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Biochemistry and molecular science > Module 6 > Flashcards

Module 6 Flashcards

overview of enzyme

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Biology 101 flashcards
1
Q

What does the configuration of enzyme do

A

Provide a specific environment i.e. active site for a given reaction to proceed rapidly

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2
Q

What are the active site of enzyme

A

They are lined with functional groups that binds to substrate

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3
Q

What is the role of enzyme

A

Lower the activation energy required and perform this function with high degree of specificity

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4
Q

How does enzyme catalyze reaction

A

By forming a complex between enzyme and substrate (ES)

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5
Q

What is a catalyzed reaction coordinate

A

E + S <> ES <> EP <> E + P

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6
Q

What are the cataliytic mechanisms

A

–acid-base catalysis:give and take protons
–covalent catalysis:change reaction paths
–metal ion catalysis:use redox cofactors, pKa shifters

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7
Q

Why are enzyme important?

A

-convert carbon fuel source into cellular energy in a appropriate timescale

-Forming ethanol from pyruvate.
Pyruvate— pyruvate decarboxylase–> acetaldehyde — alcohol dehydrogenase–> ethanol

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8
Q

What disease can be caused regarding enzyme?

A

Excessive or deficiency in enzymatic activity.

e.g. Phenylketonuria is caused by a deficiency in the enzyme Phenylalanine Hydroxylase

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9
Q

How does most drug work?

A

They target enzyme by inhibiting or activating the target

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10
Q

Does enzyme work alone

A

not all

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11
Q

What can enzyme work with?

A

cofactors (e.g. MG2+, K+)

coenzymes (carries functional groups) e.g. Coenzyme A, FAD, NAD, biocytin

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12
Q

What type of enzymes are there?

A 
8 types
– Kinases 
– Phosphorylases 
– Phosphatases 
– Dehydrogenases 
– Mutases 
– Isomerases 
– Hydratases 
– Synthases
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13
Q

What is kinase (K) for

A

Catalyses the phosphoryl transfer from one molecule (usually ATP) toanother;e.g.Hexokinase

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14
Q

What is phosphorylase (P’Lase) for

A

Catalyses the covalent addition of inorganic phosphate(Pi)to a molecule; e.g.Glycogen Phosphorylase

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15
Q

What is Phosphatase (P’Tase) for?

A

Catalyses the cleavage of a phosphate to yield the dephosphorylated product and Pi;e.g.Glucose-6-phosphatase

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16
Q

What is Dehydrogenase (DH) for?

A

Catalyses an oxidation/reduction reaction commonly using NADH/NAD+, NADPH/NADP+ or FADH2/FAD as cofactors; e.g.Glyceraldehyde-3-phosphate
dehydrogenase

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17
Q

What is Mutase (M) for?

A

Catalyses the shift of a phosphoryl group from one atom to another within the same molecule;e.g.Phosphoglycerate mutase (tetrameric in yeast and dimeric in bacteria)

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18
Q

What is isoemrase (I) for?

A

Catalyses the conversion of one isomer to another; e.g. Triose Phosphate Isomerase
(step 5 of glycolysis)

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19
Q

What is hydratase for?

A

Catalyzes the addition/removal of water
e.g. enolase
catalyses the conversion of 2-phosphoglycerate to phosphoenolpyruvate

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20
Q

What is synthase for?

A

Catalyses the synthesis of a product. e.g.citrate synthase.
Addition of an acetyl group from Acetyl-CoA to oxaloacetate to form citrate in the first step of the Krebs (citric acid, TCA) cycle

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21
Q

What prevention does enzymes have

A

energy barriers to prevent complex molecules from reverting spontaneously, reduce activation energy and thereby increase the rate of reaction

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22
Q

Characteristic of Enzyme

A

Do not affect : delta G

transition states are transient species

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23
Q

What is binding free energy?

A

the difference between the activation energies of the uncatalysed and catalysed reactions caused by the enzyme binding the transition state

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24
Q

How do enzyme reduce the activation energy and accelerate rates of reaction

A

– binding substrates in the correct orientation relative tot he active groups
-providing catalytically active groups(side chains, acids, bases, metal ions)
– Polarizing bonds, stabilising charged species (usually unstable)
– stabilizing the transition state

Weak binding interactions between the enzyme and the substrate provide a substantial driving force for enzymatic catalysis

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25
Q

The rate decreases with time due to a number of possible reasons(or a combination)

A

– (main reason) S is depleted by conversion to product
– The reaction is reversible, so as [P]↑the rate of the reverse reaction↑
– The enzyme may be unstable under the reaction conditions

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26
Q

What is the beer-lambert law

A

∆A = εx ∆c x l

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27
Q

What is the shape of the Michaelis-Menten plot

A

‘rectangular hyperbola’

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28
Q

What can is related to the rate of an enzyme catalysed reaction

A

proportional to enzyme concentration

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29
Q

What are the unit of the Michaelis-Menten plot

A

Initial velocity, Vo against subtrate concentration, [S0]

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30
Q

What is the michealis constant

A

When [S] is at ½Vmax, defined at Km, michealis constant

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31
Q

What is similar to km and [S] in enzyme kinetics

A

Kd and [L] in binding of protein and ligand e.g. Hb and O2

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32
Q

What is the michaelis-menten equation

A

Vo= (Vmax[S])/(Km+[S]

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33
Q

What is the Rate of formation of product Vo

A

V0 = k2[ES]

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34
Q

What is the Rate of ES formation

A

Rate of ES formation = k1[E].[S] = k1([Et] –[ES]) [S]

35
Q

What is the chemical equation of Michaelis Menten Theory

A

E + S k1> E + P

36
Q

What is the Rate of ES breakdown

A

k-1[ES] + k2[ES]

37
Q

What assumption do we use for the Michaelis Menten Theory

A

Assumption : ES conversion to E +P irreversible

Assumption : Steady-State Conditions [ES] constant

Assumption : [S]&raquo_space; [Et]

Assumption : [S]&raquo_space; [P] (initial conditions)

38
Q

What is the rate determining step

A

V0 =𝑘2 [𝐸𝑆] Vmax

39
Q

What is the equation for maximum velocity Vmax

A

Vmax = k2[Et]

40
Q

What is the steady-state assumption

A

Vo represents a ‘steady state’ where [ES] remain constant

The rate of formation ES = the rate of ES breakdown

41
Q

What is the ratios of concentrations OR ratios of rate constants

A

[E][S]/[ES] = (k2 + k-1)/k1, defined as Km, steady state concentration, not equilibrium concentration

42
Q

What is a double reciprocal plot

A

it is the lineweaver-burk analysis

43
Q

How is Km related to Kd

A

They have the same form for them chemical equation

44
Q

What kcat or turnover number mean

A

k cat)is defined as:• the number of molecules of substrate converted to product (S to P) per unit time per enzyme molecule saturated with substrate(i.e.when[ES]=[Et] k2, usually the rate limiting step

45
Q

What the specificity constant is and what does it mean

A

the rate constant for conversion of E + S to E + P (kcat/Km)

46
Q

What is the formation of ES at equilibrium Ka

A

1/Kd

47
Q

What is Kd

A

Kd = (k-1)/k1 = [E][S]/[ES] , how tight the enzyme tie to a substrate

48
Q

What is Km

A

The overall reaction for ES, an indication of the affinity of the enzyme for S. at steady state condition and take account of the catalytic step

49
Q

What is low Km

A

high affinity of the enzyme for its substrate

50
Q

Which Km of substrate have 30 fold difference in affinity for hexokinase

A

d-glucose = 0.05 mM, d-Fructose = 1.5 mM (in glycolysis)

51
Q

What does the Km usually related to

A

its own concentration in the environment

52
Q

When [S] &laquo_space;Km

A

Vo is proportional to kcat/Km

53
Q

What does kcat/Km reflect

A

both substrate affinity and catalytic efficiency (higher indicates more efficient use of the substrate

54
Q

Describe the difference between irreversible and reversible inhibitors

A

bind covalently to the active site, destroy a functional group essential for enzyme activity, or form a stable noncovalent complex with the enzyme.‘Suicide inhibitors’

Bind reversibly to enzymes and inhibit the enzyme either by competitive, uncompetitive or mixed modes of inhibition.

55
Q

What is the apparent Vmax and Km of competitive inhibition

A

Vmax, alphaKm

56
Q

What is the apparent Vmax and Km of uncompetitive inhibition

A

Vmax/alpha’, Km/alpha’

57
Q

What is the apparent Vmax and Km of mixed inhibition

A

Vmax/alpha, alphaKm/Alpha’

58
Q

Describe the mechanism of a competitive inhibitor

A

Inhibitor can bind to the same site, preventing substrate from binding. The activity is zero

59
Q

List the properties of the factor α competitive inhibitor

A

It is the enzyme that was used by the inhibitor. The factor of enzyme dropping.
The more enzyme removed by inhibitor

60
Q

Describe how α changes the apparent Km competitive inhibitor

A

When alpha is 1, no inhibitor.

As alpha increase, Vmax not changing, Km change, apparent Km increase.

61
Q

Generate and analyse Michaelis-Menten and double reciprocal plots that show the effect of a competitive inhibitor

A

steeper as inhibitor increase. Showing as if the enzyme is binding more weakly to substrate, but in fact it binding to inhibitor

62
Q

calculate α from kinetic data of competitive inhibitor

A

Vo = Vmax[S]/(alphaKm+[S])

63
Q

What is uncompetitive inhibitor

A

Does not compete with the same binding site but recognise and binding to the enzyme-substrate complex. No activity. IES, constant is Ki’. Decrease effectiveness of the production of product. does not contribute

64
Q

Describe how α’ changes the apparent Vmax of uncompetitive inhibitor

A

alpha become 1.5 or more, y axis increase. Vmax look smaller

65
Q

Describe how α’ changes the apparent Km of uncompetitive inhibitor

A

Decreases, but actually it does not change

66
Q

Be able to calculate α’ from kinetic data of uncompetitive inhibitor

A

Vo = Vmax[S]/(Km+alpha’[S])

67
Q

Generate and analyseMichaelis-Menten and double reciprocal plots that show the effect of an uncompetitive inhibitor

A

increase in parallel lines, Km decrease, Y axis increase.

68
Q

What is mixed inhibitor

A

It can bind to both the free-enzyme and the enzyme-substrate complex with constant of Ki and Ki’(ES complex) binding at different site. activity is zero. can bind to either side

69
Q

List the properties of the factor α and α’ in mixed inhibitor

A

alpha is binding to free-enzyme, alpha’ is to enzyme-substrate complex

70
Q

michaelis equation for mix inhibitor

A

Vo=Vmax[S]/(alphaKm+alpha’[S])

71
Q

What is the apparent Km of mix inhibitor

A

decrease(depends of the relationship between alpha and alpha’

72
Q

What is the apparent Vmax of mix inhibitor

A

decrease

73
Q

Describe the features of an allosteric enzyme

A

Regulate metabolic pathways by changing activity in response to changes in concentration of molecules around them

74
Q

Explain how positive and negative allosteric modulators control enzyme activity

A

Positive allosteric enyme bind to regulatory,change the conformation at the active site and help S bind with higher affinity

75
Q

Describe how different allosteric modulators stabilize different conformational states

A

Binds to the regulatory site

76
Q

Analyze plots of kinetic data for allosteric enzymes to identify the action of allosteric activators and inhibitors

A

High activity R state k0.5 decrease, Low activity T state K0.5 increase

77
Q

Use the example of the ATCase from E. coli as an example of allosteric regulation

A

S is Asp, sigmoidal V0 vs S, large increase in Vo. First step to produce nucleotides UTP and CTP. When high level CTP inhibit ATCase, negative modulator. ATP is the positive modulator

78
Q

What are Allosteric enzymes are regulated by

A

compounds called ‘allosteric modulators’ or ‘allosteric

effectors’

79
Q

Can allosteric modulator bind reversibly to enzyme

A

Yes, and non-covalently

80
Q

Is kinetic of allosteric regulators same as Michaelis-Menten kinetics?

A

No

81
Q

How many subunit does ATCase have

A

complex quaternary structure of 12 subunits

6 catalytic subunits, arranged as 2 x trimeric complexes. The catalytic subunits function cooperatively

And – 6 regulatory subunits, arranged as 3x dimeric complexes

82
Q

Integrate concepts of primary, secondary, tertiary and quaternary structure to describe the structure of α-chymotrypsin

A

5 disulfide bonds, hydrophobic pocket that binds the side chain of Phe,Tyr or Trpin the substrate protein. active site is described as a ‘catalytic triad’of Asp102, His57 and Ser195

83
Q

Rationalize the optimal pH for α-chymotrypsin activity with the protonation/deprotonation of His and the N-ter of the B chain

A

Below pH 7, His is protonated and cannot accept proton from Ser, kcat decrease. Above pH 8, His is all deprotonated, kcat does not change
For maximum activity ,His57 must be unprotonated (i.e. >pH7) and N-ter of the B chain (Ile16) must be protonated (ie

84
Q

What is Chymotrypsin

A

proteases that cuts peptides at specific locations on the peptide backbone, cleave the peptide bond adjacent to aromatic amino acids.

Biochemistry and molecular science (12 decks)

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