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Protein and Nucleic acid > Mechanism of Enzyme Action > Flashcards

Mechanism of Enzyme Action Flashcards

1
Q

a species inter-mediate in structure
between S and P

A

Transition State

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2
Q

TRUE OR FALSE
the enzymatic rate enhancement is
approximately not equal to the ratio of
the dissociation constants of the E-S
and E- transition-state complexes, at
least when E is saturated with S

A

False (Equal)

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3
Q

TRUE OR FALSE
the E must stabilize the Substrate complex, EX‡, more than it stabilizes the Transition State Complex, ES

A

False (transition state complex, substrate complex)

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4
Q

ensures the favorable formation of
the ES complex

A

(triangle)Gb (Intrinsic binding)

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5
Q

Gb is partially compensated by
Blank due to the binding of E
and S (TS) and by Blank
(Gd) by strain, distortion, desolvation,
and similar effects

A

entropy loss, destabilization of ES

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6
Q

TRUE OR FALSE
the smaller the difference in
energies between ES and EX‡, the
Slower the E-catalyzed reaction

A

False (faster)

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7
Q

Blank of the substrate
deepens the energy well of the ES
complex and actually lowers the
rate of the reaction

A

tight binding

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8
Q

can involve structural strain, desolvation,
or electrostatic effects

A

destabilization of the ES complex

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9
Q

a consequence of the fact that the E
is designed to bind the transition
state more strongly than the S

A

Destabilization by strain or distortion

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10
Q

E bind the transition-state structure
more tightly than the Blank

A

S (or the P)

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11
Q

How Destabilization of the E-S
Complex Affect Enzyme Catalysis?

A

Destabilization of the enzyme-substrate (E-S) complex enhances enzyme catalysis by preventing overly stable binding. When the E-S complex is less stable, the energy difference between it and the transition state is reduced, lowering the activation energy required for the reaction. This promotes the formation of the transition state and increases the overall reaction rate. By binding the substrate with moderate affinity, the enzyme facilitates a smoother transition to the enzyme-transition state complex, improving catalytic efficiency.

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11
Q

How is it that the transition state X‡
is stabilized more than S at the E
active site?

A

The favorable interactions between the substrate (S) and the amino acid (AA) residues on the enzyme (E) contribute to the intrinsic binding energy, #Gb..

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12
Q

TRUE OR FALSE
solvation of charged groups on a
substrate in solution releases
energy, making the charged
substrate more unstable

A

False (Stable)

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13
Q

if the charge on the S is diminished or lost in the course of reaction, electrostatic destabilization can result
in Blank

A

rate acceleration

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14
Q

when a S enters the active site,
charged groups may be forced to
interact (unfavorably) with charges of like sign, resulting in Blank

A

electrostatic destabilization

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15
Q
  • a “moving target”
  • exists for about 10-14 to 10-13 s
A

transition state

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16
Q

electrostatic destabilization of a substrate may arise from Blank of like charges in the active site

A

juxtaposition

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17
Q

if such charge repulsion is relieved in the course of the reaction, electrostatic destabilization can
result in a Blank

A

rate increase

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18
Q

pyrrole-2-carboxylate binds to pro racemase Blank more tightly
than L-proline, the normal S

A

160 x

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19
Q

TRUE OR FALSE
dihydroxyacetone phosphate binds 40,000 times more tightly to
yeast aldolase than the substrate Phosphoglycolohydroxamate.

A

False (Phosphoglycolohydroxamate binds 40,000 times more tightly to
yeast aldolase than the substrate dihydroxyacetone phosphate.)

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20
Q

Blank of purine ribonucleoside has been estimated to bind to adenosine deaminase with a KI of 3 x 10-13 M

A

1,6-hydrate

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21
Q

What are the Mechanism of Catalysis ?

A
  1. Near-Attack Conformations (NACs)
  2. Protein Motions
  3. Covalent Catalysis
  4. General acid-base catalysis
  5. Low-Barrier Hydrogen Bonds (LBHB)
  6. Quantum Mechanical Tunneling in Electron and Proton Transfers
  7. Metal ion Catalysis
  8. Noncatalytic Residues
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22
Q
  • the reacting atoms are in van der
    Waals contact and at an angle
    resembling the bond to be formed
    in the transition state
A

Near-Attack Conformations (NACs)

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23
Q

in the absence of an E, potential
reactant molecules adopt a NAC
only about Blank of the time

A

0.0001%

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23
Q

NACs have been shown to form in E
active sites from Blank to blank of the
time

A

1% to 70%

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24
Q
  • proteins are constantly moving
  • bonds vibrate, side chains bend and
    rotate, backbone loops wiggle and
    sway, and whole domains move
    with respect to each other
  • E depend on such motions to
    initiate and direct catalytic events
A

Protein motions

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25
Q

Protein motions may support catalysis
in several ways. Active site
conformation changes can (5)

A
  • assist substrate binding
  • bring catalytic groups into position
    around a substrate
  • induce formation of a NAC
  • assist in bond making and bond
    breaking
  • facilitate conversion of S to P
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26
Q

acceptor group on the E must be a
better attacking group than Y and a
better leaving group than X

A

Covalent catalysis

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27
Q

formation of covalent bonds
between E and S

A

BX + Y → BY + X

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28
Q

enzymatic version

A

BX + Enz → E:B + X + Y → Enz + BY
covalent intermediate

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29
Q

readily attack electrophilic centers of S,
forming covalently bonded E-S
intermediates

A

nucleophilic centers for catalysis

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30
Q

what are the side chains of AA in proteins?

A

✓ amines
✓ carboxylates
✓ aryl and alkyl hydroxyls
✓ imidazoles
✓ thiol groups

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31
Q
  • a proton is transferred in the
    transition state
  • may increase reaction rates 10- to
    100-fold
A

general acid-base catalysis

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32
Q

is often the most effective
general acid or base because the pKa
of the histidine side chain is near 7

A

histidine

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33
Q
  • when the barrier-to-hydrogen
    exchange has dropped to the point
    that it is at or below the zero point
    energy level of hydrogen
A

Low-Barrier Hydrogen Bonds (LBHB)

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34
Q

the stabilization energy of LBHBs
may approach Blank in the gas
phase and Blank or more in
solution

A

100 kJ/mol, 60 kJ/mol

35
Q

TRUE OR FALSE
as the two pKa values diverge, the
stabilization energy of the LBHB is
increased

A

False (decreased)

36
Q

a Blank in an enzyme ground
state may become an LBHB in a
transient intermediate, or even in the
transition state for the reaction

A

weak H bond

37
Q
  • if an atom or electron is transferred in a
    chemical reaction from one site to
    another across an activation barrier,
    there is a finite probability that the
    particle will appear (as part of theP) on
    the other side of the energy barrier,
    even though it cannot achieve sufficient
    energy to reach the transition state
A

quantum theory

38
Q

What are the 2 Metal Ion Catalysis?

A
  1. Metalloenzyme
  2. Metal Activated
39
Q
  • if the E binds the metal very tightly
    or requires the metal ion to
    maintain its stable, native state
A

metalloenzyme

39
Q
  • E that bind metal ions more weakly,
    perhaps only during the catalytic
    cycle
A

metal activated

40
Q

is an endoprotease (it cleaves polypeptides in the middle of the chain) with a catalytic Zn2+
ion in the active site

A

Thermolysin

40
Q

Role of a metal includes act as Blank, stabilizing the increased e- density
or (-) charge that can develop
during rxn

A

electrophilic catalysts

41
Q

coordination to a metal ion can
increase the Blank of a nucleophile
w/ an ionizable proton

A

acidity

42
Q
  • raising or lowering catalytic residue
    pKa values through electrostatic or
    hydrophobic interactions
  • orientation of catalytic residues
  • charge stabilization
  • proton transfers via hydrogen
    tunneling
A

Noncatalytic residues

43
Q

What are the 2 roles of metal?

A
  1. Act as electrophilic catalysts, stabilizing the increased e- density or (-) charge that can develop during reaction.
  2. Provide a powerful nucleophile at neutral pH.
44
Q
  • a class of proteolytic enzymes
    whose catalytic mechanism is based
    on an active-site serine residue
A

Serine Proteases

45
Q

What are the 3 digestive enzymes?

A
  1. Trypsin
  2. Chymotrypsin
  3. Elastase
46
Q

Blood-clotting enzyme

A

Thrombin

46
Q

Bacterial Protease

A

Subtilisin

47
Q

Breaks down the fibrin polymers of blood clots

A

Plasmin

48
Q
  • cleaves the proenzyme
    plasminogen, yielding plasmin
  • minimizes the harmful
    consequences of a heart attack, if
    administered to a patient w/in 30
    min of onset
A

tissue plasminogen activator (TPA)

49
Q
  • a serine esterase and is related
    mechanistically to the serine
    proteases
  • degrades the neurotransmitter
    acetylcholine in the synaptic cleft
    between neurons
A

Acetylcholinesterase (not a protease)

50
Q
  • cleaves peptides on the carbonyl
    side of the basic AAs, arg or lysine
A

trypsin

51
Q
  • cleaves peptides on the carbonyl
    side of small, neutral residues
A

elastase

52
Q
  • cleaves on the carbonyl side of
    aromatic residues, phe and tyr
A

chymotrypsin

53
Q

What are the 3 polar residues—— at the active site

A

His57, Asp102, Ser195

54
Q

Blank (red) is flanked by
Blank (gold) and by and
Blank (green)

A

His57
Asp102
Ser195

55
Q

the catalytic site is filled by
a peptide segment of Blank

A

Eglin

56
Q

is actually a depression on the surface of the
enzyme, with a pocket that the
enzyme uses to identify the residue
for which it is specific

A

the active site

57
Q

has a pocket surrounded by hydrophobic
residues and large enough to
accommodate an aromatic side
chain

A

chymotrypsin

58
Q

the pocket in trypsin has a Blank at its bottom, facilitating the binding of positively
charged Blank and Blank residues

A

negative charge (Asp189)
arginine and lysine

59
Q

has a shallow pocket with
bulky thr and val residues at the
opening; only small, nonbulky
residues can be accommodated in
its pocket

A

elastase

60
Q

in the active sites of all these
enzymes, the backbone of the
peptide substrate is hydrogen bonded
in antiparallel fashion to residues Blank to Blank and bent so that the peptide
bond to be cleaved is bound close to
Blank to Blank

A

215 to 219
His57 and Ser195

61
Q

the serine protease mechanism relies
in part on a low-barrier hydrogen
bond between Blank and Blank

A

Asp102 and His57

62
Q
  • produced by mammals, fungi and
    higher plants
  • active at acidic (or sometimes
    neutral) pH
A

Aspartic Proteases

63
Q

Digestion of dietary protein

A

Pepsin

64
Q

Digestion of dietary protein

A

Chymosin

65
Q

Lysosomal digestion of proteins

A

Cathepsin D

66
Q

Processing of AIDS virus protein

A

HIV-protease

67
Q

Conversion of angiotensinogen to angiotensin 1; regulation of blood pressure

A

Renin

68
Q
  • a hormone that stimulates smooth muscle contraction and
    reduces excretion of salts and fluid
A

angiotensoin

69
Q
  • display a variety of S specificities,
    but normally they are most active in
    the cleavage of peptide bonds
    between two hydrophobic AA
    residues
A

aspartic proteases

70
Q

Aspartic proteases is composed of Blank to Blank AA residues

A

323 to 340

71
Q

*2 homologous domains that fold to
produce a tertiary structure composed of 2
similar lobes, with approximate 2-fold
symmetry

A

aspartic protease polypeptides

72
Q

each of these lobes or domains consists of
Blank and Blank

A

2 β-sheets and 2 short a-helices

73
Q

the 2 domains are bridged and connected
by a Blank, Blank

A

6-stranded, antiparallel β-sheet

74
Q

the active site is a deep and extended
cleft, formed by the Blank and large enough to accommodate about Blank AA residues

A

2 juxtaposed domains, 7

75
Q
  • causative viral agent of AIDS
A

human immunodeficiency virus (HIV-1)

76
Q
  • cleaves the polyprotein products of
    the HIV-1 genome, producing several
    proteins necessary for viral growth
    and cellular infection
  • cleaves several different peptide
    linkages
A

HIV-1 protease

77
Q
  • a remarkable viral imitation of
    mammalian aspartic proteases
  • a dimer of identical subunits that
    mimics the 2-lobed monomeric
    structure of pepsin and other aspartic
    proteases
A

HIV-1 protease

78
Q

HIV-1 protease cleaves between the Blank and Blank residues of the sequence Ser-Gln-Asn-Tyr-Pro-Ile-Val, which joins the Blank and Blank HIV-1 proteins

A

Tyr and Pro
p17 and p24

79
Q

How many residue polypeptides that are
homologous with the individual
domains of the monomeric protease?

A

99

80
Q

structures determined by X-ray
diffraction studies reveal that the
active site of HIV-1 protease is formed
at the interface of the homodimer and
consists of 2 asp residues, designated
Blank and Blank, one contributed by
each subunit

A

Asp25 and Asp259

81
Q
  1. IN EQUILIBRIUM STATE WHAT HAPPENED TO PRODUCT AND SUBSTRATE?
A

-At equilibrium in an enzyme-catalyzed reaction, the rates of the forward and reverse reactions are equal, so there’s no net change in the concentrations of substrate, product, or enzyme. The enzyme constantly binds and releases the substrate, maintaining a steady state with stable levels of substrate and product. Although molecules continue to interact, the overall concentrations remain balanced.

81
Q
  1. WHY ENZYMES MUST BE DESTROYED?
A
  • Their degradation helps regulate metabolic pathways, ensuring that products are neither overproduced nor depleted. Enzymes, like all proteins, have a limited lifespan and are recycled to maintain cellular health by removing damaged or misfolded ones. Environmental changes, such as shifts in pH or temperature, can also denature enzymes, preventing unwanted reactions. This natural turnover allows cells to produce fresh enzymes as needed, ensuring efficiency and proper control of cellular processes, such as growth and signaling.
82
Q

in which a substrate (S) is converted to a
product (P) can be pictured as
involving a transition state

A

chemical reactions

83
Q
  • stable molecules that are chemically and structurally similar to the transition state
A

transition-state analogs

Protein and Nucleic acid (6 decks)

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