Thermo 4 Applications To Biomolecules Flashcards
What is keq
What happens to Gibbs free energy if there is equilibrium
Keq = products / reactants
The free energy is zero , no entropy, no favour between one side or the other of the reaction
What is delta G standard if keq very very big
If very very small
Delta G very negative, favourable Gibbs, reaction run to completion
Delta G very postive, unfavourable gibb, reaction doesn’t run at all
This is why Gibbs energy is characteristic of the reaction
What makes standard Gibbs only depend on the reaction equilibrium constant
Since delta G = -RT ln (Keq)
Only depends on keq , the state of the reaction after equilibrium , after the reaction has reached completion
What does regular delta G tell us
Tells us the Gibbs energy any given point in the reaction and tell us if we’re gonna roll backwards or forward in relation to delta G standard
Why does the evolution of compelx organsims not break the laws of thermodynamics
Because us as ordered beings decreasing entropy, causes our activities to make a corresponding increase in entropy on our surroundings
For example the sun gives off energy which is high entropy but we use that to survive and decrease the entropy by creating order
But we are still anomalous organisms, and very unlikely
How does a hydrogen bond still have elements of a bond
In water the h bonds are 90 % electrostatic but still 10 % covalent
How many h bond in water
Why is it like this
In water you have 3.4 h bonds on average, this value is always changing because it has a short bond lifetime
Instead of staying in the lowest energy conformation which is in the same set of bonds
They change their bonds and positions because they always have a distribution of energy in the molecules
So they occasionally go in the lowest energy state but are able to leave because of this extra energy (KbT)
When melting and boiling a crystal (solvating it) what is the Enthalpy (delta H) and why
So what has to happen for it to be solvated
Small and Positive because heat is put into the system to break the bonds
This means that delta S needs to be very large and positive (because disorder occurs, make delta G negative, and the reaction favourable)
What makes non polar things want to stick together
They only try to stick together when they are around other polar things and the alternative is to stick to them
But polar things stick together no matter what since there have electric charge interactions
What is the entropic/enthalpoc change for non polar compounds
How do they overcome this
If a nonpolar compound is in solution
Two things:
If following the minimum energy, the water makes a cage to be more ordered around the surface of the non polar compound
This makes negative entropy, Meaning needs to be a corresponding decrease in Enthalpy or the reaction won’t be spontaneus (since postive delta G)
But If the cage did not form, there’d be very large postive delta H (because breaking h bonding), this is very unfavourable and wouldn’t happen
To overcome this, the non polar molecules would aggregate to have the least interaction with the order water cage
Explain the Gibbs of non polar molecules (alkanes) in comparison to alcohol and toluene
Comparing the alkane to alcohol:
Alkane have higher Gibbs because the water is forming an ordered cage around it, decreasing entropy and making Gibbs postive
Alcohol is more polar and has less carbons so less ordered water forms a cage around it, has lower Gibbs
Comparing the alkane to Toluene:
The toluene has a more comparable Gibbs to the alkane even though it has more carbons atoms
This is because the carbon atoms in toluene are clustered tighter together
Meaning the by clustering into a ring its Gibbs lower and reduced the amount of ordered water it interacts with
Explain how the cage water structure throws of the entropy
Usually the water molecules free in solution have h bonds in place 85% of the time
But the cage molecules have them in place 88% of the time
This means the cage molecules move and exchange less, causing the to be more order, causing lower entropy and unfavourable change in Gibbs
Explain the case of amphipathic compunds (lipids) and why they aggregate
What eventually happens
They have a large hydrophobic region, meaning a water cage can also form, decreasing entropy and making an unfavourable change in Gibbs
To get over this, aggregation happens with other lipids to reduce the amount of cages forming and order water they interact with
This is entropically favoured, and makes lowest energy and highest entropy structure
This makes a micelle
Why would a micelle be a sphere
What another structure that is similar
Two reasons:
Having the tails tucked in minimizes how much ordered water the non polar region have to interact with , higher entropy
Has the lowest SA/V ratio , meaning it also minimizes how much of the surface is
interacting with ordered water molecules
Liposomes (have water on inside and outside , bilayer)
What is critical micelle concentration
The point where surfactants fully saturate the surface of the solution
After this point, adding more surfactant causes them to aggregate and make micelles
To get a negative delta g favourable spontaneous reaction Whag has to happen
Increase entropy, enthalpy small and postive
How do enzymes show change in entropy
More favourable for the to bind with their substrates because before binding there is ordered water around them, lower entropy
After binding, less ordered water interacting with them , higher entropy
How does protien folding show change in entropy
Hydrophobic collapse
Examples are amphipathic alpha helices
Makes the hydrophobic side of the helix go on the inside and not interact with ordered water and the hydrophobic side of it face the water
Explain the protien folding model
What if many micro states
The protiens fold at each peptide linkage and each linkage can have 3 possible orientation
Up down or side (so a new amino acid binds in either direction)
This means each there are 3^(N-2) configurations for that one amino acid because has can only take one of the 3 paths
N is number of amino acid residues
This gives (N-2) ln 3
Giving delta S = R (N-2) ln (3) as the molar entropy
USE R VERSION
And delta S = kb (N-2) ln (3)
If many microstates, use exponential log rule
delta S = R ln (3^N-2) then the 3^N-2 is to the power of however many residues (microstates)
What does the protien folding model neglect
The binding of water to non polar surfaces (leading to negative entropy)
Disordering of side chains that become more mobile upon unfolding (leading to postive entropy)
What is levinal paradox
If there are so many options of protien folding why is the folding so fast
Because they fall down an energy well, and stable in its folded state
What would make a protien more stable
Tighter hydrophobic packing (like in extermophiles)
Higher density of exposed charged (polar) residues
Folding with ion pairs comic together
Make the protien fall down the energy well
How is protien unfolding done
Through heat
If warm protien very slowly
Can break the interactions, make it go up the well and start unfolding the protien
Once one interaction breaks, all the other go with it meaning that is not just one interaction making the protien fold but all of them working together
Through organic solvents
Only thing keeping hydrophobic protiens together is the polar environment
If protien in a hydrophobic environment, energetically favourable for it to flip and invert to interact with solvent
What is the denaturing temp of the average monomeric protien
60 degrees
Explain the protien folding clock
A behaviour clock built into humans that is based on protien folding and unfolding
Shows how unfolding happens on purpose
Ex. KaiB switches between folded to unfolded then a diff folded state on purpose as part of a biological cycle
What are the three distributions
Max well Boltzmann
Bose eitneins (-1)
Fermi Dirac (+1)
What is the Maxwell Boltzmann distribution
Compare it to Bose einsteins
The typical distribution you’d see for a high temp molecule
High population of molecules at a lower energy, all the states have a probability of being populated for this you just have a most likely outcome
Bose Einstein is where the matter occupies the same state at low temps
so if you keep dropping the temperature the line will spike up to one specific point because each particle is only in that one state
Can’t see that they are diff particles
Compare Maxwell Boltzmann distribution fermi dirac
Fermi Dirac shows molecules that cannot be in the same state at low temps
Shows electrons, electron have to be in independent states
But if go to low enough temp,
IDK
