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BCMB2002 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What is an enzyme?

A

A biological catalyst that increases the rate of a reaction and is chemically unchanged by the reaction

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2
Q

T/F:

Enzymes are mostly protein or DNA

A

False

Protein and RNA

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3
Q

What would happen if we didn’t have enzymes

A

Chemical reactions would not occur on a useful timescale and life cannot be sustained
Life would not be possible

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4
Q

Why are proteins better than RNA as enzymes?

A

Greater scope with a protein than with an RNA molecule

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5
Q

In 1897, Eduard buchner ……

A

Showed that extracts from year cells could ferment sugar to alcohol

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6
Q

In 1926, James Summer ……

A

Isolated and crystaized urease, finding that the crystals consisted of proteins

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7
Q

In 1930s, John Northrop and Moses Kunitz…

A

crystalyzed digestive enzymes and found all were proteins

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8
Q

In 1930, J.B.S Haldane suggested that …

A

weak bonding interactions between an enzyme and its substrate might allow reactions to be catalyzed

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9
Q

Enzymes act in ordered sequences of chemical reactions known as …

A

Biochemical Pathways

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10
Q

What is Krabbe Disease?

A

Genetic disease
Deficient in enzyme galactosyleramidase
Impairment in growth and maintenance of myelin

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11
Q

Which industry are enzymes mostly used in?

A

Food and beverage industry

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12
Q

Loss of an enzyme’s _________ causes loss of activity

A

Native Structure

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13
Q

T/F:

Simple proteins require additional chemical groups for activity

A

False

They do not require additional chemical groups for activity

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14
Q

What is a holoenzyme?

A

Catalytically active enzyme with its bound metal ion and/or co-enzyme

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15
Q

What is an apoprotein/apoenzyme?

A

The protein part of the holoenzyme

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16
Q

How are enzymes classified?

A

According to the reactions that they catalyze

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17
Q

What are the six class names?

A 
Oxidoreductases
Transferases
Hydrolases
Lysases
Isomerases
Ligases
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18
Q

T/F:

Enzymes size range from 15, 20, 40 kDa

A

True

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19
Q

T/F:

The active site takes up the majority of the enzyme

A

False

It is a tiny part

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20
Q

What allows the active site to bind to the substrate?

A

The amino acid residues with R groups

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21
Q

Why is the active site structured so that it is closed during the reaction?

A

This excludes water

Most reactions take a long time with water present or don’t proceed at all

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22
Q

Define equilibrium

A

When there is no net change in the CONCENTRATIONS o REACTANTS OR PRODUCTS

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23
Q

T/F:

The enzyme affects the equilibrium

A

False

Just increases the rate of reaction

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24
Q

What is the ground state?

A

The contribution to the free energy of the system by an average molecule

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25
Q

What does a negative deltaG mean?

A

The reaction is favourable

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26
Q

The transition state is the _____ energy state as you go from substrate to product

A

Highest

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27
Q

T/F:

The transition state is a reaction intermediate

A

False

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28
Q

What is the rate of reaction dependent on?

A

The difference between the free energy of the transition state and the ground state
Activation energy= AG++
Determined by the reaction step with the highest activation energy (rate-limiting step)

29
Q

What is a reaction intermediate?

A

A chemical species on the reaction pathway that has a lifetime longer than a molecular vibration

30
Q

What is a reaction step?

A

Interconversion of two sequential reaction intermediates

31
Q

What is Keq?

A

Equilibrium constant

=[P]/[S]

32
Q

A large negative value for deltaG reflects an equilibrium that favours ____ over ____

A

Products over Reactants

33
Q

What information does this formula provide?

V=k[S]

A

Rate of reaction (V)
k= rate constant
[S]= substrate concentration

Basically the rate of a reaction is determined by the concentration of the reactions and by the rate constant

34
Q

The rate constant is ____ and _____ related to deltaG++

A

Inversely and exponentially

35
Q

What is the role of non-covalent interactions in enzyme catalyzed reactions?

A

Non-covalent interactions are critical for the formation of complexes between enzyme and substrate

36
Q

What is the role of covalent interactions in enzyme catalyzed reactions?

A

Lower the activation energy by providing an alternative lower-energy reaction path

37
Q

What is deltaGB and how does it affect deltaG++

A

deltaGB= binding energy
When the enzyme and substrate bind, there are weak interactions that release small amounts of energy to stabilize the interaction
Enzymes use this energy to lower the activation energy for the overall reaction

38
Q

T/F:

The enzyme with a completely complementary active site to its substrate would be a really good enzyme

A

False
bad enzyme
needs to be good at binding the intermediate/transition state

39
Q

Is binding energy positive or negative?

A

Negative

It is favourable

40
Q

What happens when you sum together the deltaG and deltaGB?

A

Results in a lower net activation energy
activation energy is unfavourable= positive
binding energy is favourable= negative

41
Q

How much energy does a single weak interaction provide?

A

4-30 kJ/mol of energy

42
Q

Why is it difficult to experimentally distinguish between enzyme specificity and enzyme catalysis?

A

Because they both arise from weak interactions between E and S (ie deltaGB)

43
Q

What kinds of barriers does deltaGB overcome?

A

– Entropy of molecules in solution
– Solvation shells of Hbonded water
– Need for distortion of substrates in many reactions
– Need for alignment of catalytic functional groups on the enzyme.

44
Q

What is induced fit?

A

When E interacts with S through multiple weak interactions, E itself usually undergoes a change in conformation.

The conformation changes may involve small motions near the active site or large motions of entire protein domains.

Typically, a network of coupled motions occurs throughout the enzyme structure that ultimately brings about the required changes in the active site

45
Q

Once S is bound, ________________ aid in the formation and cleavage of bonds during the reaction

A

properly positioned catalytic functional groups

46
Q

How do unstable charged intermediates affect biochemical reactions?

A

They can rapidly break down back into reactants –> unfavourable, reaction moves towards substrate rather than products

This problem can be fixed by transferring protons to or from the substrate/intermediate that will rapidly break down into products

47
Q

Why does hexokinase favour the reaction with glucose rather than water?

A

When the enzyme binds to glucose, it undergoes a conformational change to become active
when glucose is not present, it won’t be active

48
Q

Provide an example of how a metal ion can stabilize a reaction intermediate

A

Enolase acid-base reaction
Enolase= enzyme
Uses 2 Mg ions to stabilize the intermediates to allow the reaction to proceed

49
Q

How does lysozyme act as an antibacterial agent?

A

Found in tears and egg whites

Cleaves the glycosidic bond between the two types of sugar residues in the peptidoglycan cellular wall

50
Q

T/F:

There is usually equal amounts of enzyme and substrate concentration

A

False

Enzyme concentration is usually way less than substrate concentration

51
Q

What is V0?

A

Rate of the reaction at the very beginning of the experiment
Generally reflects the steady state

Michaelis-Menten Equation:
V0= Vmax[S]/Km+[S]

52
Q

What is Vmax?

A

maximum velocity the enzyme can work at under given conditions
Occurs when all the enzyme is in the form of ES (enzyme is saturated with substrate)

53
Q

What is Km?

A

[S] that gives a rate of 1/2Vmax

54
Q

T/F:

E+S –> ES is slower than ES –> E + S

A

False
Breakdown of ES into E and S is slower than the formation of ES
(it is rate limiting)

55
Q

What occurs during the steady state?

A

[ES] and [other intermediates] remain approximately constant over time
V0 generally reflects this state

56
Q

What occurs during the pre-steady state?

A

[ES] builds up over time, lasts only microseconds

57
Q

What are some limitations of Michaelis Menten equation?

A

o The real meaning of Vmax and Km differ between enzymes.
o Vmax and Km by themselves provide little information about the number, rates or chemical nature of steps in the reaction.
o Regulatory enzymes do not exhibit Michaelis-Menten behaviour.

58
Q

What can the MM equation be converted into to generate?

A

Lineweaver-Burk plot
Makes it easier to identify the Vmax and Km
Y=intercept= 1/Vmax
X intercept= -1/Km

59
Q

What happens to Km in two step reactions when K2 is less than k-1?

A

Km equation becomes k-1/k1
This is the dissociation constant Kd ie measure of the affinity of the enzyme for its substrate
Therefore Km= measure of the affinity of the enzyme for its substrate

60
Q

What is Kcat?

A

describes the limiting rate of any enzyme-catalyzed reaction that is saturated with substrate

also called the turnover number, which means the number of substrate molecules converted to product per second when the enzyme is saturated with substrate

61
Q

What are the three types of reversible inhibition of an enzyme?

A

Competitive
Uncompetitive
Mixed

62
Q

Many ________ inhibitors combine with the enzyme to form an EI complex and prevent catalysis

A

competitive

63
Q

What is alphaKm?

A

Km observed in the presence of an inhibitor

64
Q

What is KI?

A

Inhibition constant

[I] required to give half maximum inhibition

65
Q

When a competitive inhibitor is present, how can you make the reaction be favoured?

A

Add more substrate

66
Q

What do uncompetitive inhibitors bind to?

A

They only bind to the ES complex

67
Q

What do mixed inhibitors bind to?

A

Can bind to E or ES

68
Q

Uncompetitive and mixed inhibition are observed only for enzymes with ____ substrates

A

2 or more

BCMB2002 (9 decks)

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