Lecture 16
Protein and Nucleic acid binding
Announce:
bio/phys seminar today at 3:00
hand out assessment forms – please fill out over the weekend and return to...
Remember that Polik will lecture on Wed. Homework is due, but no
discussion. This wouldn’t be a bad time to get together as a group to
discuss homework.
Next homework set will be posted sometime today or over the weekend. You
must look it up, it won’t be handed out.
Outline:
Single <==> double stranded DNA
Actinomycin - DNA complex
energy conversion in photosynthesis/respiration
Review:
Maxwell relations are a mixture of fundamental thermodynamic relations and the exact
differential of an energy function.
e.g. dG = -SdT + Vdp
this implies G(T,p)... so
remember from two times ago, this showed that
Drawing on the fact that dG must be an exact differential
gives us the Maxwell relation
Finally, we finished up by talking about entropy driven processes such as protein binding.
Two proteins hook together to form one – but entropy increases, because hydrophobic
surface is reduced. Note that this is not true for all binding, but it is common. In
these cases, binding increases as T goes up.
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Nucleic acid binding:
Last time we talked about how solvent entropy can favor the attraction of hydrophobic
things to each other. Do you think this is the case for nucleic acid binding?
Probably not, because nucleic acids are very polar.
Let’s consider the single strand ö double strand DNA reaction.
What do we expect for ∆S? Solvent interacts favorably with polar single strands, so there
should be little push toward binding. Consequently, ∆S negative for single ö double
strand
So, how does binding occur? ∆H must be negative.
What drives negative ∆H? H-bonding seems likely
Anyone heard of Chargaff’s rule? It says that χA = χT and χC = χG. This came from
experimental evidence, but we know now that the molecular basis of this rule is?
Watson-Crick base pairing.
Each hydrogen bond accounts for roughly 5 kJ/mol of favorable electrostatic
interaction (relative to interaction with water)
But this is only about 1/3 of the total ∆H. What is the other 2/3? Base stacking –
dispersive interactions
So, ∆G = ∆H - T∆S
∆H - -35 kJ/mol/base pair
∆S - -88 J/K@mol/base pair
What happens at high temp? *T∆S* > *∆H*
ö ∆G is positive and DNA is all single strand
What about low temp? *T∆S* < *∆H*
ö ∆G is negative and DNA is all double strand
The details of this transition are in the next homework set, but I can give away that ∆G is
negative at normal body temperature.
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Let’s look at a slightly different DNA binding event in detail.
Actinomycin - DNA complex
What is actinomycin? chemotherapy drug – not surprisingly it has severe side effects.
Why? It is not at all selective. In fact it is a terrible poison, but it kills tumor cells
slightly more effectively than healthy cells
Anyone know how it works? It blocks transcription by plugging up and distorting the
DNA. Because tumor cells reproduce faster they are more susceptible to damaging
the transcription machinery.
It forms hydrogen bonds to guanine and it intercalates into its aromatic ring. (show nice
chime webpage from UCSF)
Binding is enthalpy-driven. Entropy is actually positive for binding (the aromatic ring
system is fairly hydrophobic) but is a much smaller effect than enthalpy at room
temperature.
Energy Flow
Photosynthesis makes carbohydrates as follows:
6CO2(g) + 6H2O(l) ö 6O2 (g) + C6H12O6(s)
∆G = + 2870 kJ/mol
With huge positive ∆G, how does this reaction happen? Energy is put into the system
from photons. (I really left out one of the reactants.) How many photons does it
take to provide this amount of energy?
roughly 16 photons per glucose. More properly then,
6CO2(g) + 6H2O(l) + 16hν ö 6O2 (g) + C6H12O6(s)
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(You should know that this doesn't happen directly and it really takes more than 16
photons. The photons and H2O are used to convert ADP to ATP and then that
ATP with CO2 is used to make glucose, so the perfect single-step energy
conversion suggested above doesn't really happen.)
Now, this weekend you can go apple picking and eat some of the yummy glucose. What
does your body do with it? Uses it to convert ADP to ATP, which is easily
transported around the body.
C6H12O6(s) + 6O2 (g) ö 6CO2(g) + 6H2O(l)
36 × ( ADP3-(aq) + H2PO4-(aq) ö ATP4-(aq) + H2O(l) )
burning glucose releases 2870 kJ/mol of free energy
making each ATP requires 30.6 kJ/mol
If ATP is stable on its own, then we know the bond formation is favorable –
exothermic. How is it that the ADP reaction above has ∆G > 0? Because
there is also the H3PO4 and H2O. The total ∆G for the reaction is positive.
Part of the reason for this is that the last phosphate bond is pretty weak. Electrostatics
and solvation play big roles in this.
Note that -2870 kJ/mol + 36*(30.6) kJ/mol = -1770 kJ/mol
We loose quite a bit of energy along the way to make sure that each little step is
spontaneous.
The key detail here is that the body has coupled the exergonic glucose oxidation
reaction with the endergonic ADP ö ATP reaction. The overall reaction is
exergonic and happens spontaneously (and rapidly). Later on we can couple the
exergonic ATP ö ADP reaction with other processes (like raising your arm) to
make the overall reactions spontaneous.
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