6 - Energy Flashcards
What does energy refer to in biological processes?
The biochemical reactions that underlie life
What does RT represent?
Thermal energy
How does RT arise?
From translation, vibrations, and rotations
What is Kd or Keq related to?
Free energy (delta G)
What are the equations for delta G?
delta G = delta H - T delta S = -RTln(Kd)
What is the common equation for an enzyme catalysis reaction?
E + S –> ES –> EP –> E + P
What is Ea (delta G dagger) in an enzyme catalysis reaction?
The energy to go from ES to EP
What does the energy of ES and EP determine?
Kd (delta G = -RTln(Kd))
How do enzymes catalyze reactions?
By lowering the activation energy (stabilize transition state)
What determines the rate of the forward reaction?
The energy barrier between ES and the transition state
What determines the rate of the reverse reaction?
The energy barrier between EP and the transition state
What determines the equilibrium between ES and EP?
Their energy levels (not the energy barrier between them)
What can be used to describe the populations of states?
The boltzmann distribution
What is the boltzmann distribution?
nES/nEP ~ exp(-(E[ES]-E[EP])/kT)
What is kT?
Thermal energy per molecule
What do the distributions of states (nES and nEP) depend on?
The temperature and energy state (how close they are)
If the energy difference between two molecules is kT, what is the ratio of concentrations?
exp(-1)
What is Ka?
An acid dissociation constant
What is the equation for Ka?
Ka = [H+][A-]/[HA]
What is Kd?
A dissociation constant
What is the equation for Kd?
Kd = [A][B]/[AB]
Why is a binding constant usually not used?
It can be ambiguous whether it is an association or a dissociation
If a reaction is favorable, what is true?
delta G < 0
What factors does delta H cover?
H-bonding, VDW, electrostatics, etc.
What happens to the reaction rate if the ES complex is stabilized?
The forward reaction decreases, because there is a higher energy barrier to overcome
What happens to the reaction rate if the ES complex is destabilized?
The forward reaction increases, because there is a lower energy barrier to overcome
How can an ES complex be stabilized?
Increase of entropy, stable electrostatics, H-bonding, VDW
How can an ES complex be destabilized?
Decrease of entropy, unstable electrostatics
If the energy of EP is the same, but the energy of ES decreases, what happens to the equilibrium constant?
It decreases (more ES)
What is the equation for delta delta G?
delta delta G = -RTln(Kd[A]/Kd[B])
What does a delta G tell you?
A large number of interactions between the ligand and enzyme
What does a delta delta G tell you?
The contribution to free energy based on one functional group
What is the range of energetics?
0-15 kcal/mol
What is the consequence of energetics occurring over a small range?
One cannot determine beforehand which interactions are the most important, since they are all comparable in energy
If a delta delta G is positive, what does that tell you?
Unfavorable energy (rise in free energy, less stable)
If a delta delta G is negative, what does that tell you?
Favorable energy (fall in free energy, more stable)
How can a water molecule influence Kd?
It can H-bond with side chains, shifting the Kd
For each 10 fold change in Kd, what is the change in free energy?
1.4 kcal/mol
What is a typical value for RT?
0.6 kcal/mol
What forces are at play for the hydrophobic effect?
- Restriction in substrate degree of freedom (unfavorable)
- Restriction in side chain motion (unfavorable)
- Release of surface bound water (favorable)
What is the second law of thermodynamics?
Isolated systems spontaneously evolve towards maximum entropy
What is the statistical definition of entropy?
S = kln(W)
What is the thermodynamic definition of entropy?
delta S = qrev/T
What is the importance of the statistical definition of entropy?
It is the common sense definition
What is the importance of the thermodynamic definition of entropy?
It relates to free energy (delta G)
For a compressed gas moving a piston, what is the work done?
-qrev = -T delta S
How does energy transfer as heat work in biological systems?
Vibrational, rotational, and translational degrees of freedom
How does energy transfer as work work in biological systems?
Changes the ordering of a protein (folding, etc.)
What is an isothermal expansion?
Heat is exchanged for constant temperature
What is an adiabatic expansion?
Heat is not exchanged, so temperature changes
Under constant pressure, what is the heat transfer equal to?
The change in enthalpy
In what energy range does biochemistry exist?
Between RT and 10 kcal/mol
If someone changes the Kd by a factor of 10, what does that mean for the energy?
It is a change in delta G slightly above RT (1.4 vs 0.6)
Is actin polymerization spontaneous or nonspontaneous?
Spontaneous
How is actin depolymerized?
Through ATP hydrolysis
What is used to correlate rate constants to activation energy?
Arrhenius equation
What is the Arrhenius equation?
k=Aexp(Ea/RT)
What does the rate of a reaction depend on?
Ea (k - Arrhenius equation) and ES (Rate = k[ES])
If thermal energy is available, can a reaction still be accomplished?
Yes, because due to boltzmann distribution some molecule will have enough energy for the reaction
What rule of thumb is for rate and temperature?
Rate doubles with every change in 10C
How can one measure activation energies experimentally?
Measure k as a function of T, and fit to ln(k) = -Ea/RT + ln(A)
How do enzymes lower the transition state?
By stabilizing the intermediate complex, thus lowering the energy
What happens if an enzyme stabilizes the ES complex?
The activation energy increases, so the reaction rate decreases
How does chymotrypsin lower activation energy?
It stabilizes the tetrahedral intermediate that forms
How does HEW lysozyme lower activation energy?
It has negative charge to stabilize the positive charge in the transition state
How are drugs designed to inhibit enzymes?
They mimic the transition state, but do not get converted into products
What does a lower Kd mean for drug design?
It has weaker dissociation, so tighter binding, so it takes more energy (delta delta G is negative)
What can binding energy be used for?
Orient substrate, exclude water, alter structure of substrate to resemble transition state
What dictates enthalpic interactions?
Coulomb’s law (electrostatics)
What is Coulomb’s law for force?
F = kq1q2/er^2
What is Coulomb’s law for potential energy?
E = kq1q2/er
In Coulomb’s law, what is e?
Dielectric constant
What does the dielectric constant describe?
How the medium between two objects shield charges
What is e for a vaccuum?
1 (no shielding)
What is e for water?
80 (dipoles can shield charge)
What is e for water plus salt?
> 80 (more shielding)
What is e for a protein interior?
2-10
How is e a fudge factor?
You do not need e if you know all the partial charges between two objects
How can electrostatic potential be calculated?
Using Poisson-boltzmann equation
How are electrostatics used in enzyme catalysis?
Active sites usually have some interesting electrostatics for chemistry
How does acetylcholinesterase use electrostatics?
It has a negatively charged funnel to attract the positively charged substrate
What is the advantage of the funnel for acetylcholinesterase?
It increases the reaction rate (faster than diffusion)
How do membrane proteins use the dielectric constant?
They can use changes to modulate electrostatic potentials
How does the MARCKS protein works?
When inserted into a membrane, it can send out positive charge to sequester PIP2 (signaling molecule)
How does MARCKS protein get removed from the membrane?
Phosphorylation
What charges are in play with the MARCKS protein?
Positive Lys interacts with negative PIP2
What is needed to calculate electrostatic interactions with Coulomb’s law?
A knowledge of geometry and partial charges
What law does delta H relate to?
Coulomb’s law
What law does delta S relate to?
Multiplicity / boltzmann
What determines orientation for Coulomb’s law?
Electron orbitals
For an NH group, where is the partial positive charge?
Localized on the H (not the N)
How can Gly participate in H-bonds?
The N and O of the amide have strong partial negative charge, so the H are strongly partial positive
What is the dipole moment?
Length times charge
What is the unit of a dipole moment?
Debye
What is the dipole moment of water?
2 Debye
What is the dipole moment of a peptide?
3.5 Debye
What is the dipole moment of retinal?
15 Debye
What is the distance dependence of monopole-monopole?
1/r
What is the distance dependence of monopole-dipole?
1/r^2
What is the distance dependence of dipole-dipole in a protein?
1/r^3
What is the distance dependence of dipole-dipole in solution?
1/r^6
What is the distance dependence of dipole-induced dipole?
1/r^4
What is the distance dependence of induced dipole-induced dipole?
1/r^6
What is the distance dependence of steric clashes?
1/r^12
What is the most favorable distance for two elements found?
At the lowest energy (maximize attractive forces)
Is a repulsive force positive or negative?
Positive
Is an attractive force positive or negative?
Negative
What is the energy of an induced dipole depend on?
Polarizability (how easy to move electrons)
What is the purpose of calculating electrostatic interactions?
All based on Coulomb’s law, can be calculated, and can stabilize enzyme complex
How can the pKa of an acid be increased?
Destabilize A-, hydrophobic environment
How can the pKa of an acid be decreased?
Stabilize A-
Which dipole dominates in an alpha helix?
The C=O dipole (as opposed to the NH dipole)
Which direction does the alpha helix dipole point?
From the C (+) to the O (-)
What is the importance of the alpha helix dipole?
It can modulate pKas
What is an example of a protein that uses alpha helix dipoles?
K+ channel
How does a K+ channel use alpha helix dipoles?
It orients them to interact with cation (selectivity barrier)
If an activity profile is bell-shaped, what does this mean?
There are two groups being titrated - one acid and one base
What is an example of an enzyme with a bell-shaped activity profile?
Ribonuclease
What is the mechanism for ribonuclease?
- His119 acts as a catalytic acid to give up H
- His12 acts as a catalytic base to take H
- Lys41 stabilizes phosphate intermediate
What is the purpose of Asp121 for ribonuclease?
It stabilizes His119 as a catalytic acid
What is the purpose of Lys41 for ribonuclease?
It destabilizes His12 acid, so it remains a catalytic base
Is a catalytic acid active at high pH or low pH?
Low pH
Is a catalytic base active at high pH or low pH?
High pH
For a titration curve, where is protein activity?
The area underneath where both curves intersect
In a titration curve, what happens if pKa increases?
The curve shifts to the right
In a titration curve, what happens if pKa decreases?
The curve shifts to the left
What is the optimal pH of an enzyme with a bell-shaped activity profile?
The average of the pKas
