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enzymes Flashcards

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1
Q

What is an Enzyme?

A

Globular protein

Biological catalyst that differs from a chemical catalyst

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2
Q

enzymes: ribozymes

A

catalytic RNA molecules with no protein component

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3
Q

enzymes are biological catalysts that

A
  • Catalyses very high reaction rates
  • Shows great reaction specificity
  • Work in mild temperature/pH conditions
  • Can be regulated
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4
Q

Cofactor =

A

Non-protein component needed for activity

eg- ions

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5
Q

cofactor in glucose-6-phosphate

A

Mg2+

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6
Q

cofactor in pyruvate kinase

A

K+

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7
Q

cofactor in catalase, peroxidase

A

Fe2+, Fe3+

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8
Q

Coenzyme

A

Complex organic molecule, usually produced from a vitamin

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9
Q

coenzyme from riboflavin

A

FAD

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10
Q

coenzyme from Niacin

A

NAD+

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11
Q

coenzyme from pantothenate

A

Coenzyme A

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12
Q

Prosthetic group =

A

Cofactor covalently bound to the enzyme or very tightly associated with the enzyme
eg- haem in haemoglobin

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13
Q

Apoenzyme =

A

The protein component of an enzyme that contains a cofactor

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14
Q

Holoenzyme =

A

“whole enzyme” – the apoenzyme plus the cofactor(s)

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15
Q

Substrate =

A

Molecule acted on by the enzyme

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16
Q

Active site =

A

Part of the enzyme in which the substrate binds and is acted upon

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17
Q

Oxidoreductases - type of reaction

A

Transfer e-

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18
Q

Transferases - type of reaction

A

Group transfers

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19
Q

Hydrolases - type of reaction

A

Hydrolysis (transfer chemical groups to water)

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20
Q

Lyases - type of reaction

A

Form, or add groups to double bonds

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21
Q

Isomerases - type of reaction

A

Transfer groups within molecules (form isomers)

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22
Q

Ligases - type of reaction

A

Formation of C-C, C-S, C-O and C-N bonds (coupled to ATP cleavage)

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23
Q

Enzymes do not

A
  • Move reaction equilibria

- Make a non-spontaneous reaction spontaneous

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24
Q

Enzymes do

A
  • Increase rates of spontaneous reactions
  • Lower the activation energy of biochemical reactions
  • Accelerate movement towards reaction equilibrium
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25
Q

“Useful” energy generated from cellular reactions is termed

A

Gibbs Free-Energy (G), originally called “available energy”

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26
Q

Spontaneous reactions must have a

A

–ve ΔG value as they will decrease enthalpy (H) and/or increase entropy (S)

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27
Q

Spontaneous reaction isn’t

A

instantaneous because of the energy barrier

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28
Q

Energy barrier =

A

energy required to position chemical groups correctly, bond rearrangements, e- rearrangements, etc…

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29
Q

Transition state shows

A

the moment that chemical bonds are formed and broken. the top bit of curve.

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30
Q

Addition of an enzyme to a spontaneous reaction

A

lowers the activation energy

Enzymes allow the reaction to proceed via different route

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31
Q

Enzymes form non-covalent bonds with

A

substrate molecules, called the “binding energy” allowing them to take the reaction through a different path of reaction intermediates

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32
Q

No enzyme =

A

high activation energy ( high delta G)

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33
Q

CATALYSIS =

A

Active site complementary to transition state

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34
Q

How do enzymes reduce activation energy?

A
  • Entropy reduction
  • Desolvation
  • Induced fit
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35
Q

Explain Entropy reduction

A
  • Molecules in free solution will only react by “bumping” into one another
  • Enzymes “force” the substrate(s) to be correctly orientated by binding them in the formation they need to be in for the reaction to proceed
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36
Q

Explain Desolvation

A

Weak bonds between the substrate and enzyme essentially replace most or all of the H-bonds between substrate and aqueous solution

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37
Q

Explain Induced fit

A

Conformational changes occur in the protein structure when the substrate binds

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38
Q

If we changed the substrate concentration [S] we would change

A

the initial rate of a reaction.
More substrate = higher initial rate of reaction
- As the reaction proceeds, the substrate is used up and the rate of reaction changes
- Initial velocity (V0) can be studied if we assume that initial [S] does not change – this only really works if you have loads of S

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39
Q

When substrate concentration becomes so large that V0 changes are vanishingly small you get

A

maximum reaction velocity, Vmax.

Vmax occurs because all of the enzyme active sites are saturated with substrate

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40
Q

Michaelis-Menten equation

when you plot V0 against substrate concentration you get a

A

hyperbolic curve.

formation of an enzyme-substrate complex (ES)

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41
Q

Michaelis-Menten equation

A

Model states that the first part of the reaction (to produce ES) occurs reversibly
Second part of the equation (to produce E and P) occurs more slowly than the first part - rate limiting step

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42
Q

Michaelis-Menten equation:

If 2nd part is slower it must

A

limit the rate of the overall reaction, so the overall rate of reaction must be proportional to the amount of ES
- In other words, more ES would give a higher overall reaction rate and less would give a slower overall reaction rate

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43
Q

V0 usually equates to the

A

steady state of a reaction, so study of these initial rates of reaction is termed “steady state kinetics”

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44
Q

M-M equation was derived from their hypothesis that t

A

he rate-limiting step of an enzymatic reaction is the breakdown of the ES complex to give free enzyme and product

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45
Q

V0 =

A

initial reaction velocity

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46
Q

Vmax =

A

maximum reaction velocity

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47
Q

What’s the point of the M-M equation?

A

The equation accounts for the hyperbolic curve you see when a reaction proceeds
- At low [S] (i.e. the [S] is much less than Km) the M-M equation looks like,

V0 = Vmax[S]
Km

At high [S] ([S] is much greater than Km) the equation looks like,

V0 = Vmax

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48
Q

Km is equivalent to

A

the substrate concentration at which the initial reaction rate is half of the maximum reaction rate

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49
Q

The “better way” of experimentally defining the Vmax and the Km is to

A

draw a Lineweaver-Burk plot using the same data as was used to draw the M-M hyperbolic curve

50
Q

Lineweaver-Burk equation makes a

A

straight line graph

51
Q

Km = k-1 /k1

A

This can also be termed the dissociation constant, Kd of the ES complex

52
Q

Km is the

A

ratio of rate constant for breakdown of ES to E + S compared to the rate constant for formation of ES from E + S

53
Q

larger Km values indicate

A

a less stable ES complex

54
Q

smaller Km values indicate

A

a more stable ES complex

55
Q

Km gives you a clue to the

A

affinity of the enzyme with it’s substrate

56
Q

Vmax tells you

A

how fast a reaction is proceeding when the enzyme is saturated with substrate

57
Q

when [S] is equal to the Km, the M-M equation looks like,

A

V0 = Vmax

2

58
Q

isozymes

A

are different proteins but they catalyse the same reaction

59
Q

Glucokinase and hexokinase are

A

isozymes.

both catalyse
Glucose + ATP —> Glucose-6-phosphate + ADP

however have different kinetics

60
Q

When [blood glucose] goes UP after a meal,

A

the glucokinase activity increases but hexokinase activity does not respond as it is already working at its Vmax – this property allows glucokinase to respond proportionally depending on the [blood glucose]

61
Q

When [blood glucose] is LOW,

A

gluconeogensis releases glucose from the liver, but glucokinase cannot catalyse glucose back into glucose-6 phosphate under these conditions allowing glucose to be used by the body

62
Q

Glucokinase km(affinity for glucose) and Vmax are

A

high

63
Q

hexokinase Km (affinity for glucose) and Vmax are

A

low

64
Q

Enzymes in the wrong place

A

tell us about disease.

eg- increased plasma levels of intracellular enzymes are due to cell damage

65
Q

enzyme activity can be measured through

A
  • Measure initial rate
  • Have substrate in excess
  • Check that activity is proportional to enzyme concentration
66
Q

In clinical samples, normal activity is

A

often given an arbitrary value

67
Q

hexokinase is found in

A

muscle

68
Q

glucokinase is found in

A

liver; aka hexokinase D

69
Q

Isoenzymes can be studied by

A

electrophoresis as they are products of different genes.

- sometimes alternative combinations ofdifferent gene products

70
Q

Electrophoresis - a useful way to

A

separate plasma proteins

71
Q

electrophoresis cathode

A

negative side - sample is placed here

72
Q

electrophoresis anode

A

positive side - sample moves in this direction

73
Q

Creatine kinase (CK) is a

A

dimer, made up from two polypeptides B and M

74
Q

CK2 isoform is

A

abundant in the heart; elevation of plasma CK2 is diagnostic for myocardial infarction

Note: troponins I and T are now considered more useful

75
Q

hexokinase catalyses the production of

A

glucose-6-phosphate from glucose and ATP

76
Q

Catalysing a reaction with two or more substrates usually

A

involves transfer of groups from one substrate to the other

This can occur in several ways:

  • Random order or Ordered with a ternary complex
  • No ternary complex formation
77
Q

Lactate dehydrogenase exhibits

A 
an *ordered sequential mechanism*to its catalysis of pyruvate to lactate.
The coenzyme (NADH) binds first and the lactate is always released first,
78
Q

In a ordered sequential reaction mechanism the enzyme exists in

A

a ternary complex, first with the substrates of the reaction and then (after catalysis) with the products of the reaction

79
Q

Aspartate aminotransferase shows a

A

double displacement or ping-pong reaction pathway when it transfers an amino group from aspartate to α-ketoglutarate.

The term “ping-pong” comes from the fact the substrates bounce on and off the enzyme as they are catalysed. Aspartate “bounces” to oxaloacetate and α-ketoglutarate “bounces” to glutamate

80
Q

Allosteric enzymes do not follow

A

M-M kinetics

81
Q

Allosteric enzymes are made up of

A

many subunits, which contain many active sites.
One substrate binding to an enzyme subunit can cause changes in other active sites on other subunits

  • This can lead to the concept of “cooperative binding” of substrate molecules
  • Haemoglobin is a good example of cooperative binding of a substrate
82
Q

What will affect an enzyme?

A
  • Temperature
  • pH
  • Inhibitors
83
Q

pH effects on enzyme

A
  • pH changes the charge of amino acids
  • If the active site amino acids charge changes the enzyme will cease to function correctly
  • Extreme pH will denature most enzymes
  • pH will also affect the substrates of the reaction, some of which may require H+ or OH- groups to be involved in the reaction
84
Q

Competitive inhibitors bind to

A

enzymes non-covalently and will usually resemble the substrate molecule, therefore competing with the active site

85
Q

competitive inhibition leads to

A

decrease in the affinity between the active site and the substrate, so the Km of the substrate-enzyme complex increases

86
Q

how can you overcome competitive inhibition

A

Increasing substrate concentration can overcome this inhibition, so the same Vmax can be achieved

Therefore competitive inhibitors exhibit increased Km values but the Vmax remains unchanged – this gives a Lineweaver-Burke plot that look like line above original

87
Q

(Azidothymidine) AZT acts by

A

competitive inhibition of the reverse transcriptase enzyme.

- Reverse transcriptase is used by HIV to produce a dsDNA molecule from it’s ssRNA

88
Q

AZT undergoes

A

triphosphorylation in the body, and thus mimics the ordinary DNA precursor thymidine triphosphate (TTP)

89
Q

maximal interaction occurs between

A

enzyme and the transition state

90
Q

In the body oseltamivir is

A

hydrolysed in the liver to it’s active form, which is then able to block the activity of neuraminidase enzyme.
- Neuraminidase normally cleaves sialic acid (found on the surface of cells) that allows the release of new virus particles from the cells

91
Q

transition states are

A

intermediate step between an enzyme-substrate complex and an enzyme-product complex - difficult to replicate

92
Q

naturally occurring catalytic antibody lupus erythematosus is characterised by

A

autoantibodies attacking the connective tissue of the joints, skin, kidneys, heart and lungs

93
Q

Non-competitive inhibitors bind to

A

enzymes non-covalently and will usually attach to a site other than the active site of the enzyme.
The substrate is usually still able to bind the active site, so the Km of the substrate-enzyme complex remains unchanged

94
Q

Non-competitive inhibitors and increasing substrate concentration

A

Increasing substrate concentration does not change the inhibition so the Vmax will decrease
- Therefore non-competitive inhibitors exhibit unchanged Km values but the Vmax decreases – this gives a Lineweaver-Burke plot that look like line above original

95
Q

Irreversible inhibitors bind to

A

enzyme in a covalent, and therefore irreversible way

96
Q

CN- binds to Fe3+ of

A

cytochrome c oxidase and disrupts the terminal respiratory system
- Blocking the terminal respiratory system will effectively “starve” cells of ATP causing the individual with cyanide poisoning to exit the carbon cycle post haste

97
Q

often the first enzyme in pathway holds

A

regulatory step for that pathway – makes sense as you don’t want to regulate something half way down a pathway

98
Q

Two main ways regulatory enzymes modulate reactions:

A
  • Allosteric enzymes
  • Covalently modified enzymes

Both classes of regulatory enzymes tend to be multi-subunit proteins

99
Q

Allosteric effectors are usually

A

cell metabolites that bind non-covalently to a site on the enzyme that is not the active site

  • This changes the enzymes structure
  • Some effectors are activators and some are inhibitors
100
Q

Allosteric effectors are examples of

A

non-competitive inhibitors

101
Q

Allosteric enzymes :

low [S] (between A and B)

A

sensitises the enzyme so it responds more efficiently at higher [S] (between B and C)

102
Q

2 models explain allosteric enzyme kinetics

A
  • Concerted model

- Sequential model

103
Q

Concerted model:

A
  • Each sub-unit can exist in two different conformations
  • One binds substrate well the other doesn’t
  • With no substrate the enzyme flips between the two conformations
  • All sub-units must be in the same conformation (so they flip in concert)
104
Q

Concerted model explains the

A

sigmoidal curve

105
Q

According to the concerted model, Allosteric activators will

A
  • stabilise the ‘open’ conformation allowing S to bind more effectively
106
Q

According to the concerted model, Allosteric inhibitors will

A
  • stabilise the ‘closed’ conformation and make it difficult for S to bind effectively
107
Q

Sequential model assumes

A
  • No flipping between different conformation states
  • Sub-units exist in a conformation that can bind S, activators, inhibitors
  • It is the binding that causes a conformational change
108
Q

In Sequential model, Substrate binding causes

A

a change in one sub-unit

  • This causes a change in another sub-unit allowing it to bind S more readily
  • Like the first model, binding of some substrate sensitises the enzyme to bind more
109
Q

In Concerted model, Substrate binding causes

A

‘locking’ of the other binding sites, stopping them flipping, allowing other S to bind easily

  • Low [S] sensitises the enzyme to bind more S
  • Explains the sigmoidal curve
110
Q

Many ways enzymes (and other proteins) can be regulated through

A

reversible covalent modification

- most important covalent modifications is phosphorylation

111
Q

Approx. 30% of all eukaryotic proteins are phosphorylated

A
  • At a single site
  • Multiple sites
  • Multiple phosphorylations at one site
112
Q

Enzymes catalyse the phosphorylation of enzymes

A

Protein kinases – add phosphoryl groups to proteins

Protein phosphatases – remove phosphoryl groups

113
Q

Multiple phosphorylation sites allow

A

very fine control of enzyme function depending on the requirement of the particular enzyme at a given time
- has finely tuned activity dependant on the signals it receives

114
Q

Enzymes can exist as an inactive precursor protein, called

A

a proprotein or proenzyme

- Proproteins can be cleaved to give active enzyme by proteases

115
Q

zymogens - Proteolytic Cleavage

A

Digestive enzymes are regulated in this way – if they weren’t they would digest the parts of the gut where they are made

116
Q

can insulin be cleaved

A

yes

117
Q

Inhibitors can affect enzymes in different ways:

A
  • Competitive inhibitor
  • Non-competitive inhibitor
  • Irreversible inhibitor
  • Feedback inhibition
118
Q

Feedback inhibition

A

caused by build up of something

119
Q

Enzymes can be modulated in different ways:

A
  • Allosterically
  • Covalent modifications
  • Proteolytic cleavage
120
Q

Electrophoresis can be used as a

A

diagntstic tool to separate complex mixtures of enzymes

Science for Medicine (16 decks)

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