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BSCI330 SPRING > exam 2 protein structure and function: enzymes > Flashcards

exam 2 protein structure and function: enzymes Flashcards

1
Q

how does enzyme catalysis work

A

by stabilizing the reaction’s transition state

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2
Q

what are some non-protein components that enzymes require for function

A

cofactors and prosthetic groups

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3
Q

what are the ways enzymes are highly regulated

A

by covalent modification and binding of non-substrate ligands

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4
Q

what type of proteins are enzymes

A

catalytic proteins - speeding up cellular reactions to allow life

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5
Q

do enzymes alter delta G

A

NO

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6
Q

what can enzymes link to each other

A

an energy producing reaction with an energy-requiring reaction to directly transfer the energy from one to the other

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7
Q

what can enzymes not do

A

cannot make a reaction occur spontaneously if it is thermodynamically unfavorable

cannot alter the concentrations of reactants and products in a reaction mixture that is at equilibrium

cannot extract more useful energy per mole of reactants - they can only extract it faster

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8
Q

what do enzymes do kinetically

A

they change the kinetics of a reaction, not the thermodynamics

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9
Q

what exactly is a chemical reaction

A

break some bonds to start a reaction, which requires an input of energy

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10
Q

what do you recover if a reaction is spontaneous

A

all activation energy + more energy

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11
Q

what do you recover if a reaction requires energy

A

you will get some back but not as much as you put in

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12
Q

what do enzymes lower and why

A

the amount of activation energy because the energy is a main barrier to initiating a reaction, which sets the speed of the reaction

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13
Q

as a catalyst, what is an enzyme also

A

only required in small amounts

must be left uncharged at the end of a reaction so that it can cycle back to bind more substrate

catalyzes equally the forward and reverse reactions

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14
Q

how does enzyme function begin

A

by binding the substrate through reversible, weak bonding to a stereo-specific active site, which forms an enzyme-substrate complex

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15
Q

where can ribosomes make peptide bonds form

A

between L amino acids

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16
Q

what can enzymes of metabolism only work with

A

D glucose

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17
Q

what happens after enzyme function has begun

A

the substrate is chemically converted to product, forming an enzyme product complex

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18
Q

what is the last step of enzyme function

A

the product is released and enzyme can bind another molecule of substrate

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19
Q

what is the reaction of enzymes all together

A

enzyme binds to substrate, making enzyme-substrate complex
then enzymes performs catalysis to convert substrate to product
then enzyme releases product to generate enzyme and product separately and repeats

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20
Q

what is the limiting rate for enzyme

A

the first step of binding of enzyme to substrate

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21
Q

what happens with more substrate

A

the more there is, the easier it is to bang into an enzyme and begin the reaction

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22
Q

what is the rate of a reaction limited by

A

the ability of the substrate to interact with the enzyme

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23
Q

what is V(max)

A

the rate when enzyme is saturated with substrate

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24
Q

what is V(max) dependent on

A

how many molecules of enzyme is in solution

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25
Q

what is turnover rate

A

the number of molecules of substrate that can be converted to product per second per molecule of enzyme

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26
Q

what is K(m)

A

the Michaelis Constant - approximately equal to the dissociation constant for the enzyme-substrate complex

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27
Q

what does a low K(m) mean

A

enzyme has a high affinity for its substrate

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28
Q

what is the equation for K(m)

A

1/2 V(max)

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29
Q

what does V(max) represent

A

how fast the enzyme can convert substrate to product

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30
Q

what is K(m) a measure of

A

how well the enzyme binds to the substrate

31
Q

what happens if the K(m) is reduced

A

the binding interaction between the enzyme and substrate becomes stronger and the amount of substrate required to half-saturate the enzyme is lowered

32
Q

what is the amount of substrate required to half-saturate the enzyme dependent on

A

the binding affinity of the substrate for the enzyme

33
Q

what has to happen for a reaction to occur

A

substrate molecules have to pass through a series of intermediate states

34
Q

what happens in intermediate states

A

3D geometry of reactants needs to be adjusted for optimal interaction

electrons among reacting atoms must begin to become redistributed

35
Q

what happens with higher energy of a system

A

it’s less stable

36
Q

what happens when you lower the energy of a transition state

A

you stabilize it, allowing a reaction to proceed more rapidly

37
Q

what is the transition state for a reaction

A

an intermediate form between product and reactant with a specific structure

38
Q

how can you reduce activation energy using a transition state

A

by providing an alternative pathway to reach a product

39
Q

how do enzymes function

A

by stabilizing specific transition states of the substrate

40
Q

what state has a higher energy than either reactants or products

A

as they react, substrates will go through a state with a higher energy level before the reaction occurs

41
Q

what happens when enzymes stabilize transition states

A

they lower activation energy

42
Q

what is the result of products binding to enzymes

A

they’re oriented in the correct way and can reach transition states

43
Q

what do enzymes facilitate

A

redistribution of electrons - will bring in positively and negatively charged amino acids to help change electrons

44
Q

what happens when enzymes put physical stress on molecules

A

they favor the formation of the transition state - transition state relives the stress

45
Q

what is the full way enzymes mechanisms of stabilizing the transition state works

A
  • enzymes binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them
  • binding of substrate to enzyme rearranges electrons in the substrate creating partial negative and positive charges that favor a reaction
  • enzyme strains the bound substrate molecules, forcing it toward a transition state to favor a reaction
46
Q

what are prosthetic groups

A

non-protein (non-organic) molecules which aid in some protein function

47
Q

how can prosthetic groups be used

A

covalently or non-covalently bound by the protein

48
Q

what are cofactors

A

enzyme prosthetic groups

49
Q

what are coenzymes

A

organic molecules that act as cofactors

50
Q

what are molecular tunnels

A

the structures of enzymes that perform multiple sub-reactions that must occur at distinct active sites to direct intermediate products from one active site to the next

51
Q

what do molecular tunnels do

A

they prevent diffusion of intermediates and decomposition of unstable molecules and speed up reaction rates

52
Q

what do molecule tunnels do for intermediates

A

they provide a direct route for intermediates to go from one catalytic site to the next one without interacting with other reactive components, thus speeding up the reaction rate over all

53
Q

what do metabolic pathways require from reactions

A

reactions to occur in specific , highly regulated order

54
Q

how are enzymes in the metabolic pathway organized

A

into higher-order multi-enzyme complexes

55
Q

what occurs within a multi-enzyme complex

A

the product of the first enzyme is passed to the second enzymes, where it is the substrate, and so on

56
Q

what does regulation of key enzymes involve

A

multiple inputs to be turned on and off when needed

57
Q

what is feedback control with enzymes

A

a downstream product regulates an upstream enzyme in a given pathway

58
Q

when is feedback control implemented

A

when product concentrations reach sufficient levels and there’s no more need for more product

59
Q

what do irreversible inhibitors do

A

covalently bind to an amino acid residue, which usually lowers Vmax by inactivating and removing active enzyme molcules

60
Q

how common are irreversible inhibitors

A

rare in nature

61
Q

what do competitive reversible inhibitors do

A

reversibly bind to active site and compete with substate, though can be displaced by a very high [S]

62
Q

how common are reversible inhibitors

A

common in nature

63
Q

what do competitive reversible inhibitors do to Km

A

increase Km - lower affinity

Vmax is not affected, but Km is

64
Q

what do non-competitive reversible inhibitors do

A

reversibly bind away from active site to cause change in enzyme structure that lowers catalytic efficiency

65
Q

what do non-competitive reversible inhibitors do to Km

A

lowers Vmax, but does not affect Km or substrate binding

66
Q

what does phosphorylation allow for

A

a rapid, reversible mode of regulation that can be coded by a short, linear amino acid sequence

67
Q

what is an allosteric regulator

A

a regulatory molecule that binds at a site away from the catalytic site

68
Q

what is conformational change in protein structure

A

the binding of one molecule to one region of an enzyme influences the binding of another molecule to a different region of the enzyme

69
Q

what can an allosteric site be a part of

A

the same protein chain as the active site or may be in a regulatory subunit

70
Q

what does binding result in

A

a change in the conformation of the catalytic site

71
Q

what can conformational changes in the catalytic site do

A

activate (promote substrate binding/catalysis) or inhibit (prevent substrate binding/catalysis)

72
Q

are allosteric inhibitors competitive or non-competitive

A

both - competitive affects substrate binding and non-competitive affects catalysis

73
Q

what does allosteric regulation change

A

the shape of the enzyme to control its function and that can be either negative or positive

BSCI330 SPRING (24 decks)

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