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BCHEM > enxyme test > Flashcards

enxyme test Flashcards

1
Q

what is mean by kinetically favourbale

A

this means that the reaction will happen spontaneously, the free energy of the system is negative

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2
Q

what is meant by thermodynamically favorable

A

this means that the natural change in free energy is from high to low.
the products have slow energy and are more stable than in reactants

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3
Q

absolute vs group specificity

A

the pickiness of an enzyme. High specificity means that it can only bind to one type or very few substrates (that are alike).

group specificity means that an enzyme is able to bind to a larger group of enzymes that share similar characteristics

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4
Q

free energy

A

the measurement of energy that is able to do work in a system

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5
Q

transition state

A

a very high-energy intermediate where the substrate is no longer the reactant, but not yet the product. During this state, bonds are partially broken and formed

note at this stage an ES complex HAS NOT FORMED. rather its the state between the ES and the EP

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6
Q

free energy of activation

A

the difference between the reactant energy and the free energy of the transition state. This is the amount of energy that needs to be input into the system to allow the reaction to proceed

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7
Q

what is the purpose of an enzyme catalyst

A

make a reaction kinetically favorable by lowering the free energy of activation by stabilizing the transition state

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8
Q

what is the binding energy

A

the release of free energy when bonds are formed between the enzyme and substrate. enzymes lower the binding energy of a system.

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9
Q

what are the features of an active site?

A

1) comprised of many residues found @ different positions along the chain (folding)
2)very small
3) unique environment= specificity
4) has the ability to form weak interactions with substrates
5) the arrangement of residues in the active site contribute ti specificity too

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10
Q

what are cofactors why are they needed

A

nonprotein moles that bind to enzymes to increase their overall chemistry

they can be coenzymes or metals

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11
Q

what is a prosthetic group

A

a tightly bound cofactor to its enzyme

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12
Q

what is a coenzyme

A

they are cofactors derived from vitamins

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13
Q

what is a co substrate

A

a loosely bound cofactor to its enzyme

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14
Q

explain the induced model fit

A

the idea that the active site of an enzyme is not a rigid structure and is able to conform to the shape of the substrate upon binding. this model is much more dynamic

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15
Q

explain the lock and key model

A

the concept that each enzyme has an active site that is perfectly complementary to one substrate. it’s a perfect match

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16
Q

what is an apoenzyme

A

an enzyme without its co facotrs

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17
Q

what is a holoenzyme

A

an enzyme with its co factors

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18
Q

initial velocity

A

the rate of the reaction when time ~0
this is the slope of the curve

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19
Q

how does enzyme concentration impact intial vel

A

it doesn’t! substrate concentration impacts it. this is because enzyme conc is typically constant within a system

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20
Q

what needs to form before an rxn can be catalyzed

A

an ES complex

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21
Q

what are the assumptions for the MM plot

A
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22
Q

what is Vmax

A

the velocity of the reaction when ll enzymes are saturated

ES=Et, at this point generally [S]>km

note that Vmax directly depends on the [E]

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23
Q

what is Km

A

the concentration of S to REACH 1/2 Vmax. Note it is not = to 1/2Vmax

it is the [S] to allow for 1/2of the E to be occupied

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24
Q

what is the turnover number

A

the # of mole per unit time (rate) that product is made when enzymes are fully saturated (ES=Et)

this is Kcat=K2

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25
Q

what is Kcat/Km

A

this is the specificity constant used when [S]«Km and describes the affinity of a particular enzyme has for an enzyme

high values means that the sub and enzyme work well together, even at low concentrations

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26
Q

catalytic perfection

A

to the notion that all encounters a substrate has with a particular enzyme will result in product. it is the Kcat/Km value of which cannot go any hight (the rate of the reaction cannot increase with minimal amounts of moles)

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27
Q

temperature optimum

A

the temp at which an enzyme is functioning at peak efficientcy. Any hotter and the enzyme will become denatured

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28
Q

pH optimum

A

the Ph at which the enzyme functions the more effectively. Ph dictates the charge and ability for weak interactions to occur in the active site. this impacts the ability for the enzyme to interact with its substrate

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29
Q

pseudo-first-order reaction

A

a reaction that depends on the [S]

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30
Q

zero order reaction

A

a reaction that doesn’t depend n [S]

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31
Q

what is steady state kinetics

A

the idea that ES is constant through a period of a reaction. ES form ation= ES breakdown

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32
Q

on a burk plot… what is the Vo, the Km, Vmax, Km/Vmax

A

1/Vo=y
Km/Vmax=slope
-1/km=x int
1/Vmax= y int

33
Q

what is the rate-limiting step of a reaction?

A

k1: the rate of the ES formation as products can only be made as fast a reactants collide

34
Q

what is allostery

A

the regulation of an enzyme via the binding of effectors to effector sites. this in turn controls the abundance of biochemicals found within a system

35
Q

feed forward activation

A

where the binding of an effector enhances the activity of an enzyme

36
Q

feedback inhibition

A

where an inhibitor binds to an enzyme to repress activity, to stop catalyzing the committed step of a reaction.

37
Q

what is the committed step of a pathway

A

generally, the first step of a pathway, where the catalysis of the substrate initiates the production of the final product.
this step is important as all intermediates are biologically useless, so all ‘ingredients’ to make product must be available.

38
Q

what is a concerted reaction model for allosteric enzymes

A

this idea is that all active sites of an enzyme must be of the same conformation. Where the conversion to R from T will happen to all sites, vastly interrupting the RT equb.

this abides by the symmetry rule

39
Q

what is the sequential reaction model for allosteric enzymes

A

the idea that active sites can be either R or T, though the conformation of one sight will influence the state of the neighboring sites.

40
Q

In what direction do inhibitors shift a sigmoidal curve? activators?

A

INH= right
Acti= left (less {s}needed to hit Vmax

41
Q

what is a homotropic effect

A

the presence of substrate affects that allostery of the enzyme and disrupts the tP qub

42
Q

what is a heterotropic effect

A

the influence regulators have on enzymes. Inhibitors stabilize the T while activators stabilize the R

43
Q

what do allosteric enzymes do?

A

catalyze the commtted step of a reaction

44
Q

what is the allosteric constant

A

Lo=T/R commonly 100:1

45
Q

what is the threshold effect

A

the idea that allosteric enzyme are more sensitive to Km than MM w/ that same Vmax

less d[S] is needed to reach the same Vmax than MM

46
Q

what are the 4 types of enzyme mechanisms?

A

Covalent catalysis
general acid base catalysis
metal ion catalysis
catalysis by approximation

47
Q

what is covalent catalysis

A

the formation of at least one temporary covalent bond between the enzyme and substrate

48
Q

what is general acid base catalysis

A

when an acid or basic residue in the active site is sed to facilitate the transfer of protons

49
Q

what is metal ion catalysis

A

metal ions used as cofactors commonly to stabilize other molecules in the active site

50
Q

what is catalysis by approximation

A

bringing two substrate close together in a proper orientation to increase the rate of reaction

51
Q

what are irreversible inhibitors?

A

moels that become tightly bound to an enzyme and dissociate very slowly

may be covalent or non covalent

52
Q

what are reversible inhibitors

A

moles that bind but are able to dissociated very quickly from an enzyme in the EIC

53
Q

what are the types of reversbale inhibit

A

competitive
uncompetitive
noncompetitive

54
Q

what are the types of irreversible inhibitor

A

group specific
affinity labels
suicide inhibit
transition state analogs

55
Q

competitive inhibit

A

those that bind directly to the acitve site.

effects can be undone by increase [S]

Km inc but Vmax stays the same (as the [E] functional stays the same)

56
Q

un competitive inhibit

A

a mole that binds to the ESI completely, after the ES has been formed. No product is formed

Both Km and Vmax dec

57
Q

non competative inhibt

A

moles that bind to the enzyme or the ESI changing the conformation of the enzyme

no product is made

km stays the same while Vmax dec

58
Q

group specific inhibition

A

bind to the side chains of AA, preventing the interaction with sub

59
Q

affinity labels

A

moles that mimic the functional properties of a substrate but will covalently bond with enzyme and not let go

60
Q

suicide inhibitors

A

the substrate is converted into a chemically reactive intermediate which remains bound to the enzyme via covalent bonding.

61
Q

transition state analogs

A

moles that resemble the transition state of the substrate and there for bind tighter to the enzyme

62
Q

what are the 7 major classes of enzymes

A

1) oxidoreductases
2) transferases
3) hyrdrolases
4) lyases
5)isomerases
6) transolcases
7) ligases

63
Q

oxidoreductases

A

enzymes that cata oxidation-reduction reactions by transferring electrons between moles

64
Q

transferases

A

transfer functional groups between moles

65
Q

hydrolases

A

cleave moles by adding water

66
Q

lysates

A

add moles or FG to double bonds or will removed moels to make double bonds

67
Q

isomerases

A

move FG within the same mole

68
Q

ligases

A

join moles together via using ATP

69
Q

translocases

A

cata movement of ions or mole across membranes

70
Q

what kind of mole is chymotrypsin

A

protease = protein tr over. chymotrypsin specifically does this via hydrolysis

chy cleaves on the carboxyl side of a bulky hydrophobic chain. this is because of a high specificity constant

71
Q

what kind of curve are oxygen binding curves

A

sigmoidal bc of the cooperatvity of the multiple active sites on the subunits

72
Q

how does the biding of oxygen affect the binding ability of the other sites

A

O2 into the 5th coord site on the heme group causes a structural change. the heme becomes planar and the aB group rotates 15deg. this induces R charter into the neighboring sites. a sequential like application

73
Q

what regulates the release of O2 from hemoglobin

A

2,3 BPG. this mole bind to a pock of the T form (deoxY) and stabilizes it. this reduces O2 affinity

74
Q

how does fetal hemoglobin differ from adult hemoglobin

A

the fetus gets their O2 from their mother. TF their hemoglobin has a very high affinity for O2 and a low affinity or 2.3 BPG. this is to ensure the fetus gets enough oxygen from the already limited supply.

75
Q

what is the bhor affect

A

the regulation of O2 affinity through the present of CO2 and H+

76
Q

what happens to O2 affinity with increased resp?

A

increase rep= ^CO2=^H+ in the blood. the lower the pH the lower the affinity hemoglobin has or oxygen. this is because hemo is trying to deliver more O2 to the muscles.

77
Q

how does an abundance of H= allow from the decreased affinity of O2?

A

H+ stabilizes the deoxy. the H+ ion is ale to bind to redu=isude in the active site and form salt bridges between other residues.
specifically, the His146 is protenates at low pH and forms brings with Lys 40 and Asp 94

78
Q

how does CO2 alone decrease O2 affinity??

A

CO2 reacts with terminal amono groups to form carbamate anions
these groups in hand can form salt brigdes between residues in the subunits, stabilizing the T form

79
Q

what are the mutations that cause sickle cell

A

the B chain, Glu 6 is changed to Val 6. Val 6 is associated heavily with the Phe 85 and Leu 88 pocket (where O2 would bind) and reduces the binding ability with oxygen.

these cells aggregate together and can not bind to oxygen

BCHEM (23 decks)

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