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CHE 541 > 6 - Energy > Flashcards

6 - Energy Flashcards

1
Q

What does energy refer to in biological processes?

A

The biochemical reactions that underlie life

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2
Q

What does RT represent?

A

Thermal energy

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3
Q

How does RT arise?

A

From translation, vibrations, and rotations

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4
Q

What is Kd or Keq related to?

A

Free energy (delta G)

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5
Q

What are the equations for delta G?

A

delta G = delta H - T delta S = -RTln(Kd)

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6
Q

What is the common equation for an enzyme catalysis reaction?

A

E + S –> ES –> EP –> E + P

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7
Q

What is Ea (delta G dagger) in an enzyme catalysis reaction?

A

The energy to go from ES to EP

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8
Q

What does the energy of ES and EP determine?

A

Kd (delta G = -RTln(Kd))

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9
Q

How do enzymes catalyze reactions?

A

By lowering the activation energy (stabilize transition state)

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10
Q

What determines the rate of the forward reaction?

A

The energy barrier between ES and the transition state

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11
Q

What determines the rate of the reverse reaction?

A

The energy barrier between EP and the transition state

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12
Q

What determines the equilibrium between ES and EP?

A

Their energy levels (not the energy barrier between them)

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13
Q

What can be used to describe the populations of states?

A

The boltzmann distribution

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14
Q

What is the boltzmann distribution?

A

nES/nEP ~ exp(-(E[ES]-E[EP])/kT)

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15
Q

What is kT?

A

Thermal energy per molecule

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16
Q

What do the distributions of states (nES and nEP) depend on?

A

The temperature and energy state (how close they are)

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17
Q

If the energy difference between two molecules is kT, what is the ratio of concentrations?

A

exp(-1)

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18
Q

What is Ka?

A

An acid dissociation constant

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19
Q

What is the equation for Ka?

A

Ka = [H+][A-]/[HA]

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20
Q

What is Kd?

A

A dissociation constant

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21
Q

What is the equation for Kd?

A

Kd = [A][B]/[AB]

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22
Q

Why is a binding constant usually not used?

A

It can be ambiguous whether it is an association or a dissociation

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23
Q

If a reaction is favorable, what is true?

A

delta G < 0

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24
Q

What factors does delta H cover?

A

H-bonding, VDW, electrostatics, etc.

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25
Q

What happens to the reaction rate if the ES complex is stabilized?

A

The forward reaction decreases, because there is a higher energy barrier to overcome

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26
Q

What happens to the reaction rate if the ES complex is destabilized?

A

The forward reaction increases, because there is a lower energy barrier to overcome

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27
Q

How can an ES complex be stabilized?

A

Increase of entropy, stable electrostatics, H-bonding, VDW

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28
Q

How can an ES complex be destabilized?

A

Decrease of entropy, unstable electrostatics

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29
Q

If the energy of EP is the same, but the energy of ES decreases, what happens to the equilibrium constant?

A

It decreases (more ES)

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30
Q

What is the equation for delta delta G?

A

delta delta G = -RTln(Kd[A]/Kd[B])

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31
Q

What does a delta G tell you?

A

A large number of interactions between the ligand and enzyme

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32
Q

What does a delta delta G tell you?

A

The contribution to free energy based on one functional group

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33
Q

What is the range of energetics?

A

0-15 kcal/mol

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34
Q

What is the consequence of energetics occurring over a small range?

A

One cannot determine beforehand which interactions are the most important, since they are all comparable in energy

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35
Q

If a delta delta G is positive, what does that tell you?

A

Unfavorable energy (rise in free energy, less stable)

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36
Q

If a delta delta G is negative, what does that tell you?

A

Favorable energy (fall in free energy, more stable)

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37
Q

How can a water molecule influence Kd?

A

It can H-bond with side chains, shifting the Kd

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38
Q

For each 10 fold change in Kd, what is the change in free energy?

A

1.4 kcal/mol

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39
Q

What is a typical value for RT?

A

0.6 kcal/mol

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40
Q

What forces are at play for the hydrophobic effect?

A
  1. Restriction in substrate degree of freedom (unfavorable)
  2. Restriction in side chain motion (unfavorable)
  3. Release of surface bound water (favorable)
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41
Q

What is the second law of thermodynamics?

A

Isolated systems spontaneously evolve towards maximum entropy

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42
Q

What is the statistical definition of entropy?

A

S = kln(W)

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43
Q

What is the thermodynamic definition of entropy?

A

delta S = qrev/T

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44
Q

What is the importance of the statistical definition of entropy?

A

It is the common sense definition

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45
Q

What is the importance of the thermodynamic definition of entropy?

A

It relates to free energy (delta G)

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46
Q

For a compressed gas moving a piston, what is the work done?

A

-qrev = -T delta S

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47
Q

How does energy transfer as heat work in biological systems?

A

Vibrational, rotational, and translational degrees of freedom

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48
Q

How does energy transfer as work work in biological systems?

A

Changes the ordering of a protein (folding, etc.)

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49
Q

What is an isothermal expansion?

A

Heat is exchanged for constant temperature

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50
Q

What is an adiabatic expansion?

A

Heat is not exchanged, so temperature changes

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51
Q

Under constant pressure, what is the heat transfer equal to?

A

The change in enthalpy

52
Q

In what energy range does biochemistry exist?

A

Between RT and 10 kcal/mol

53
Q

If someone changes the Kd by a factor of 10, what does that mean for the energy?

A

It is a change in delta G slightly above RT (1.4 vs 0.6)

54
Q

Is actin polymerization spontaneous or nonspontaneous?

A

Spontaneous

55
Q

How is actin depolymerized?

A

Through ATP hydrolysis

56
Q

What is used to correlate rate constants to activation energy?

A

Arrhenius equation

57
Q

What is the Arrhenius equation?

A

k=Aexp(Ea/RT)

58
Q

What does the rate of a reaction depend on?

A

Ea (k - Arrhenius equation) and ES (Rate = k[ES])

59
Q

If thermal energy is available, can a reaction still be accomplished?

A

Yes, because due to boltzmann distribution some molecule will have enough energy for the reaction

60
Q

What rule of thumb is for rate and temperature?

A

Rate doubles with every change in 10C

61
Q

How can one measure activation energies experimentally?

A

Measure k as a function of T, and fit to ln(k) = -Ea/RT + ln(A)

62
Q

How do enzymes lower the transition state?

A

By stabilizing the intermediate complex, thus lowering the energy

63
Q

What happens if an enzyme stabilizes the ES complex?

A

The activation energy increases, so the reaction rate decreases

64
Q

How does chymotrypsin lower activation energy?

A

It stabilizes the tetrahedral intermediate that forms

65
Q

How does HEW lysozyme lower activation energy?

A

It has negative charge to stabilize the positive charge in the transition state

66
Q

How are drugs designed to inhibit enzymes?

A

They mimic the transition state, but do not get converted into products

67
Q

What does a lower Kd mean for drug design?

A

It has weaker dissociation, so tighter binding, so it takes more energy (delta delta G is negative)

68
Q

What can binding energy be used for?

A

Orient substrate, exclude water, alter structure of substrate to resemble transition state

69
Q

What dictates enthalpic interactions?

A

Coulomb’s law (electrostatics)

70
Q

What is Coulomb’s law for force?

A

F = kq1q2/er^2

71
Q

What is Coulomb’s law for potential energy?

A

E = kq1q2/er

72
Q

In Coulomb’s law, what is e?

A

Dielectric constant

73
Q

What does the dielectric constant describe?

A

How the medium between two objects shield charges

74
Q

What is e for a vaccuum?

A

1 (no shielding)

75
Q

What is e for water?

A

80 (dipoles can shield charge)

76
Q

What is e for water plus salt?

A

> 80 (more shielding)

77
Q

What is e for a protein interior?

A

2-10

78
Q

How is e a fudge factor?

A

You do not need e if you know all the partial charges between two objects

79
Q

How can electrostatic potential be calculated?

A

Using Poisson-boltzmann equation

80
Q

How are electrostatics used in enzyme catalysis?

A

Active sites usually have some interesting electrostatics for chemistry

81
Q

How does acetylcholinesterase use electrostatics?

A

It has a negatively charged funnel to attract the positively charged substrate

82
Q

What is the advantage of the funnel for acetylcholinesterase?

A

It increases the reaction rate (faster than diffusion)

83
Q

How do membrane proteins use the dielectric constant?

A

They can use changes to modulate electrostatic potentials

84
Q

How does the MARCKS protein works?

A

When inserted into a membrane, it can send out positive charge to sequester PIP2 (signaling molecule)

85
Q

How does MARCKS protein get removed from the membrane?

A

Phosphorylation

86
Q

What charges are in play with the MARCKS protein?

A

Positive Lys interacts with negative PIP2

87
Q

What is needed to calculate electrostatic interactions with Coulomb’s law?

A

A knowledge of geometry and partial charges

88
Q

What law does delta H relate to?

A

Coulomb’s law

89
Q

What law does delta S relate to?

A

Multiplicity / boltzmann

90
Q

What determines orientation for Coulomb’s law?

A

Electron orbitals

91
Q

For an NH group, where is the partial positive charge?

A

Localized on the H (not the N)

92
Q

How can Gly participate in H-bonds?

A

The N and O of the amide have strong partial negative charge, so the H are strongly partial positive

93
Q

What is the dipole moment?

A

Length times charge

94
Q

What is the unit of a dipole moment?

A

Debye

95
Q

What is the dipole moment of water?

A

2 Debye

96
Q

What is the dipole moment of a peptide?

A

3.5 Debye

97
Q

What is the dipole moment of retinal?

A

15 Debye

98
Q

What is the distance dependence of monopole-monopole?

A

1/r

99
Q

What is the distance dependence of monopole-dipole?

A

1/r^2

100
Q

What is the distance dependence of dipole-dipole in a protein?

A

1/r^3

101
Q

What is the distance dependence of dipole-dipole in solution?

A

1/r^6

102
Q

What is the distance dependence of dipole-induced dipole?

A

1/r^4

103
Q

What is the distance dependence of induced dipole-induced dipole?

A

1/r^6

104
Q

What is the distance dependence of steric clashes?

A

1/r^12

105
Q

What is the most favorable distance for two elements found?

A

At the lowest energy (maximize attractive forces)

106
Q

Is a repulsive force positive or negative?

A

Positive

107
Q

Is an attractive force positive or negative?

A

Negative

108
Q

What is the energy of an induced dipole depend on?

A

Polarizability (how easy to move electrons)

109
Q

What is the purpose of calculating electrostatic interactions?

A

All based on Coulomb’s law, can be calculated, and can stabilize enzyme complex

110
Q

How can the pKa of an acid be increased?

A

Destabilize A-, hydrophobic environment

111
Q

How can the pKa of an acid be decreased?

A

Stabilize A-

112
Q

Which dipole dominates in an alpha helix?

A

The C=O dipole (as opposed to the NH dipole)

113
Q

Which direction does the alpha helix dipole point?

A

From the C (+) to the O (-)

114
Q

What is the importance of the alpha helix dipole?

A

It can modulate pKas

115
Q

What is an example of a protein that uses alpha helix dipoles?

A

K+ channel

116
Q

How does a K+ channel use alpha helix dipoles?

A

It orients them to interact with cation (selectivity barrier)

117
Q

If an activity profile is bell-shaped, what does this mean?

A

There are two groups being titrated - one acid and one base

118
Q

What is an example of an enzyme with a bell-shaped activity profile?

A

Ribonuclease

119
Q

What is the mechanism for ribonuclease?

A
  1. His119 acts as a catalytic acid to give up H
  2. His12 acts as a catalytic base to take H
  3. Lys41 stabilizes phosphate intermediate
120
Q

What is the purpose of Asp121 for ribonuclease?

A

It stabilizes His119 as a catalytic acid

121
Q

What is the purpose of Lys41 for ribonuclease?

A

It destabilizes His12 acid, so it remains a catalytic base

122
Q

Is a catalytic acid active at high pH or low pH?

A

Low pH

123
Q

Is a catalytic base active at high pH or low pH?

A

High pH

124
Q

For a titration curve, where is protein activity?

A

The area underneath where both curves intersect

125
Q

In a titration curve, what happens if pKa increases?

A

The curve shifts to the right

126
Q

In a titration curve, what happens if pKa decreases?

A

The curve shifts to the left

127
Q

What is the optimal pH of an enzyme with a bell-shaped activity profile?

A

The average of the pKas

CHE 541 (20 decks)

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