatalyzed unimolecular reactions
A
Flexible reactant → rigid transition state conversion is entropically unfavorable for flexible reactants.
17
Q
when is the entropy cost paid during catalyed reaction
A
binding
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.
19
Q
how do you lower delta G
A
with catalyst
20
Q
enzymes bind what state best
A
transition state
21
Q
enzyme active sites are _____ to the transition state of the reaction
A
complimentary
22
Q
enzymes bind ______ _____ better than substrates
A
transition states
23
Q
delta H stands for
A
chagne in enthalpy
24
Q
understand the graph and slide on pg 8
A
look up in biochem book for add’l help
25
coupling reactions with ATP does what
makes it much lower energy - s omakes delta G much lower, and reaction s proceed more and with less energy
26
can the enzyme actually change delta G
no
27
acid-base catalysis
give and take protons
28
covalent catalysis:
change reaction paths
| think nucleophilic catalysis
29
metal ion catalysis:
use redox cofactors, pKa shifters
30
what is hydroxide in water
10^-7
31
look up acid-base catalysis in biochem book and youtube
pg 10
32
in covalent catalysis what happens
form covalent bond b/w enzyme and substrate
33
draw the reaction pathway for uncatalyzed and catalyzed covalent catalysis
pg 12
34
covalent catalysis required what on the enzyme
nucloephile
35
what are example nucleophiles taht can be on enzye for covalent catalysis
can be a reactive serine, thiolate, amine, or carboxylate
36
metal ion catalysis involves a what bound to enzyme
metal ion
37
metal ion stabilizes
negative charge
38
what kind of reaction does metal ion catalysis participate in
oxidation reactions
39
by breaks down small peptides
proteases
40
what does chymotrypsin do
breaks peptide bonds that contain aromatic amino acids. more generally, ,it cuts peptides at specific locations on the peptide backbone
41
show what kind of bond chymotrypsin cuts
pg 14
42
in chymotrypsin reactions they are
oxidized
43
chymptrypsin uses what enzymatic mechanisms
most of them
44
Asp102, His57, Ser195 are referred to as
triad
45
what is step one of the chymotrypsin mechanism
substrate binding
46
how does substrate bind in first ste pof chymotrypsin mechanism
Hydrolytic cleavage of a peptide bond by chymotrypsin.
47
draw out or at least underestand step one of chymotrypsin mechanism
pg 16
48
what is the second step of chymotrypsin mechanism
nucleophilic attack
49
look at/draw/understand the second step of chymotrypsin mechanism
pg 17
50
what is step three of chymotrypsin mechanism
substrate cleavage
51
draw out/understand step 3 of chymotrypsin mechanism
pg 18
52
what is step four of chmotrypsin mechanism
water comes in
53
draw out/understand the fourth step of water coming in for chymotrypsin mechanism
pg 19
54
what is step five of chymotrypsin mechanism
water attacks
55
draw out/understand water attack -s tep 5 of chymotrypsin mechanism
pg 20
56
what is step 6 of chymotrypsin mechanism
break off from enzyme
57
draw out/understand the 6th step of chymotrypsin mechanism
pg 21
58
what is step 7 of chymotrypsin mechanism
product dissociates
59
draw out understand the 7th step of chymotrypsin mechanism
pg 22
60
list the main reaction mechanisms
```
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)
```
61
draw example of nucleophilic carbon-carbon bond formation
pg 25
62
draw example of addition-elimination reaction
pg 26
63
in isomerizations and eliminations there is no change in
oxidation state
64
draw out isomerization and elimination
pg 27
65
what are the two types of interaction b/w enzyme and substrate
Specificity: lock-and-key model
Specificity: induced fit
66
what is included in complementary in lock and key model
size
shape
charge
hydrophobic/hydrophilic character
67
describe induced fit
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
in steady state, rate of formation =
rate of breakdown
69
total enzyme concentration is
constant
70
what is the mass balance equation for enzymes
Etot = [E] + [ES]
71
Stot =
[S] + [ES]
72
what does S stand for
substrate
73
what is steady state assumption
concentration of substrate doesn't change over time
74
rate of formation of ES - rate of breakdown of ES =
0
75
Kcat is?
constant for catalysis
76
km =
k-1/k1
77
km is important why
affinity of enzyme for substrate
78
if Km is very high what does it mean
enzyme has low affinity for substrate
79
if km is very low what does it mean
enzyme has high affinity for substrate
80
write out the michaelis-menten equation
v = kcat [Etot][S]\Km +[S] = Vmax[S]/Km + [S]
81
what is the turnover number
kcat
82
what does Kcat stand for
how many substrate molecules one enzyme molecule can convert per second
83
what is michaelis constant
km
84
what does Km stand for
an approximate measure of a substrate’s affinity for an enzyme
85
during steady state, maxium velocity occurs when?
all of the enzyme is in the ES complex and is dependent on the breakdown of that complex (k[ES])
86
what does Vmax stand for
maximum velocity
87
microscopic meaning of km and kcat depend on what
details of the mechanism
88
small km for an enzyme reflects what
high affinity of enzyme for substrate
89
large km for an enzyme reflects what
low affinity of enzyme for substrate
90
below km the velocity of the reaction is most sensitive to what
changes in [S]
91
if there is a mutation that reduces affinity for substrate, it does what to km?
what is needed to move reaction forward
increases km
| higher [S] is needed to move reaction toward vmax
92
does km vary with concentration of enzyme?
no
93
describe what km means on the graph, esp in terms of velocity
Substrate concentration at which the initial reaction velocity is equal to ½ Vmax
94
what is the linear equation that is modification of michaelis-menten
1/v0 = km/Vmax[S] + 1/Vmax
95
why is it beneficial to have the linear graph of km vs. the hyperbolic
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
what is the function of the linear modification of michaelis-menten aka what can you determine
km and vmax and can determine mechanism of action of enzyme inhibitors
97
biotin is
vitamin
98
avidin is
protein
99
if you eat a lot of avidin you will have what deficiency
biotin (the avidin and biotin have high affinity, so they will bind and then the body can't use the biotin)
100
if you eat a lot of raw eggs you have a lot of
avidin
101
at very high concentrations v0=
vmax
102
at high concentrations of substrate, then concentration of substrate is much higher than
km
103
what is zero order rxn
rxn doesn't depend on concentration of substrate
104
what factors affect reaction velocity
temperature
higher concentration of reactants
variable optimal pH
105
inhibitors are compounds that do what
decrease enzyme's activity
106
what is irreversible inhibitors
one inhibitor molecule can permanently shut off one eynzyme molecule
107
what are examples of irreversible inhibitors
powerful toxins
| drugs
108
what are reversible inhibitors
bind to enzyme and then can detatch.
| often structural analogs of substrates or products
109
what are examples of reversible inhibitors
drugs → slow down specific enzyme
110
what can reversible inhibitor bind to
the free enzyme and prevent the binding of the substrate
the enzyme-substrate complex and prevent the reaction.
111
aspirin is an
inhibitor
112
when there is competitive inhibiton what happens to km
increases
113
with competitive inhibition what happens to vmax
no change
114
does competitive inhibition affect catalysis
no
115
where does competitive inhibitor bind
active site - competitively binds
116
draw cartoon of competitive inhibition
pg 40
117
understand lineweaver-burk graph
lines intersect at y axis
| pg 40
118
what is affect on noncompettitive inhibition on vmax
decrease vmax
119
what is noncompetitive inhibition affect on km
no affect
120
what do you use to analyze noncompetitive inhibition
Lineweaver-Burk plot:
121
draw graph of no inhibitor vs. noncompetitive inhibitior
pg 41
122
where does non compettiive inhibitor bind
to active site or anther site on the enzyme
| it inactivates the enzyme
123
how can enzyme activity be regulated in body
```
noncovalent modification (allosteric)
covalent modification - irreversible or reversible
```
124
Allosteric effectors or modulators are generally
small chemicals
125
what is an allosteric effector
Binding of a ligand to one site affects the binding properties of a different site on the same protein
126
what are the two kinds of allosteric effects
homotropic
| heterotropic
127
what is homotropic
The normal ligand of the protein is the allosteric regulator.
128
what is heterotropic
A different ligand affects binding of the normal ligand
129
sigmoidal curve
fusion of low and high affinity
130
what are zymogens
proteins that are invactive
131
how are zymogens actiated
irreversible covalent modification
132
What is delta G
the energy required to overcome the activation barrier
133
enzymes catalyze reactions by lowering
activation barrier
134
enzymes bind what better than substrates
transition states
135
what does trypsin cleave
arginine & lysine
136
in acute pancreatitis & cystic fibrosis there will be elevated levels of what in blood
trypsin & trypsinogen
137
immunoreactive trypsinogen is used for screening for
cystic fibrosis
138
what does chymotrypsin cleave
aromatic a.a.
| leucine
139
what is chymotrypsin used for medically
digestion
| treats soft tissue injuries, sprains, sport injuries
140
alpha1 antitrypsin protects lungs from
elastase
141
what is used to treat pancreatic insufficiency
trypsin, chymotrypsin, carboxypeptidase
142
V =
vmax [S]/km +S
143
in equation V = vmax [S]/km +S if S is very high, what can you do
ignore km - it will be so low it is insignificant
144
draw graph V = vmax [S]/km +S vs. Vo= Vmax
pg 36
145
COX is responsible for
inflammation, pain, coagulation
146
how does asprin work?
acetylates COX which irreversibly inactivates it
147
what part of COX is acetylated
serine
148
what does NSAID stand for
non-steroidal anti inflammatory drug
149
HMG makes
cholesterol
150
how does pravastatin work
competitive inhibitor for HMG - stops it from making cholesterol
151
what is Km
concentration of substrate that produces half the Vmax
152
competitive inhibitor vs. noncompetatitive inhibitor and how they affect km and vmax
competitive: no change in Vmax, increase in Km
noncompetitive: no change in Km, decrease in Vmax
153
name reversible covalent modifications
```
phosphorylation
adenylation
acetylation
myristoylation
ubiquitination
ADP-ribosylation
methylation
```
154
draw out adenylation
pg 46
155
draw out acetylation
pg 46
156
draw out myristolylation
pg 46
157
draw out uniquitination
pg 46
158
draw out ADP-ribosylation
pg 46
159
draw out methylation
pg 46
160
polypeptide chains of chymotrypsin are linked by
disulfide bonds
161
blood coagulation cascade uses irreversible
covalent modification
