Chapter 8 Flashcards
(102 cards)
1
Q
All enzymes are proteins that:
A
- Accelerate spontaneous reactions
- Not consumed in reaction which will allow…
- Catalysis -> individual enzyme molecule can sequentially accelerate multiple rounds of reaction
- Enzymes have an active site where they bind substrates
- Stabilize substrate transition states
2
Q
Enzyme active site
A
bind substrates and bring them in proximity of each other
3
Q
Highest energy species in a reaction pathway
A
transition states
4
Q
Chemical reactions go in
A
both directions
5
Q
Non specific enzyme
A
Papain
6
Q
Specific enzyme
A
trypsin
7
Q
What group is proteases belong to
A
Hydrolase group
8
Q
Why is proteases a hydrolase
A
ass H2O to cleave molecule
9
Q
Trypsin
A
cleaves the peptide bond carboxy-terminal to K or R
10
Q
blood clotting enzyme
A
thrombin
11
Q
Thrombin is specific for the
A
R-G peptide bond
12
Q
The specificity of the enzyme is determined by
A
interaction of the substrate with the enzyme
13
Q
Cofactors
A
small molecules that are needed for a specific enzyme to be active
14
Q
inactive specific enzyme
A
apoenzyme
15
Q
active enzyme
A
holoenzyme
16
Q
Coenzymes are often derived
A
vitamins
17
Q
Groups that bind to coenzymes are called
A
prosthetic groups (e.g. heme)
18
Q
Free energy change provides information about
A
spontaneity of reaction
19
Q
∆G
A
the energy available to do work and needed to understand enzyme activity
20
Q
Energy formula for enzyme
A
∆G = G(P) - G(S)
21
Q
∆G<0
A
reaction can occur sponaneously
22
Q
Spontaneous reaction is
A
exergonic
23
Q
∆G>0
A
Endergonic
24
Q
∆G=0
A
no work is being done and system is at equilibrium
25
The rate of the reaction is related to the
energy required to initiate the chemical reaction
26
Enzymes always affect
rate of reaction, not ∆G and equilibrium
27
the free-energy difference between reactants and products accounts for t
equilibrium of the reaction
28
Enzyme does not change
equilibrium constant of the reaction
29
Uncatalyzed reactions do not
reaction velocity increase as increase substrate concentration
30
At "maximal velocity"
substrate is starting to saturate all available active sites
31
Simple enzyme with single substrate and products curve shape
hyperbolic
32
Active site contains
catalytic group including specific aa side chains and cofactors
33
Active site form
a cleft (as in lysozyme) and are not necessarily adjacent on the protein's primary structure
34
lysozyme
cleft formed from active site
35
first event in enzyme reaction
formation of an enzyme substrate complex (E +S -> ES)
36
Fischer Lock and Key
proposes that there is shape complementary between the active site and the substrate `
37
The binding of S depends on
weak forces, including hydrogen bonds, hydrophobic forces, charge
interactions, and van der Waals forces.
38
Koshland’s Induced Fit
the substrate binds, the enzyme changes shape to bind it and the substrate changes shape to bind the enzyme
39
What provides activation energy
binding specificity
40
ES compared to E+S
ES has a lower free energy state
41
Velocity formula
(-∆A/∆T) or (∆P/∆T) or k*[A]*[B]
42
k (second order rate constant) units
M-1s-1
43
A low Km implies
tight binding between E and S
44
A high Km implies
loose binding (slower reaction)
45
in general, low Km’s make better more active enzymes at
low substrate concentration
46
E+S ->ES : k?
k1
47
ES -> E+P : k?
k2
48
k-1 >> k2
Km = Kd
49
Kd
(k^-1)/(k1)
50
when k2 is small
Km is a measure of ES binding strength
51
Low Km's means
tight ES binding
52
High Km's and high Kd's means
ES binding is weak and the ES complex is likely to fall apart
53
Vmax reveals
turnover number of an enzyme
54
turnover number
number of substrate molecules converted into P by one enzyme molecule in a unit time when the enzyme is fully saturated with S
55
turnover number (kcat) =
k2
56
turnover number units
s^-1
57
Vmax =
kcat[E]t
58
concentration of active sites
[E]t
59
fraction of active sites filled f(ES)
V / (Vmax) or [S] / ([S]+Km)
60
Rates cannot be faster than
diffusion-controlled rate of encounter of an enzyme and its substrate
61
Kcat/Km cannot be over
10 E8 or 10 E9 s^-1M-1
62
Allosteric enzymes are like hemoglobin because
they have multiple sub-units, multiple active sites,
cooperative
63
Allosteric enzyme curve
"sigmoidal" curve not hyperbola
64
Michaelis-Menten kinetics do not apply to (not Km)
Allosteric enzyme
65
Michaelis constant
Km
66
Enzyme inhibitors can be
reversible and irrversible
67
Reversible inhibitors
I rapidly diffuses on and off E
68
Irreversible inhibitors
I is slowly diffusing or covalent bound to E
69
Competitive inhibitor
binds reversibly and competes for the same binding site as S
70
Competitive inhibitor effect on [ES]
lowers [ES]
71
Competitive inhibitors may bind E with binding constants that are higher or lower than S. It can overcome by
increasing [S]
72
Uncompetive inhibitor
traps the substrate in the active site to get ESI
73
In Uncompetive inhibitors, binding of I is dependent on S
cannot be overcome by increasing [S]
74
Noncompetive inhibitor
binds anywhere, but the active site, and inactivates the enzyme while still allowing substrate to bind
75
Noncompetive inhibitors has the effect of
decreasing the concentration of functional enzyme molecules
76
The effect of Noncompetive inhibitors results in
decrease turnover number and in not overcome by increased [S]
77
Ki
dissociation constant for the EI complex
78
EI -> E+I
Ki = [E] [I] / [EI]
79
whenever [I] = Ki
half of E is in the EI complex
80
When ESI is formed uncompetive inhibitors
[ES] decreases
81
UNCOMPETITIVE INHIBITORS BIND ES,
REDUCE Vmax AND KM^app
82
When more S binds to E to form ES
k1 (forward rate constant) and decreases Km
83
Inhibitor only binds as
ternary ESI complex
84
Noncompetive inhibitors E and ES
reduce Vmax (lower enzyme concentration) , but not Km
85
double-reciprocal plots distinguish
inhibitors
86
Example of competive
ibuprofen
87
Non-competive
doxycyclin lead
88
uncompetive
glphosate
89
irreversible inhibs can identify
residues in an active site
90
Group-specific reagents react with
unique targets like aa side-chains
91
Affinity label (or reactive substrate analogs)
more specific to an enzyme's active site because they resemble the enzyme's natural substrate
92
Inhibitor DIPF targets
S residue
93
Inhib TPCK targets
H residue
94
Bacterial cell walls consist of
peptidoglycan
95
Peptidoglycan is a
macro-molecule of linear polysaccharide chains that are cross-linked by short peptides
96
Short peptides that cross-link peptidoglycan
pentaglycines and tetrapeptides
97
Glycopeptide transpeptidase (TP)
catalyzes the formation of the cross-links
98
Bacterical cells walls are unique because
they contain D-amino acids which form the cross linkes
99
TP activates
D-ala polypeptide by making an acyl intermediate (Enz-Ser-OH attack) on C=O
100
TP's (Enz-Ser-OH attack) activates
carbonly C for further attack by the amino group of polyglycine to form the X-link
101
lactam ring
an amide formed with B carbon of carbonyl
102
Penicillin irreversibly inactivates
glycopeptide transpeptidase
