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1) Biochemistry I > Enzymes > Flashcards

Enzymes Flashcards

1
Q

Define enzymes.

A

Proteins that function to increase the rate of a reaction.

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2
Q

What type of proteins are enzymes?

A

most are globular

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3
Q

What type of specificity do they have? How?

A

Strict specificity, many weak interactions between the E-S

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4
Q

Why is it important to understand enzymes?

A

Are the functional entities of many cells

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5
Q

How are enzymes categorized?

A

According to the reactions they catalyze

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6
Q

What is the enzyme suffix?

A
  • ase
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7
Q

What can they catalyze (reactions)?

A

Forward and backward reactions

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8
Q

What is catalyzed in oxidoreductases?

A

Addition or reduction of electrons (oxido-reduction)

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9
Q

What is catalyzed in transferases?

A

Transfers of groups

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10
Q

What is catalyzed in hydrolases?

A

Hydolysis reactions where a molecule is split into two or more smaller molecules by the addition of water

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11
Q

What can the enzyme hierarchy be compared to?

A

Taxonomy

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12
Q

What is catalyzed in lyases?

A

Addition of groups across a double bond or elimination of groups to generate double bonds

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13
Q

What is catalyzed in isomerases?

A

Atomic rearrangements within a molecule (trans vs cis)

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14
Q

What is catalyzed in ligases?

A

Reaction which joins 2 molecules and drives the formation of a new bond (condensation reactions)

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15
Q

What is particular about ligases?

A

Use energy derived from ATP

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16
Q

Do enzymes catalyze by themselves? What do they require? Why?

A

Some can
Others require quaternary structure, important for controlling allisteric effect
Some need cofactors

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17
Q

How will apoenzymes bind to a cofactor?

A
  • Non covalent bonds: can dissociate

- Covalent bonds: cannot dissociate

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18
Q

What is an apoenzyme?

A

Enzyme with minimal activity which will bind to a cofactor to have full activity (holoenzyme)

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19
Q

What are the two kinds of enzyme cofactors?

A
  • Inorganic: metal ions

- Organic: coenzymes or prosthetic groups (vitamins)

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20
Q

Which are bound more tightly: coenzymes or prosthetic groups?

A

Prosthetic more tight than coenzymes

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21
Q

Do enzymes change the chemistry of the reaction?

A

NO

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22
Q

How do they accelerate the reaction?

A

Lowering the energy of activation

Stabilizing the transition state intermediate

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23
Q

How is the transition state intermediate in solution?

A

Highly unstable

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24
Q

Define energy of activation.

A

Amount of energy required to achieve the transition state

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25
Q

In an exothermic reaction, which rate is faster?

A

Forward > backward

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26
Q

In an endothermic reaction, which rate is faster?

A

Backward > forward

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27
Q

What delta G is spontaneous?

A

Negative

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28
Q

When does the cleavage of a peptide bond occur?

A

when reactions acquire sufficient collision E to enter the transition state

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29
Q

If Ea is high, how is the speed of Rx?

A

slow

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30
Q

What do enzymes do to speed things up?

A

decrease ea

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31
Q

What are the 3 things that make enzymes lower the Ea and speed Rx?

A

1) Catalytic pockets that orient substrates to be positioned properly in the reactive conformation of the active side
2) Amino acids that bring acids/bases for bond making/breaking into close proximity of the bonds
3) The transition state intermediate forms multiple contact points which is stabilized

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32
Q

Are enzymes consumed in a reaction?

A

Catalysts, by definition, are NOT consumed in a reaction

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33
Q

What do serine proteases do?

A

Catalyze the hydrolysis of the peptide bond

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34
Q

What is the catalytic triad?

A

Histidine 57, Aspartate 102, Serine 195

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35
Q

What is the catalytic triad’s function?

A

Charge is moved to a region where it can drive catalysis (turns serine into a nucleophile)

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36
Q

What do site specific mutations of the triad do?

A

alanine for ex would kill the relay network

changing alignment would also decrease

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37
Q

Where are serine proteases found?

A

In GI, break down peptides into amino acids

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38
Q

What determines serine proteases specificity?

A

The shape of the binding pocket determines the types of substrates or peptides the enzyme can cleave

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39
Q

What can chymotrypsin cleave?

A

Bulky sidechains (Phenylalanine, Tryptophan, Isoleucine, Tyrosine)

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40
Q

What can Trypsin cleave?

A

Long sidechains + charge (Lysine, Arginine)

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41
Q

What can elastase cleave?

A

small side chain (Alanine, Glyine, Valine)

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42
Q

Where do serine proteases cleave?

A

At the C terminus by hydrolyzing the peptide bond

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43
Q

Which serine protease has an ionic sidechain?

A

Trypsin

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44
Q

What happens if a substrate has more than 1 AA that a protease could cleave?

A

It will cleave multiple times

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45
Q

What mother group are proteases?

A

Hydrolases

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46
Q

Describe the charge transfer relay network.

A

Learn it.

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47
Q

What is the name of the intermediate that needs to be cleaved?

A

Acyl intermediate

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48
Q

What are the transition states?

A

1) Cleaving peptide bond

2) Cleaving acyl intermediate

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49
Q

Name the 3 factors that influence Rx rate.

A

1) Temperature
2) pH
3) Enzyme concentrations

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50
Q

What is the Q10 rule?

A

Activity doubles with ever 10oC

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51
Q

What are the Q10 rule limitations?

A

at a certain T, proteins will denature

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52
Q

What will pH change?

A

Ionization state of substrate

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53
Q

What do optimal curves look like? Not optimal?

A

Learn it.

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54
Q

Name the 3 reasons why pH curves aren’t usually optimal.

A

1) pH extremes denatures proteins
2) amino acid required for catalysis = ionized
3) Substrates become ionized and no longer bind to enzyme

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55
Q

How does enzyme concentration influence rate?

This holds provided what?

A
  • reaction rates increase linearly with amount of enzyme

- provided that the enzyme concentration is much lower than the substrate concentration

56
Q

Define enzyme kinetics.

A

Chemistry involved in converting substrate to product. Study of reaction rates

57
Q

What do kf and kr depend on?

A

Constant, specific to enzyme, pH and temp

58
Q

What is initial velocity?

A

rate of rx shortly after you add enzyme to substrate

total product formed/time elapsed

59
Q

Name 2 Michaelis and Menton discoveries.

A

1) If you hold substrate, increase enzyme, increase rate

2) If you hold enzyme, increase substrate, will reach concentration where you can’t get it to go faster

60
Q

Why can’t the reaction go faster sometimes?

A

Intermediate: all of the enzymes were bound and couldn’t produce more product

61
Q

What did Michaelis and Menton suggest?

A

That Rx proceed via the formation of the ES intermediate.

62
Q

Describe Michaelis and Menton chem equation.

A

E + S ->k1 k2 -< ES -> P + E

  • E: free enzyme
  • S: substrate
  • ES: Michaelis and Menton complex
  • P: product
63
Q

What happens in the Michaelis and Menton equation?

A

ES stays constant until substrate concentration drops, then ES drops, while E will rise and P will rise

64
Q

Is E free at the end of Michaelis and Menton?

A

Not really, will convert products back.

65
Q

Describe Michaelis and Menton initial velocity equation.

A

vo = Vmax (S)/km + (S)

66
Q

Explain the concentration over time graph.

A

As substrate decreases, product increases
ES will increase, reach a steady state, until substrate drops
E will decrease, then exponentially increase an reach a steady state

67
Q

ES is at steady state until when?

A

Until substrate decreases

68
Q

What are km and vmax specific to?

A

Particular to specific enzymes

69
Q

What does the curve look like for a single substrate reaction?

A

Hyperbolic

70
Q

What are the 2 stages to a single substrate reaction?

A

1) E + S -km-> ES (binding and formation of ES complex)

2) ES -kcat-> E + P (catalysis and breakdown of ES to products)

71
Q

What is the rate limiting step?

A

vmax

72
Q

How is km expressed?

A

as a concentration

73
Q

Name the 2 meanings of km.

A

1) The concentration of substrate at 1/2 vmax - WHEN 50% of the enzyme is bound to substrate
2) The dissociation constant for the ES complex when k3 &laquo_space;k2. Under these conditions km = k2/k1 = ks

74
Q

When (S)&raquo_space; km, what is vo?

A

Vo = Vmax

75
Q

When (S) = km, what is vo?

A

Vo = Vmax/2

76
Q

What forms are the substrate in at km?

A

50% is ES, other 50% is free enzyme

77
Q

For km’s function as a dissociation constant, what needs to hold true?

A

Dissociation constant for ES when k2&raquo_space;» k3

78
Q

What is km’s formula?

A

km = k2/k1 (k3 can be ignored)

79
Q

What is the range of km?

A

10^-2 (weak binding) to 10^-7 (tight binding) M

80
Q

Km is the concentration of substrate to keep _____ in the _____.

A

50% of enzyme in the ES complex

81
Q

How do we make TSI more populated?

A

You need more substrate

82
Q

Which step is rate limiting?

A

k3

83
Q

What does Vmax describe? When?

A

Describes the efficiency of the catalyst when all of the enzyme is in the ES complex

84
Q

What is the Vmax formula?

A

ES -> E + P

Vmax = k3 (E)

85
Q

What does (E) depend on? Units?

A

depends on enzyme, concentration of product formed/time

86
Q

What is kcat? Units?

A

How many reactions that each molecule of enzyme can catalyze over unit time

87
Q

Differentiate the kcats catalase and lysozyme.

A

Catalase: 40 000 000 s^-1
Lysozyme: 0.5s^-1

88
Q

How do you determine km and vmax experimentally?

A

Series of 6 tubes, each will have a different substrate concentration

  • Add fixed amount of enzyme to each tube
  • Then you need to plot
89
Q

How do you figure out the initial velocity experimentally?

A

Plot and draw a tangent at the curve

90
Q

What are the effects of increasing (S) on enzyme kinetics?

A

1) When substrate concentration is low, an increase in (S) causes a proportional increase in enzyme activity
2) At high (S), when the enzyme is already saturated, increasing (S) has no effect on activity because vmax has already been attained.

91
Q

What are the effects of increasing (E) on enzyme kinetics?

A

Increasing (E) will always increase vmax regardless of the starting concentration of enzyme.

92
Q

What happens when km increases?

A

An enzyme’s affinity for its substrate decreases

93
Q

How do you get an M-M curve? What does it plot?

A
  • Plot initial velocities

- Vo (y) vs S (x)

94
Q

Name the 4 types of enzyme inhibition.

A

1) Competitive
2) Mixed inhibition or Noncompetitive
3) Uncompetitive
4) Irreversible Inhibition

95
Q

Which type of enzyme inhibition bond covalently?

A

Irreversible inhibition

96
Q

Which type of enzyme inhibition do not bond covalently?

A

Competitive, Mixed Inhibition or Noncompetitive, Uncompetitive

97
Q

What do competitive enzyme inhibitors bind to? How do they influence Km and Vmax?

A
  • Binds to E
  • Increases Km
  • Vmax stays the same
98
Q

What do noncompetitive enzyme inhibitors bind to? How do they influence Km and Vmax?

A
  • Bind to E or ES
  • Km stays the same
  • Vmax decreases
99
Q

What do uncompetitive enzyme inhibitors bind to? How do they influence Km and Vmax?

A
  • Bind to ES ONLY when substrates are bound
  • Km decreases
  • Vmax decreases
100
Q

What happens if you decrease ES?

A

You decrease the rate at which substrate is converted to product

101
Q

Provide two examples of competitive inhibition.

A

1) Protease inhibitors to treat HIV/AIDS

2) Alcohol dehydrogenase

102
Q

How do protease inhibitors to treat HIV/AIDS work?

A
  • Block protease -> stops maturation of virus, but does not eliminate
  • Protease sits at the interface between two enzymes (diamer) -> disrupts function, since precursor for viral protein cannot fit into catalytic pocket
103
Q

How does alcohol dehydrogenase work?

A
  • If you drink methanol, enzyme will convert to formaldehyde

- Shooting ethanol into your veins will out compete methanol and minimize toxic effects

104
Q

Provide an example of non-competitive inhibition.

A
  • Hepatitis C Virus RNA Polyerase Enzyme
  • Drug shuts down polymerase -> stops production of Hepatitis C
  • Binds to cleft outside catalytic region of protein
105
Q

When does uncompetitive inhibition work best?

A

When substrate concentration is high

106
Q

What is the formula for uncompetitive inhibition?

A

V = ((Vmax ^app)(S)) / ((km^app) + (S))

107
Q

What is another name for irreversible inhibitors?

A

Suicide inhibitors

108
Q

Name 2 examples of irreversible inhibitors

A

1) Sarin Gas

2) Aspirin

109
Q

What does Sarin gas look like?

A

similar to acetylcholine

110
Q

What will sarin gas react with?

A

enzyme will clear acetylcholine in synaptic cleft, sarin will react with serine -> kill enzymes by irreversible inhibitor

111
Q

What does sarin gas provide physiologically?

A

Diaphragm muscles = continuously contracted -> stops breathing -> death

112
Q

How do you treat sarin gas?

A

You need to allow the body time to generate new acetylcholenesterase

113
Q

How does aspirin work?

A
  • Decreases inflammation
  • Cyclooxygenase 2 acts on arachidonic acid -> prostaglandin
  • Aspirin forms a bond with reactive serine -> acetylate serine -> kills the enzyme
  • decreases production of prostoglanding by modifying enzyme
114
Q

What kind of information does km give you?

A

Gives you information on the affinity in which the substrate binds to an enzyme

115
Q

What enzyme class do dehydrogenase and catalase belong to?

A

Oxidoreductase

116
Q

What enzyme class do methylase, protein kinase and polymerase belong to?

A

Transferase

117
Q

What enzyme class does Enoyl-CoA hydratase belong to?

A

Lyase

118
Q

What enzyme class does peptide synthase and aminoacyl-tRNA synthetase belong to?

A

Ligase

119
Q

Are cofactors proteins?

A

No, non-protein

120
Q

Which enzyme does not require cofactors?

A

Trypsin

121
Q

Name 4 examples of cofactors and their roles.

A

a) Vitamin C (ascorbic acid): collagen synthesis
b) Folic Acid: cell growth, nucleic acid synthesis
c) Thiamin (B1): deficiency = beriberi, nerve degeneration, muscle disease
d) Vitamin K: prothrombin formation clotting protein

122
Q

Name the 5 serine proteases.

A 
Chymotrypsin
Trypsin
Elastase
Thrombin
Subtilisin
123
Q

Discuss the roles of Aspartate 102 in the catalytic triad.

A
  • Provides the negative charge to the serine to turn it into a nucleophile and start the reaction chain that will cleave the peptide bond.
  • The aspartate side chain holds the histidine in the correct orientation promotion general acid-base catalysis
124
Q

Discuss the role of Histidine 57 in the catalytic triad.

A

The histidine side chain becomes protonated and unprotonated promoting general acid-base catalysis

125
Q

Discuss the role of Serine 195 in the catalytic triad.

A

Negatively charged so it will carry a nucleophilic attack to cleave the peptide bond (will attack the carbonyl carbon)

126
Q

What kind of enzyme is phosphoglycerate mutase?

A

Isomerase

127
Q

What kind of enzyme is aldolase?

A

Lyase

128
Q

What kind of enzyme is enolase?

A

Lyase

129
Q

What is the equation for catalytic efficiency?

A

cat efficiency = kcat/km

130
Q

What is the lineweaver-burk equation?

A

1/vo = km/vmax + 1/vmax

131
Q

When k3 «&laquo_space;k2, what is km?

A

km = k2/k1

132
Q

What is the equation for kcat?

A

kcat = vmax/Et

133
Q

What is the equation for vmax?

A

vmax = k3 (E)

134
Q

Name two examples of enzymes that do not have the suffix “ase”.

A
  • Lysozyme
  • Trypsin
  • Chymotrypsin
135
Q

Define allosteric enzyme.

A

Subtle regulations to control and meet cells metabolic processes

1) Biochemistry I (12 decks)

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