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Molecular biochemistry > Enzyme kinetics > Flashcards

Enzyme kinetics Flashcards

1
Q

What is catalysis?

A

Catalysis is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst, which is not consumed in the catalyzed reaction and can continue to act repeatedly.

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2
Q

What are enzymes?

A

Enzymes are macromolecular biological catalysts that accelerate chemical reactions.

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3
Q

How can an enzyme catalysed reaction be written out?

A

E+S <=> E.S –> E+P
First reaction K^1/K^-1 equilibrium

Second reaction K^2

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4
Q

How do enzymes speed up reactions (overall, in simple terms)?

A

Enzymes act by binding to their substrate in order to provide a lower energy pathway of the reaction.

This makes the reaction more thermodynamically feasible so it is favoured and the reaction will reach equilibrium at a faster rate

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5
Q

What does an enzyme form when bound to substrate?

A

Enzyme substrate complex

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6
Q

What are the two theories of how enzyme-substrate complexes form?

A

Lock and key mechanism

Induced fit

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7
Q

How does the induced fit model work?

A

The structures are specific but not perfectly complimentary.

Therefore a conformational shape change takes place that repositions residues to promote reaction by causing strain or bond formation in specific places.

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8
Q

What are the two ways that an enzyme can be triggered to undergo a conformational change?

A

Substrate binding to the active site

Third party molecule binding away from the active site, which triggers an allosteric change.

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9
Q

) When the substrate concentration is much greater than Km, the reaction is?

A

0th order

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10
Q

In an enzyme catalysed reaction, the rate

A

Has an optimal pH

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11
Q

The Km (Michaelis-Menten constant)

A

Is a combined rate constant, (K-1+K2)/K1, related to the formation and dissociation of the enzyme-substrate complex

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12
Q

When the substrate concentration equals 2Km what is the rate relative to Vmax?

A

When substrate concentration = 2Km, the rate is 2/3 of Vmax

Why: Use MM, Vmax x 2km = 2km Vmax / Km+2km
Cancel Km = 2Vmax/ (1+2) = 2/3 Vmax

2/3 Vmax

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13
Q

In the enzyme active sites what do AA functional groups do?

A

Functional groups on amino acids in the active site participate in the reaction

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14
Q

What about the active site makes it suited for function?

A

Specific shape and residue arrangement

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15
Q

What does the substrate form when it binds to the enzyme?

A

Transition state complex

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16
Q

What is the transition state complex?

A

TSC is an intermediate form of the substrate where all the bonds are maximally strained, and it has the highest energy

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17
Q

What does the enzyme provide to the TSC, why?

A

Stability, as the TSC binds tighter to the enzyme than the substrate.

Without the enzymes support, the TSCs are very unstable so it is kinetically favourable to form products that are more stable

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18
Q

What is activation energy?

A

The energy difference between the substrate and the TSC

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19
Q

How do enzymes lower the activation energy?

A

Enzymes lower the energy at which the TSC can form (Ea), as the TSC forms more bonds with the active site than the substrate

Bonds release energy, same TSC can form at lower energy

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20
Q

What is Hydrolysis?

A
  • the chemical breakdown of a compound due to reaction with water.
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21
Q

What is Ligation?

A

The joining of two DNA strands or other molecules by a phosphate ester linkage (phosphodiester bond).

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22
Q

What is Condensation

A

Two smaller molecules join to form a larger one by removing functional groups that form a small molecule, often water.

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23
Q

What is Group transfer?

A

A group transfer reaction is a pericyclic (cyclic compounds) process where one or more groups of atoms is transferred from one molecule to another.

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24
Q

What is Redox?

A

The transfer of electrons, reduction (electron gain), oxidation (electron loss).

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25
Q

What is Isomerisation?

A

One molecule is transformed into another molecule which has exactly the same atoms, but the atoms have a different arrangement

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26
Q

What must the active site be?

A

Complimentary to the TSC

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27
Q

How can metal ions contribute to an active site?

A

Positive charge - stabilising properties to groups that are negative.

Large electron cloud - act as electrophiles to withdraw electrons in reactions

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28
Q

How can specific residues contribute to an active site?

A

Facilitate mechanisms by transferring electrons.

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29
Q

Why is it beneficial in a reaction to form an intermediate?

A

Formation of an intermediate in the mechanism means the route has lower energy.

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30
Q

What is an oxyanion hole?

A

Pocket in the active site of an enzyme that stabilizes transition state negative charge on a deprotonated oxygen or alkoxide.

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31
Q

What are co-factors?

A

Bind to enzymes and transport chemical groups between them

32
Q

What is an activation transfer co-enzyme?

A

Form a covalent bond with the substrate and the enzyme.

This physically encourages catalysis

33
Q

What is an example of an activation transfer co-enzyme?

A

Thiamine pyrophosphate.

34
Q

What is an oxidation reduction co-enzyme?

A

Involved in redox reactions catalysed by enzymes

35
Q

What is an example of an oxidation reduction co-enzyme?

A

Dehydrogenases, transfer hydrogen from the substrate to an electron accepting co-enzyme like NAD+.

36
Q

What is the rate of an enzyme controlled reaction dependent on?

A

Substrate concentration and the amount of active enzyme

37
Q

What do rate calculations assume?

A

K^1

K^-1 are in rapid equilibrium

38
Q

What is the michaelis-menten equation?

A

Vo= Vmax.[S]/Km+[S]

39
Q

What is Vmax?

A

Maximum enzyme velocity

40
Q

What is Km?

A

Substrate concentration at ½ Vmax

41
Q

Are enzyme catalysed reactions saturable?

A

Yes

42
Q

Because enzyme catalysed reactions are saturable, how does rate increase as [S] increases?

A

Hyperbola

At an infinite substrate concentration the enzyme is fully saturated and the rate will plateau.

Increasing the substrate concentration past a certain value will have no regulatory effect on the enzyme rate.

43
Q

The … the Km, the more the substrate concentration has an effect on rate

A

Lower

44
Q

Why does a lower Km increase the amount [S] affects rate?

A

Enzyme has a greater affinity for the transition state complex at lower [S] so less overall substrate is needed to affect the increase in Vi.

45
Q

What is a lineweaver burk plot?

A

Linear graph of 1/[S] by 1/v

46
Q

What are inhibitors?

A

Enzyme Inhibitors are substances that bind to the enzyme and reduce its activity.

47
Q

What is a competitive inhibitor?

A

Compete for the binding site, they therefore share a similar structure to the TSC.

48
Q

How can competitive inhibition be overcame?

A

Increasing concentration of substrate

49
Q

Do competitive inhibitors affect the Vmax?

A

No

50
Q

Do competitive inhibitors affect the Km, how?

A

Km increased

More substrate is needed to saturate the enzyme

51
Q

What is a non-competitive inhibitor?

A

Bind away from the active site, at another area (allosteric site).

This causes an allosteric conformational shape change that alters the active site from an active R (relaxed) state to an inactive T (tense) state.

This means the enzyme active site can no longer bind to the substrate so it cannot lower TSC energy.

52
Q

How do non-competitive inhibitors affect the Vmax?

A

Lower the Vmax

Decreasing concentration of active enzyme.

53
Q

How do non-competitive inhibitors affect the Km?

A

None

54
Q

What is an irreversible inhibitor?

A

Covalently modify an enzyme so that a substrate can no longer bind. It denatures the enzyme.

55
Q

What is allostery?

A

A substance binds away from the active site, which causes a conformational shape change, can be an allosteric activator or an allosteric inhibitor.

56
Q

What is cooperativity?

A

Binding of one molecule (can be allosteric) increases chances of another bind.

Changes dependent on one another, as one change will induce other domains to change too

57
Q

What type of enzymes can cooperativity occur in?

A

Multimeric enzymes

58
Q

Compare and contrast graphs of normal enzyme activity, competitive inhibitor and non-competitive inhibitor

A

Normal - hyperbola

Competitive - same Vmax, less curved and steep as lower Km

Non-competitive - lower Vmax, same curve and gradient as normal

59
Q

How do allosteric activators work?

A

Allosteric activators bind more tightly/ have a higher affinity to the enzymes relaxed (R) state than the tense (T) state.

The result leads to a greater proportion of the enzyme population being in an activated state so the reaction rate is faster.

60
Q

How do allosteric inhibitors work?

A

In an allosteric inhibition, a competitive inhibition occurs for the allosteric site

T shape change, so less of the enzyme is in the relaxed state. Lowering the Vmax.

61
Q

What is the shape of an cooperative enzyme?

A

Sigmoidal

Representing how the binding of successive substrates activates other subunits.

62
Q

When an activator is added to a cooperative enzyme what happens to the graph, why?

A

Graph more closely models the Michaelis-Menten hyperbola with a decrease in Km as the affinity of enzyme for substrate increases, as more enzymes are in an active state.

63
Q

How can phosphorylation regulate an enzyme?

A

Transfer of phosphate groups to activate.

Phosphate groups are highly negative and can altering enzymes charged residues.

Kinase catalyzes the transfer of phosphate

64
Q

What is mevinolin, what is it used for and why?

A

Mevinolin is an inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, an enzyme involved in the production of sterols in eukaryotes.

This enzyme catalyses the synthesis of mevalonate, which is the immediate precursor of cholesterol.

Hence this drug is used as a statin.

65
Q

What is a zymogen?

A

An inactive enzyme precursor, that undergoes a biochemical change in order to activate it in the correct environment.

66
Q

Describe the difference between non-competitive inhibitors and allosteric inhibition?

A

Non-competitive inhibition always stops an enzyme working, by sitting on the enzyme in a location which changes the active site.

Allosteric inhibition focuses more on the use of chemicals which sit on an enzyme and by doing so can switch On or OFF the enzymes activity.

67
Q

What is Kcat?

A

Number of molecules of substrate converted to product in unit time

68
Q

Which macromolecules have been shown to display biological enzymatic activity?

A

Proteins and RNA

69
Q

A feature of allosteric enzymes that allow for efficient regulation of enzyme activity…

A

Cooperativity between subunits

70
Q

Do enzymes alter the equilibrium of a reaction?

A

No

71
Q

Mechanism by which ATP regulates phosphofructokinase activity…

A

Allosteric inhibition

72
Q

Residues involved in protein phosphorylation

A

Serine, tyrosine, threonine

73
Q

What do lyases do?

A

Catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure.

74
Q

What is an apo-enzyme?

A

An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.

75
Q

What is a holo-enzyme?

A

Holoenzyme- An apoenzyme together with its cofactor.

76
Q

Where can/does phosphorylation occur?

A

Cytoplasm

77
Q

What type of inhibitor is irreversible?

A

Non-competitive

Molecular biochemistry (5 decks)

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