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381 - Biochemistry (COMPLETED) > Tutorial - Week 9 - Enzymes > Flashcards

Tutorial - Week 9 - Enzymes Flashcards

1
Q

________: catalyse and promote sequences of chemical reactions

A

Enzymes

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2
Q

___________: consecutive reactions catalysed by enzymes
The products of one reaction become the reactants of the next one

A

Pathways

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3
Q

Describe Catabolic pathways:

A

pathways that degrade organic nutrients into
simple end products to extract chemical energy and convert it into a
form useful to the cell (e.g. ATP, NADH, NADPH, FADH2)

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4
Q

Describe Anabolic pathways:

A

pathways that start with small precursor
molecules and convert them into more complex molecules (e.g.
proteins, nucleic acids). These require the use of energy.

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5
Q

___________: the overall network of enzyme catalysed pathways
(anabolic & catabolic)

A

Metabolism

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6
Q

What are enzymes? (4 points)

A
  • Under biologically relevant conditions, uncatalysed reactions tend to be slow (for example reactions required to
    digest food would take a very long time if not catalysed)
  • Life depends on powerful and specific catalysts: Enzymes
  • Almost every biochemical reaction is catalysed by an enzyme
  • Most enzymes are proteins (a few exception are RNA molecules: ribozymes)
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7
Q

What are enzymes? Simple explanation

A

Enzymes are proteins that catalyse biochemical reactions by
lowering their activation energy

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8
Q

Enzymes affect the _______________, not the_____________

The reaction equilibrium is dependent on…?

A

rate of the reaction

equilibrium

the thermodynamics of the
reaction (remember ∆G !” = −RT ln K #$ )

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9
Q

Enzymes are classified according to…/

A

the type of reaction they catalyse

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10
Q

Name the type of reaction catalyzed by each enzyme class

A
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11
Q

How enzymes work:

Enzymes have an _______:
* It provides a specific…?
* It binds and recognises a…?

A

active site

environment that helps accelerate the reaction

specific substrate(s

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12
Q

What are the four parts required for enzyme catalyzation? Draw the process

A
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13
Q

Many enzymes require non-protein ________ for their ________ function

A

cofactors

catalytic

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14
Q

What is a cofactor?

A

Cofactor = a non-protein chemical component needed for the biological activity of an enzyme. Cofactors can
be inorganic ions, Fe 2+ , Mg 2+ , or complex organic molecules, also referred to as coenzymes

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15
Q

What is a coenzyme?

A

Coenzyme = are cofactors that are organic molecules and bind loosely to the active site of an enzyme to help
with the catalysis, such as NADH and vitamins.

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16
Q

What is a prosthetic group?

A

Prosthetic group = are cofactors that are tightly bound, or even covalently bound, to the enzyme (e.g. FAD in
flavoproteins).

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17
Q

What is Apoenzyme

A

is an enzyme without the cofactor, and therefore is inactive.

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18
Q

What is holoenzyme

A

Holoenzyme = is an enzyme with cofactors attached and catalytically active

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19
Q

What are the three features that make a protein an enzyme?

A
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20
Q

Describe catalytic power

Give simple description and the difference between no enzyme in the reaction and an enzyme

A
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21
Q

What is the transition state?

A

highest energy
arrangement of atoms during a reaction

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22
Q

∆G‡ free energy of activation,
Activation energy (Ea): energy = ?

A

difference between the substrate and
the transition state.
Determines the rate of the reaction

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23
Q

∆G‡ free energy of activation (Ea)
catalysed: explain

A

When the enzyme is
complementary to the transition
state, it helps destabilise the
substrate (bend stick), reduces the Ea
and accelerates the reaction.

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24
Q

Enzymes catalyse reactions: how?

A

substrates bind to the active site
of the enzyme, which accelerates the chemical reaction,
products are formed, and then allow products to dissociate

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25
Q

The function of enzymes is to…?

A

lower the activation energy (Ea) to accelerate the reaction

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26
Q

Enzymes selectively recognise specific _________
* Substrates bind to the __________ of the enzyme via __________
bonds (______________________)
* Specificity is controlled by __________ and ____________ in
the active side.

A

substrate (s).

active site

non-covalent

H-bonds, van der Waals and ionic interactions

the 3D structure

specific amino acids

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27
Q

The substrate binds to the __________.
* The active site is…?
* The active site of an enzyme is the place where…?.
* The active site provides…?

A

active site (or binding site)

a region in the enzyme uniquely suited to bind specific substrate(s)

a reaction is catalysed

catalytic groups to facilitate the chemistry that stabilises the
formation of the transition state

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28
Q

Enzymes act as…?

A

a template for the reaction to occur, they bind to specific substrate (s),
stabilise the transition state, lower the activation energy and accelerate the reaction.

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29
Q

What are the two models of enzyme specificity?

A
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30
Q

Explain the Lock and key model

A
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31
Q

Explain the induced fit model

A
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32
Q

Weak bonds (non-covalent) between the substrate and binding site of an enzyme normally
involve:

A
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33
Q

Interactions between the enzyme and substrate, optimised in the _________

  • Reduction of _______ by constraining the substrate(s) in the proper orientation to react in the active site
  • Desolvation of the substrate(s) (many organic molecules are surrounded by…?
  • Change in the enzyme conformation when the …?
  • The induced fit serves to…?
A

transition state

entropy

a shell of water molecules that
can reduce interactions between substrates)

substrate binds (induced fit).

bring specific functional groups on the enzyme into the proper position to catalyse the reaction

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34
Q

Inhibitors: describe

A

inhibit the activity (i.e. interfere with the kinetics of the reaction
catalysed by the enzyme)

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35
Q

Activators: do what?

A

Increase the activity of the enzyme

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36
Q

Enzyme inhibitors: are…?

A

molecules that interfere with the catalysis, by slowing or stopping enzymatic
reactions

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37
Q

Type of enzyme inhibitors?

A
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38
Q

Describe what the competitive inhibitor does?

A

Competitive inhibitor: competes with the substrate for the active site. If the inhibitor occupies the active site, the substrate cannot bind

39
Q

Uncompetitive inhibitor: what does it do?

A

Binds to a different site, but binds only to the ES complex.

40
Q

What are Noncompetitive (or mixed) inhibitor also referred to as?

What do they do?

A

Allosteric inhibitors

Binds to a different site, it can bind to the E or to the ES complex.

41
Q

Irreversible inhibitors bind _________ with, or ________, a functional group that is essential for the enzyme’s activity, or they form a…?

A

covalently

destroy

highly stable noncovalent association.

42
Q

Label these types of activation

A
43
Q

What do allosteric inhibitors do?

A

Allosteric inhibitor: induces a conformational
change that reduces the enzyme’s affinity for its
substrate. Noncompetitive and uncompetitive
inhibitors are examples of allosteric inhibition.
Vmax is reduced

44
Q

What do allosteric activators do?

A

Allosteric activators: bind to locations on an enzyme
away from the active site, inducing a conformational
change that increases the affinity of the enzyme’s
active site(s) for its substrate(s).
Vmax is increased

45
Q

Describe Product accumulation:

A

excess of product, might inhibit the enzyme activity.

46
Q

Describe Substrate availability:

A

if no substrate is available, the reaction does not occur; increased concentration accelerates the
enzyme activity

47
Q

Describe Genetic control:

A

it can induce more or reduce the expression of enzymes

48
Q

Describe Covalent modification:

A

attachment of a chemical group by covalent bond can modify the enzyme activity (e.g.
phosphorylation of specific amino acid residues can activate or inactivate enzymes)

49
Q

Describe Expression of enzymes as Zymogens:

A

inactive enzyme precursors that only become active after specific proteolytic
cleavage

50
Q

Describe Expression of several isoenzymes:

A

enzymes with similar function and overall 3D structure, that differ in the primary
sequence of the polypeptides that make up their quaternary structure (e.g. LDH1, LDH2, LDH3, LDH4, LDH5)

51
Q

Modulator proteins:

A

proteins that bind to enzymes and influence the activity of the enzyme

52
Q

Most enzymes have certain _________ properties in common: Substrate concentration, [S], affects…?

A

kinetic

the rate of the reaction

53
Q

The rate of an enzymatic reaction depends on….? which depends on…?

A

the formation of enzymesubstrate complex (ES)

the concentration of substrate,
until all the enzyme binding sites are occupied with substrate

54
Q

As we increase the amount of substrate there is a higher rate of?

A

Product production

55
Q

The rate of an enyzmatic reaction depends on…?

A

the concentration of substrate we have when we first start the reaction

56
Q

The reaction is faster at the beginning when there is
more…?

A

substrate (initial rate, V0)

57
Q

T/F: As the reaction proceeds and substrate(s) is(are) consumed,
the rate slows down

A

True

58
Q

The ___________________ can be determined by the
variation of product produced over time

A

rate of an enzymatic reaction

59
Q

The initial rate of an enzymatic reaction, V0, can be determined
by…?

A

the variation of product produced over time, at the beginning
of reaction (as shown in the figure, is the tangent at the
beginning of the reaction/linear part of the curve)

60
Q

Label the arrows

A
61
Q

What is this yellow arrow pointing to?

A

The initial rate (Vo)

62
Q

Describe the Michaelis-Menten enzymatic reaction:

A

a model that describes the kinetics of many enzymatic reactions

63
Q

In the Michaelis-Menten enzymatic reaction, the Vmax represent?

Km is? (2 points)

A
64
Q

Kinetic parameters (KM and Vmax) are used to compare…?

A

enzyme kinetics

65
Q

Kinetic parameters: A traditional approach to determine these parameters is by using the _________________ to linearise the MichaelisMenten plot, an approach that takes the reciprocal of both sides of the Michaelis-Menten equation

A

Lineweaver-Burk plot

66
Q

Label

A
67
Q

Competitive inhibitor: Explain

A

competes with the substrate for the active site. If the inhibitor occupies the
active site, the substrate cannot bind

68
Q

List what happens to Km and Vmax

A
69
Q

The lines in the
Lineweaver Burk
representation intersect at the…?

A

Y-axis

70
Q

We need a lot more substrate to overcome
the inhibitor and obtain the _______

A

Vmax

71
Q

Describe what happens to the Km and Vmax when there is an uncompetitive inhibitor

A

Km^App decreases
Vmax^App decreases

72
Q

Define Uncompetitive inhibitor:

A

Binds to a site different from active site, but binds only to the ES complex.

73
Q

Describe what happens to the lines in the Lineweaver Burk representation when uncompetitive inhibitors are binding?

A

The inhibition cannot be overcome by
increasing the [S], Vmax is lower

74
Q

Non-competitive (or mixed) inhibitor: Define

What happens to the Km and Vmax, and the lines and their intersections

A

Binds to a site different from Binds to a site different from
active site , but binds to E or to the ES complex

75
Q

How fast an enzyme molecule convert a substrate into a product?

A

The higher the Kcat, the faster the enzyme at catalyzing the reaction

Specificity constant (kcat/KM): is the best way to compare the catalytic efficiencies of different enzymes

76
Q

Types of enzyme reaction, based on the number of substrates:

  • True unimolecular reaction: Explain
A

A single substrate rearranges to
a single product (e.g. isomerases catalyse reactions that
normally are true unimolecular)

77
Q

Pseudo unimolecular reaction: What is it?

A

A single substrate molecule is separated into two or more
products (e.g. hydrolases that break a chemical bond; water is a substrate, but is in large
excess, and is not a limiting substrate)

78
Q

Describe bimolecular reactions

A
79
Q

Describe sequential bimolecular reactions

A
80
Q

Describe Non-Sequential biomolecular:

A
81
Q

Mechanisms of enzyme catalysis:

Describe general acid and base catalysis

A
82
Q

Describe covalent catalysis

A
83
Q

Describe metal ion catalysis

A
84
Q

Give example of general base catalysis

A
85
Q

Give an example of covalent catalysis

A
86
Q

Give an example of metal ion catalysis

A
87
Q

Key concept: What are enzymes?

A

Enzymes are proteins that catalyse biochemical reactions by lowering their activation energy

88
Q

Key concept:

The active site, cofactors, and how enzymes work: (3 points)

A
89
Q

Key concept:

Features that distinguish enzymes from other proteins: (3 points)

A
90
Q

Key concept:

Enzyme regulation and types of enzyme inhibitors (2 types and explain)

A
91
Q

Key concept:

Enzyme kinetics, initial rate, Michaelis-Menten model, and kinetic parameters (explain 4 points)

A
92
Q

Key concept:

Lineweaver-Burk plot and their use to determine kinetic parameters and type of enzyme inhibitor (explain)

A

To linearise the Michaelis-Menten plot, an approach that takes the reciprocal of both sides of the Michaelis-Menten
equation, comparison of kinetics with and without inhibitor

93
Q

Key concept:

List the different types of enzyme reaction, based on number of substrates

A
94
Q

Key concept:

Mechanisms of enzyme catalysis (3 points)

A

381 - Biochemistry (COMPLETED) (47 decks)

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