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Enzymes Flashcards

1
Q

Highly specific, extremely fast, biological catalysts

-Proteins

A

Enzymes

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2
Q

Mutations in proteins and enzymes are the cause of many

A

Diseases

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3
Q

Enzymes can be used as drugs, an example of this is the clot buster

A

Activase

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4
Q

Enzymatic reactions are multi-step reactions. The first step in an enzyme reaction is the enzyme binds

A

Substrate (forms the ES complex)

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5
Q

The second step in an enzyme reaction is the

A

conversion of ES to EP

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6
Q

The third step of an enzymatic reaction is the

A

Dissociation of P and regeneration of E

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7
Q

A molecule that accelerates a chemical reaction and is regenerated at the end of the reaction

A

Catalyst

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8
Q

Says that an enzyme has an active site that fits only a specific substrate

-ex: yeast fermented the D- but not L- forms of glucose, mannose, and galactose

A

Fisher’s lock and key model

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9
Q

A three dimensional cleft formed by catalytic amino acids that come from different parts of the protein sequence

A

Enzymes active site

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10
Q

Bind substrates but don’t carry out a chemical reaction

A

Receptors

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11
Q

Bind substrates and carry out chemical reactions

A

Enzymes

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12
Q

Close together in tertiary structure, but not in primary structure

A

Catalytic amino acids

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13
Q

Only a very small portion of an enzymes aminos function in the active site, the rest serve as a

A

Scaffold

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14
Q

Small pockets lined with a few catalytic amino acids that participate in substrate binding and catalysis

A

Active site

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15
Q

Small part of the total volume of the enzyme and is non-polar (excludes water unless water is a reactant)

A

Active site

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16
Q

The nonpolar characteristics of active sites enhances substrate binding by increasing

A

Electrostatic interactions

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17
Q

Substrates bind active sites by way of many

A

weak non-covalent interactions

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18
Q

What is the energy for a

  1. ) Covalent interaction?
  2. ) Non-covalent interaction
A
  1. ) 50 kcal/mol

2. ) 0.5-2 kcal/mol

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19
Q

Enzymes can undergo many catalytic cycles because substrates and products bind

A

reversibly

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20
Q

Precise active site conformation of glucokinase explains specific binding and reaction of ATP with glucose but not galactose. Why does galactose not bind even though the two differ by only a single hydroxyl?

A

Cooperative binding

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21
Q

The lock and key model proved to be inadequate when looking at glucokinase and hexokinase because

A

Since they bound glucose, they should have been able to bind water and react with ATP, but they could not

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22
Q

The lock and key model failed to explain why ATP did not react with water, which paved the way for the

A

Induced-fit model

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23
Q

Summarize the induced fit model

A

Substrate binding causes a conformational shift in the enzyme, which stabilizes the active conformation and allows catalysis

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24
Q

In the induced fit model, a specific substrate activates the enzyme by

A

Orienting catalytic groups on the enzyme

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25
Q

What was the experimental evidence supporting the induced fit model?

A

The binding of glucose induced a large conformational change in glucokinase

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26
Q

In the case of ATP transferring a phosphate to NMP rather than water, we see that the induced fit conformational change assures that a catalytically competent complex is formed only when

-prevents the reaction with water

A

Both ATP and NMP are bound to NMP kinase

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27
Q

Enzymes increase the rates of reactions by a factor of

A

10^6-10^17 times

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28
Q

The minimum energy required for two molecules to react

-inversely proportional to reaction rate

A

Activation energy

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29
Q

Enzymes work by decreasing the

A

Activation barrier (transition state energy)

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30
Q

Enzymes have no effect on the

A

Gibbs free energy

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31
Q

Enzymes create a new reaction pathway with a lower activation energy through specific binding to the

A

Transition state

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32
Q

How do enzymes lower the transition state energy?

A

Tighter binding to transition state than to substrate

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33
Q

What are five ways enzymes speed up the rate of a reaction?

A
  1. ) Proximity (all)
  2. ) Stabilization of transition state (all)
  3. ) Covalent or nucleophilic catalysis (some)
  4. ) Acid-base catalysis (most)
  5. ) metal ion catalysis (many)
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34
Q

Increase the effective concentration of reactants that are in the proper orientation

A

Proximity

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35
Q

In a chain of successive reactions, the rate enhancement due to proximity increases as the

A

Products structure becomes more rigid (less ability to be in improper orientation)

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36
Q

What are the three enzymatic strategies employed by the protease enzyme chymotrypsin?

A
  1. ) Nucleophilic or covalent catalysis
  2. ) General acid-base catalysis
  3. ) Transition state stabilization (oxyanion hole)
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37
Q

The serine residue in the active sight of chymotrypsin is a powerful

A

Nucleophile (but must be deprotonated)

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38
Q

The pKa of the side chain of serine is

A

pKa = 13

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39
Q

The serine residue in the active site of chymotrypsin is turned into a potent nucleophile by deprotination using

A

Acid-base catalysis

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40
Q

The extremely reactive serine residue in chymotrypsin is created by the

A

Catalytic triad (Ser, His, Asp)

-His accepts a proton to become HisH+

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41
Q

In the chymotrypsin active site, once serine is deprotonated, it

A

Nucleophilically attacks the carbonyl carbon of amino acid, forming the tetrahedral intermediate (oxyanion hole), which then reforms the double bond and kicks off the amine

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42
Q

Serine nucleophilically attacking the carbonyl carbon is an example of

A

Covalent Catalysis

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43
Q

Binds the transition state tightly and stabilizes the transition state by way of H-bonds which were not possible in the reactant

A

Oxyanion hole

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44
Q

A space in the enzyme active site that is ready to bind a negatively charged group

A

Oxyanion hole

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45
Q

Summarize how chymotrypsin cleaves at the C-terminal end of the aromatic amino acids (Phe, Tyr. Trp)

A

Aspartate H-bonds w/ histidine, the His Nitrogen attacks the serine OH,allowing the SerO- to nucleophilically attack the carbonyl carbon of the amino, forming the tetrahedral intermediate. The oxyanion hole stabilizes the intermediate until the carbonyl is reformed, breaking the amide bond and the amine fragment is released. His then takes a proton from water, which generates OH, which attacks the carbonyl carbon of the residue still bound to serine, forming the tetrahedral intermidiate. The electrons reform the double bond, releasing a now carboxylic acid from serine. Serine takes a proton back from histidine.

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46
Q

A reaction where ΔG

A

Exergonic Reaction

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47
Q

A reaction where ΔG > 0

-Non spontaneous reaction

A

Endergonic reaction

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48
Q

An endergonic reaction can be driven forward by

A

Coupling it to an exergonic reaction

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49
Q

What is the ΔG˚ of ATP hydrolysis?

A

-30.5 kJ/mol

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50
Q

What are three reasons that ATP hydrolysis is so favorable?

A
  1. ) ADP and Pi (products) are more stable than ATP (reactant)
  2. ) Electrostatic repulsion (ADP has -2 charge and ATP has -3)
  3. ) Resonance stabilization of Pi
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51
Q

What is a great example of a coupling reaction?

A

Coupling the phosphorylation of Glucose to form glucose-6-phosphate with ATP hydrolysis

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52
Q

The ΔG˚ value provides absolutely no information about

A

Reaction rates

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53
Q

Kcat is the rate constant of

A

ES —> E + P

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54
Q

The velocity of an enzyme reaction is proportional to the

A

Concentration of the ES complex i.e. [ES]

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55
Q

How can we use the MM equation to determine Kcat and Km?

A

Measure velocity of the reaction

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56
Q

How do we measure the velocity (speed) of the reaction?

A

Measure the change in concentration of substrate or product over the time of the enzymatic reaction

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57
Q

The MM equation shows that enzymatic rate/ velocity increases linearly with

A

Enzyme concentration

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58
Q

The MM equation shows that enzymatic rate increases asymptomatically with

A

Increasing [S]

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59
Q

On a plot of velocity vs [S], Km can be thought of as

A

Vmax/2

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60
Q

On a plot of velocity vs [S], Kcat can be thought of as

A

Vmax/[E]

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61
Q

The ratio of Kcat/Km is called the

-measure of enzyme efficiency

A

Specificity constant

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62
Q

From a definition standpoint, we can think of Km as being inversely proportional to the

A

The enzymes affinity for substrate

  • Large Km = small affinity
  • Small Km = Large affinity
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63
Q

Result in a high specificity constant

A
  1. ) Rapid Turnover (large kcat)

2. ) High enzyme affinity for substrate (Low Km)

64
Q

A measure of the affinity of the substrate for the enzyme

A

Km

65
Q

Characteristic for an enzyme for a particular substrate

-Changes with pH or Temperature

A

Km

66
Q

Km values are usually close to

A

Physiological substrate concentration

67
Q

The maximum velocity with which the enzyme can catalyze the reaction

A

Vmax (units = M/s)

68
Q

The turnover number of an enzyme, representing the number of moles of substrate converted to products persecond per mol of enzyme

A

Kcat (units s^-1)

69
Q

Vmax is linearly dependent on

A

[E]

70
Q

Some enzymes require cofactors. An enzyme and it’s cofactor are called a

A

Holoenzyme

71
Q

Small organic molecules, mostly derived from vitamins, that are either noncovalently bound to the enzyme, or covalently bound (prosthetic groups)

A

Coenzymes

72
Q

Apoenzymes without their cofactor are

A

Inactive

73
Q

Provide the functionalities not found in the natural amino acids

A

Coenzymes

74
Q

Have different primary structures or amino acid sequence, but catalyze the same chemical reaction and act upon the same substrate

-Thought to have evolved from gene duplication and divergence

A

Isozymes

75
Q

Allow fine tuning of metabolism to meet the needs of a given tissue or developing stage

A

Isozymes

76
Q

Do isozymes have the same Km and kcat as their enzyme isomers?

A

No

77
Q

Measurement of isozyme levels helps in

A

diagnosis

78
Q

What happens within one day of heart muscle damage?

-indicates myocardial infarction

A
  1. ) LDH isozyme H4 increases within 12-24 hrs.

2. ) Level of MB creatine kinase in the blood increases

79
Q

Enzyme activity is affected by temperature. Explain how temperature increases rate.

A

As temp increases, there are more molecular collisions between E and S

80
Q

Enzyme activity is affected by temperature. Explain how temperature decreases rate.

A

When temp gets too high, proteins are denatured, causing the decrease in rate

81
Q

What are the two negative effects that pH can have on an enzyme?

A
  1. ) extreme pH’s irreversibly denature the enzyme and activity is lost forever
  2. ) Can reversibly affect the enzyme by ionizing the functional groups involved in catalysis
82
Q

Enzymes in different organs have different pH optimum, but most intracellular enzymes have a pH optimum of

A

pH = 7.2

83
Q

Enzyme concentration is regulated by

A
  1. ) Synthesis (transcription, translation, etc.)

2. ) degradation (proteolysis)

84
Q

Enzyme activity is regulated by compartmentalization in

A

Cell organelles

85
Q

Enzyme activity is regulated by post translational modifications such as

A

Phosphorylation, glycosylation, methylation, etc.

86
Q

Enzyme activity is regulated by regulatory proteins such as

A

Transcription Factors

87
Q

Enzyme activity is inhibited by

A

Feedback inhibitors, enzyme inhibitors, and products

88
Q

ADP-ribosylation of EF2 blocks its capacity to carry out translocation of the growing polypeptide chain, thus

-Accounts for remarkable toxicity of diptheria toxin

A

Protein synthesis ceases

89
Q

Over 95% of protein phosphorylation occurs on

A

Serine resiues

90
Q

Highly negatively charged phosphoryl group can alter

A

Substrate binding and catalytic activity

91
Q

Is reversible and fast and it can either activate or inhibit the enzyme

A

Phosphorylation

92
Q

Abnormal levels of protein phosphorylation are a cause or consequence of major diseases such as

A

Cancer, diabetis, and arthritis

93
Q

What is an irreversible way to activate enzymes?

A

Proteolysis

-apoptosis mediated by caspases from procaspases

94
Q

A prime example of feedback regulation of an enzyme is that of the allosteric enzyme Aspartate Transcarbamylase, which is activated by? inhibited by?

A

Activated by ATP

Inhibited by CTP

95
Q

Enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site.

A

Allosteric Enzymes

96
Q

All allosteric enzymes are

A

Oligomeric

97
Q

Allosteric molecules (bind in the allosteric site) do not resemble the

A

Substrate

98
Q

Allosteric enzymes can be distinguished kinetically because they show

A

Sigmoidal curves

99
Q

Do allosteric enzymes follow MM kinetics?

A

No

100
Q

Enzymes following MM kinetics show a

A

Hyperbolic curve

101
Q

Allosteric curves are sigmoidal due to the allosteric enzyme’s

A

Cooperative binding

102
Q

Allosteric enzymes exist in which two equilibrium conformations?

A
  1. ) Active (R) state

2. ) Inactive (T) state

103
Q

Binds substrate better and/or has higher catalytic activity

A

R-state

104
Q

How does an allosteric activator increase substrate binding and/or activity?

A

Binds to the allosteric site and stabilizes the R-state

105
Q

How does an allosteric inhibitor decrease substrate binding and/or activity?

A

Binds to the allosteric site and stabilizes the inactive T-state

106
Q

In AcT, the inactive T-state is favored by

A

CTP binding

107
Q

Inhibitors shift the allosteric sigmoidal curve to the?

A

Right

108
Q

Activators shift the allosteric sigmoidal curve to the?

A

Left

109
Q

The basis for clinical drug therapies: antiviral, antibacterial, and antitumor therapies

A

Enzyme inhibition by small molecules

110
Q

What are the two main classes of inhibitors?

A
  1. ) Irreversible inhibitors (bind covalently)

2. ) Reversible inhibitor (bind reversibly)

111
Q

What are the three types of reversible inhibitors?

A
  1. ) Competitive
  2. ) Noncompetitive
  3. ) Uncompetitive
112
Q

Substrate analogs that form a covalent bond with and active site amino acid

-ex: penicillin bonding to transpeptidase

A

Irreversible inhibitors

113
Q

Aspirin is an example of an

A

Irreversible inhibitor

114
Q

Bind the same active site as the substrate

A

Competitive inhibitor

115
Q

Bind to a site separate from the active site

A

Noncompetitive inhibitor

116
Q

Stable molecules that resemble geometric and/or electronic features of the highly unstable transition state.

-Potent inhibitors

A

Transition state analogues

117
Q

What are the kinetic features of a competitive inhibitor?

A
  • Vmax is unchanged
  • Km increases

No inhibition at high [S]

118
Q

What are the kinetic features of a noncompetitive inhibitor?

A
  • Km is unchanged
  • Vmax decreases

-High [S] does not overcome inhibition

119
Q

Where do the lines intersect on a linweaver-burke plot for

  1. ) competitive inhibition?
  2. ) noncompetitive inhibition?
A
  1. ) y-axis

2. ) negative x-axis

120
Q

The most widely prescribed drug that lowers cholesterol

A

Statins (competitive inhibition)

121
Q

Statins act by inhibiting

A

HMG-CoA reductase

122
Q

What is Pi?

A

Inorganic Phosphate

123
Q

The gibbs free energy represents the

A

Maximal work under a set of conditions

124
Q

ATP is so reactive because it has three phosphates and a charge of

A

-3 or -4, averaging to -3.5

125
Q

Where do coupled reactions occur in the enzyme?

A

On the same active site

126
Q

The dissociation constant of [ES]

A

Kcat

127
Q

What are the trends of the [ES] dissociation constant Km?

A

The smaller the Km, the faster the reaction typically is

-Small Km means enzyme does not dissociate from [ES] and reaction proceeds

128
Q

What is the rate limiting step of an enzymatic reaction?

A

Kcat

129
Q

When [S] is in excess, the velocity increases linearly with

A

[E]

130
Q

Why does the rate increase asymptomatically with increasing substrate concentration?

A

At some point all of the enzyme active sites are saturated with substrate, and Vmax has been reached

131
Q

The higher the value of Km, the

A

slower the reaction

132
Q

Mutations in enzymes that affect the ability of substrate to bind will also effect

A

Km

133
Q

What are the units of Km?

A

M, mM, or uM

134
Q

Is roughly equal to the physiological substrate concentration

A

Km

135
Q

What is the fastest known enzyme?

-Called the perfect enzyme

A

Carbonic anhydrase

136
Q

An inactive enzyme without its cofactor

A

Apoenzyme

137
Q

Allow variability that expands beyond that of the 20 amino acids in enzymes

A

Coenzymes

138
Q

What is a common example of isozymes?

A

Hexokinase and Glucokinase

139
Q

The liver synthesizes and utilizes

A

Glucokinase

140
Q

The optimum temperature of human enzymes is

A

38 degrees celcius

141
Q

Km and Kcat values are affected by

A

Temperature and pH

142
Q

Why is pH so important to enzymes?

A

The H-bonds that form from the catalytic aminos will not be possible if pH is outside of optimum range

143
Q

We don’t want to have to synthesize an enzyme every time we need it, because that will take to long. So, we synthesize enzymes and keep them in the inactive form called a

A

Zymogen

144
Q

The activation of a zymogen to an enzyme is

A

Irreversible

145
Q

Can be used to turn an enzyme off by inactivating a Ser, Thr, or Tyr in the active site

A

Phosphorylation

146
Q

An example of enzyme regulation by specific proteolysis

A

Zymogen activation

147
Q

Regulation of an enzyme at a distance (how many metabolic pathways are regulated)

A

Allosteric Regulation

148
Q

All allosteric enzymes are oligomeric, meaning they are

A

Dimers, trimers, tetramers, etc

149
Q

Do not look like the enzymes substrate, thus they do not bind to the active site. Instead, they bind to a regulatory site and cause some form of conformation change in the enzyme which either activates or inhibits the enzyme

A

Allosteric Effectors

150
Q

Their association with an enzyme is not allosteric because they actually bind to the active site

A

Cofactors

151
Q

Instead of a Km, allosteric enzymes have a

A

K0.5

152
Q

What type of allosteric inhibitor or activator affects K0.5 but not Vmax?

A

K-type

153
Q

What type of allosteric inhibitor or activator affects Vmax but not K0.5?

A

V-type

154
Q

AcT is a hexamer, the active site is at the interface of two subunits in the T-state. When an activator is added, the interface is broken, freeing the active sites and stabilizing the

A

R states

155
Q

Most drugs are

A

Inhibitors that target enzymes

BMS (62 decks)

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