Exam 3 Flashcards
(116 cards)
1
Q
Catalysts of biochemical reactions
A
Enzymes
2
Q
Enzymes are _________ of biochemical reactions.
A
catalysts
3
Q
What is a catalyst’s function
A
Increases the rate or velocity of a chemical reaction without being changed following the reaction
4
Q
Most biological catalysts are __________
A
Proteins
5
Q
Only exception currently known for biological catalysts
A
certain types of RNA molecules that can function as enzymes (ribozymes)
6
Q
Enzyme concentration in cells
A
Very Low
7
Q
Molecules that modulate enzyme activity
A
Effectors
8
Q
Number of known enzymes
A
Over 1 million
9
Q
Different species of organisms produce different __________ ___________ of the same enzymes
A
structural variants
10
Q
Effectors can be either …
A
Activators or Inhibitors
11
Q
Each enzyme has a
A
Specificity for a very narrow range of chemically similar substrates
12
Q
Substrates bind to the enzyme at a region of the enzyme known as the
A
Active Site
13
Q
The active site occupies
A
less than 5% of the surface area of the enzyme
14
Q
________________ in the active site determines the type of substrate molecule that can bind and react there
A
The arrangement type of amino acid R-groups
15
Q
There are usually about __ such R-groups per active site
A
5
16
Q
Non-covalently bound _______ or covalently bound ____________ are non-protein molecules associated with enzymes at or near the active site
A
Cofactors (ex. Sugars, Lipids, Nucleic Acids)
Prosthetic Groups
17
Q
Function of cofactors or prosthetic groups
A
Help to determine substrate specificity along with the enzyme’s active site
18
Q
Enzymes are named according to…
A
the type of reaction they catalyze
19
Q
Enzyme name =
A
4 integer EC number and a name
20
Q
EC
A
Enzyme Commission: a group of expert enzymologists from all over the world who come up with the rules of nomenclature
21
Q
1st integer of the EC number
A
indicates to which of the 6 major enzyme classes and enzyme belongs
22
Q
2nd integer of the EC number
A
indicates the type of bond acted on
23
Q
3rd integer of the EC number
A
indicates a subclassification of the bond type or group transferred
24
Q
4th integer of the EC number
A
serial number
25
Enzyme that catalyzes the phosphorylation of D-glucose
Hexokinase
26
Why do we have EC numbers?
So that when you publish about a specific enzyme, people can use the exact enzyme
27
Catalyzes oxidation-reduction reactions
Oxidoreductase
| A Hydrogen or electron donor is one of the substrates
28
Group Transfer A--X + B--> A + X--B
Transferase
29
Hydrolytic Cleavage of C--C, C--N, C--O, and others
Hydrolase
30
Non-hydrolytic cleavage of C--C, C--N, C--O, and others
Lyase
| Results in a double bond or the addition to a double bond
31
Molecular geometrical rearrangement
| Transfer of groups within a molecule to yield isomeric forms
Isomerase
32
Ligation (joining) of 2 molecules with accompanying hydrolysis of a high-energy bond (Condensation coupled to ATP hydrolysis)
Ligase
33
Activation energy is
the energy required for a reaction to proceed
34
Energy needed to drive a reaction
Energy Barrier
35
Binding the enzyme to the substrate ______ the activation energy
Lowers
36
If a reaction requires less energy, it is __________ to happen
more likely
37
When the enzyme binds to its substrate
Transition state
38
What is transformed into the transition state?
The substrate
39
Less energy is required for the reaction to proceed when
the substrate is in the transition state
40
The rate of a chemical reaction depends on
how efficiently the reactants can reach a transition state
| If it does it easily we will have a high rate enhancement
41
The transition state is an ____________ ___________ arrangement of atoms in which bonds are being formed or broken
Unstable energized
| Electrons are shifting when bonds are being formed and broken
42
The transition state is NOT a
reaction intermediate
Rection intermediates are stable structures formed as a result of a reaction series, so when it forms it is a stable molecule
43
Reactants are normally in the _______ ________ and have ________ potential energy for reacting
Ground State
Little
(Energy must be added to allow a reaction to occur)
44
The energy required to reach the transition state from the ground state is called the
Energy of Activation, or Activation Barrier, or Energy Barrier, or Activation Energy
45
Enzymes _______ the activation energy required to reach the transition state
Lower
46
The reaction is more likely to occur, thus the reaction rate is _______ if you lower the energy
increased
47
Circumstantial evidence comes from the use of molecules known as
Transition State Analogs
48
Stable structures that resemble the postulated (what we think) transition state structure
Transition State Analogs
49
Transition state analogs are _____ inhibitor enzymes
Powerful
50
If an enzyme has an analog stuck in the active site, the enzyme is now permanently bound to the analog and inactive, which makes the analogs such
Powerful Inhibitors
51
If we find a molecule that's an analog of our transition state and we add that analog to our substrate the enzyme is going to...
bind to that transition state analog
Structurally the enzyme believes the analog is substrate. So now nothing happens because the analog is stable (there's nothing left to happen) so the enzyme does not work.
52
The enzyme doesn't release the substrate until
the product is formed (NOT when the transition state hits)
53
How to test to see if you have the correct transition state?
Look for molecules that are stable and are similar to the proposed transition state
54
Enzymes bind to analog and are no longer able to bind which...
inhibits enzyme activity
55
Mechanisms by which enzymes increase reaction rates
Facilitation of proximity, Covalent catalyst, Acid-base catalysis, and Molecular Distortion/Strain
56
Also known as the Propinquity Effect
Facilitation of Proximity
57
Reaction rate between 2 molecules is enhanced when the enzyme removes them from dilute solution and holds them in close proximity to each other in the enzyme active site
Facilitation of Proximity
| This raises the effective concetration of reactants
58
An enzyme can increase the reaction between two molecules when...
an enzyme binds to them and takes them out of solution and holds them together
(Facilitation of Proximity)
59
A means to artificially raise reactive concentration so the reaction is faster
Facilitation of Proximity
60
Amino acids in the active site with nucleophilic R-groups attack electrophilic parts of the substrate forming covalent bonds between the enzyme and substrate
Covalent Catalyst
61
Nucleophilic groups include
COO- NH2, Aromatic OH, Histidyl groups, R-OH, S-
62
This mechanism is particularly evident in transferases (enzymes that most often use this mechanism)
Covalent Catalyst
63
Transfer of a proton in the transition state
Acid-Base Catalysis
64
Rate enhancement is only about a factor of 100 in this mechanism
Acid-Base Catalysis
65
Clu, His, Asp, Lys, Tyr, and Cys act as acid catalysts when they are protinated during this mechanism
Acid-Base Catalysis
| When unprotinated the same amino acids can act as base catalysts
66
This mechanism is dependent on pKa of the R-groups that are in the active site and on pH optimum of the enzyme
Acid-Base Catalysis
67
Strain is induced in the bond system of the reactants and the release of the strain as the transition state converts to products provides the rate enhancement
Molecular Distortion/Strain
| When the substrate is removed and converts into products
68
When the enzyme binds to the active site, strain is placed on the reactant
Molecular Distortion/Strain
69
Substrate in highly energized state, stressed state, enzyme lets go and that releases the energy in the transition state which helps push the substrate into product in this mechanism
Molecular Distortion/Strain
70
Discipline that describes the properties and characteristics of enzymes in mathematical terms
Enzyme Kinetics
71
When an enzyme is first mixed with a large excess of substrate there is an initial periods during which the concentration of ES complex builds up. It then...
finds substrate molecules and binds to them:ES
72
The enzyme complexed with the substrate
ES
73
The initial period where ES builds up is called
The pre-steady state
74
Usually too short to be easily observed
Pre-steady state
75
The reaction quickly achieves a ____________ in which the concentration of ES and the concentration of any other intermediates remains approximately constant overtime
Steady-state
76
Concerned themselves with the steady-state rate, and analysis of this type (referred to as Steady-State Kinetics)
Michaelis and Menten
77
Steady-state rate and analysis of this type
Steady-state Kinetics
78
Every time E converts S to a product, the enzyme binds to a new
substrate
79
Pioneer of science for women
Maude Menten
80
Enzyme + Substrate -->
ES--> E+P
81
E + S-->
ES k1
82
ES-->
E + S k1
83
Rate constant
k
84
The catalytic rate
Product formation rate = k2
85
Measures the number of S molecules turned over per enzyme molecules per second; number of substrates that get used for each enzyme in given time
k2
86
(Michaelis-Menton Equation) Vo=
Vmax[S] / Km + [S]
87
Every enzyme in the reaction is bound to a substrate
Enzyme saturation
| If just on enzyme wasn't bound to a substrate you would not achieve maximum product
88
Combined rate constant (Michaelis-Menten Constant)
Km
89
Total enzyme in reaction
Et
90
Maximum Velocity
Vmax
91
Initial velocity
Vo
92
k2[ES] =
Vo
93
Velocity increases with
increased substrate
94
A direct measure of _______ _________ can be judged by k2/Km
Reaction Efficiency (Enzyme Efficiency)
95
The theoretical maximum efficiency would fall between 10^8-10^9 s/mol/L assuming
every possible collision between E and S gives ES
96
Can also be directly assessed by k2/Km
Substrate specificity
97
Higher value for k2/Km if
enzyme is in solution with substrate it likes to bind with
98
Lower value for k2/Km if
Enzyme is in solution with substrate it doesn't prefer to bind with
99
Almost a zero value for k2/Km if
enzyme can't bind with substrate
100
Michaelis-menten Equation
Vo=Vmax[S]/Km + [S]
101
When Vo is 1/2 Vmax
```
Vmax/2 = Vmax [S]/ Km +[S]
Km= [S]
```
102
A direct measure of _________ _________ can be judged by k2/Km
Reaction efficiency or enzyme efficiency
103
Theoretical maximum efficiency would fall between
10^8-10^9 assuming every possible collision between enzyme and substrate gives ES
104
Can also be directly assessed by k2/Km
Substrate specificity
105
Higher value for k2/Km if enzyme is in solution with...
Substrate it likes to bind with
| It would be almost zero if it can't bind with the substrate
106
Allows for a more accurate determination of Vmax using reciprocals and does not effect Km accuracy
Double reciprocal plots
107
Most popular double reciprocal plot
Lineweaver-Burk Plot
108
Reciprocal transformation of Michaelis-Menten equation
Double reciprocal plots
109
1/[S] on x-axis and 1/Vo on y-axis
Double reciprocal plots
```
Slope = Km/Vmax
Y-int = 1/Vmax
X-int = 1/Km
```
110
Reactions that usually involve the transfer of one atom or a group from one substrate to the other substrate
Bi substrate reactions
111
2 common mechanisms for bi substrate reactions
Ternary complex formation (random and ordered binding)
| Ping-pong (aka double displacement)
112
Random or ordered binding mechanism
Ternary complex formation
113
Enzyme catalyzed before substrate comes in. Enzyme can only bind to S2 in its modified form. When enzyme binds to S2 it modifies it back to original enzyme.
Ping pong mechanism
114
Bi substrate reactions can be analyzed using
Steady state kinetics
115
Bi substrate graph with three separate starting points
Ternary complex formation
116
Bi substrate graph with parallel lines
Ping pong
