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Biochem 1 (WPH) > Enzymes 1 - catalysis 09/16 Spencer > Flashcards

Enzymes 1 - catalysis 09/16 Spencer Flashcards

1
Q

what is a common suffix attached to enzyme names

A

-ase

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2
Q

in enzyme classification numbers of the form EC.n1.n2.n3.n4, what does n1 refer to?

A

type of reaction (6 possible)
1 - oxidoreductase (oxidation/reduction)
2 - transferase (transfer of functional group)
3 - hydrolase (cleaves by hydrolysis)
4 - lyase (add or remove groups to form double bond)
5 - isomerase (intramolecular group transfer)
6 - ligase (covalently join molecules with energy from ATP hydrolysis)

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3
Q

what is an oxidoreductase enzyme

A

catalyzes an oxidation/reduction reaction

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4
Q

what is a transferase enzyme

A

catalyzes the transfer of a functional group from one molecule to another

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5
Q

what is a hydrolase enzyme

A

catalyzes cleavage of bonds by hydrolysis, the addition of water

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6
Q

what is a lyase enzyme

A

catalyzes addition or removal of a functional group to form a double bond

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7
Q

what is an isomerase enzyme

A

catalyzes the transfer of a functional group from one part of a molecule to another part of the same molecule

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8
Q

what is a ligase enzyme

A

catalyzes the covalent joining of molecules with energy from the hydrolysis of ATP

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9
Q 
A- + B  A + B-
what class of enzyme is involved
A

oxidoreductase

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10
Q 
AX + B  A + BX
what class of enzyme is involved
A

transferase

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11
Q 
AB + H2O  AOH + BH
what class of enzyme is involved
A

hydrolase

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12
Q 
XABY  A=B + XY
what class of enzyme is involved
A

lyase

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13
Q 
D-A  L-A (D-A and L-A are isomers)
what class of enzyme is involved
A

isomerase

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14
Q 
X + Y + ATP  XY + ADP + Pi
what class of enzyme is involved
A

ligase

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15
Q

in enzyme classification numbers of the form EC.n1.n2.n3.n4, what do n2 and n3 refer to?

A

some details of the enzyme reaction, we are not required to know these details

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16
Q

in enzyme classification numbers of the form EC.n1.n2.n3.n4, what does n4 refer to?

A

the substrate of the enzyme reaction

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17
Q

how much do enzymes increase physiologic reaction rates?

A

by a factor of 10^6 or more

uncatalyzed reaction rates are not consistent with life

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18
Q

enzyme cofactor

A

small non-protein molecules that bind and facilitate catalytic activity of enzymes

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19
Q

what are two types of enzyme cofactors

A 
inorganic cofactors (metals)
organic cofactors or coenzymes (from vitamins)
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20
Q

what are inorganic cofactors?

A

metals that bind and facilitate catalytic activity of enzymes

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21
Q

what are organic cofactors?

A

coenzymes derived from vitamins that bind and facilitate catalytic activity of enzymes

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22
Q

what are 2 types of organic cofactors?

A 
co-substrate (loose, changed by rxn)
prosthetic group (tight, not changed by rxn)
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23
Q

map the kinds of enzyme cofactors together

A

cofactor
______|______
inorganic organic
(metals) (coenzymes)
(vitamin derived)
_______|_______
co-substrate prosthetic group
(loose, changed) (tight, unchanged)

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24
Q

a coenzyme is another name for…

A

an organic co-factor

vitamin derived

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25
Q

what is a co-substrate

A

organic cofactor that is bound loosely and changed by the reacton

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26
Q

what is a prosthetic group

A

an organic cofactor that is bound tightly and unchanged by the reaction

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27
Q

holoenzyme

A

active enzyme with cofactor

28
Q

apoenzyme

A

non-active enzyme without cofactor

29
Q

active enzyme with cofactor =

A

holoenzyme

30
Q

non-active enzyme without cofactor =

A

apoenzyme

31
Q

T/F enzymes are highly specific to the reactions they catalyze

A

true - (to some varying degrees, e.g. cleaving peptide bonds vs only cleaving peptide bonds between R and G)

32
Q

∆G refers to…

A

change in (Gibbs) free energy

33
Q

T/F ∆G of a reaction is dependent on the path that is followed in converting reactants to products (e.g. transition state energies)

A

false - ∆G is dependent only on G products - G reactants

34
Q

T/F ∆G is concerned only with initial state of reactants and final state of products

A

true

35
Q

what does ∆G tell you about the rate of a reaction?

A

nothing. no info on rate, only spontaneity

36
Q

∆G < 0

A

spontaneous reaction

37
Q

∆G > 0

A

non-spontaneous reaction

38
Q

∆G = 0

A

reaction at equilibrium (no net change)

39
Q

what is ∆G for a spontaneous reaction

A

< 0

40
Q

what is ∆G for a non-spontaneous reaction

A

> 0

41
Q

how do you calculate ∆G for a given temperature?

A 
∆G = ∆Go + RT ln (products/reactants)
∆Go = ∆G @ standard conditions
42
Q

what are temperature, pressure, concentration, and pH at standard reaction conditions?

A 
T = 298 K (room temp)
P = 1 atm
[X] = 1 M
pH = 7
43
Q

how can you calculate ∆Go (∆G @ standard conditions) for a reaction at equilibrium conditions?

A 
∆Go = -RT ln Keq
Keq = [products]/[reactants]
44
Q

Keq =

A

equilibrium constant

[products]/[reactants]

45
Q

Keq > 1 favors the..

A

products

46
Q

Keq < 1 favors the…

A

reactants

47
Q

if ∆Go is negative, is the reaction spontaneous?

A

not necessarily. reaction is spontaneous at standard conditions but at different conditions, ∆G may be non-spontaneous

48
Q

T/F enzymes alter equilibrium

A

false - enzymes only accelerate the attainment of equilibrium by catalyzing the reaction

49
Q

what is the activation energy of a reaction?

A

∆G transition state - ∆G reactants

50
Q

how is reaction velocity related to activation energy?

A

lower activation energy, greater reaction velocity

51
Q

T/F small changes in activation energy can result in large changes in reaction velocity

A

true

52
Q

what is a catalytic group in an enzyme

A

a group of 2-3 residues in an active site that participate directly in the making or breaking of bonds

53
Q

what is the active site of an enzyme

A

region that binds substrates and cofactors and contains catalytic groups that participate in the making / breaking of bonds

54
Q

describe the general characteristics of an enzyme active site with respect to:

  • 3D shape
  • % of enzyme
  • substrate binding interactions
  • specificity of binding
A
  • 3D shape usually cleft with unique microenvironment (e.g. H2O excluded)
  • small % of total enzyme volume
  • binds substrate with many weak interactions (electrostatic, van der Waals, H-bonds)
  • controls binding specificity with orientation of atoms in the site
55
Q

how does an enzyme lower activation energy?

A

numerous weak enzyme-substrate interactions and eventually formation of the transition state release free energy (binding energy)

56
Q

what is the binding energy of an enzyme?

A

the free energy released (equivalent to the lowering of activation energy) by numerous weak interactions and eventually transition state formation between enzyme and substrate

57
Q

why does maximum binding energy require close contact between enzyme and substrate?

A

many of the interactions contributing to binding energy are weak, short-range interactions - more interactions = greater release of energy and lower activation energy

58
Q

which enzyme-substrate binding model accounts for specificity but not for stabilization of transition state?

A

lock & key

rigid, does not account for conformational change / flexibility

59
Q

which enzyme-substrate binding model accounts both for specificity and for stabilization of transition state?

A

induced fit

enzyme has flexible active site that becomes complementary to substrate shape

60
Q

in induced fit model of enzyme-substrate binding, which is flexible.. enzyme or substrate?

A

enzyme

61
Q

4 catalytic strategies of enzymes

A

covalent catalysis
acid-base catalysis
metal ion catalysis
catalysis by approximation

62
Q

describe covalent enzyme catalysis

A

a reactive group (usually a powerful nucleophile) in the active site makes a temporary covalent attachment to the substrate during the reaction

63
Q

describe general acid-base enzyme catalysis

A

an enzyme or substrate residue becomes an H+ donor or acceptor

64
Q

describe 3 mechanisms of metal ion enzyme catalysis

A

metal ions can:

  • promote nucleophile formation
  • act as electrophiles and stabilize neg charge
  • serve as enzyme-metal-substrate bridge
65
Q

describe enzyme catalysis by approximation

A

enzyme brings two distinct substrates together in the right conformation so they can react with one another

66
Q

what amino acid residues make up the catalytic triad in chymotrypsin and what kind of catalysis do they facilitate?

A

asp, his, ser
asp makes his a better base
his accepts an H+ from ser (basic catalysis)
ser becomes a good electrophile (covalent catalysis)

Biochem 1 (WPH) (15 decks)

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