Thermodynamics - Chemistry of Life
What is the internal energy of a system
This is the sum of work energy and heat energy in the system
U= w+q
The total energy of a system is its internal energy
What are the forms of energy
Kinetic energy - For a particle with mass and velolicty can use Kinetic energy
Ke= 1/2mv^2
Potential energy - Graviattional potential energy and chemical bond energy, which is the energy stored in chemical bonds that is released when bonds broken and cleaved when bonds made
What are the 3 types of systems
Open- Both energy and matter can enter and leave the system
Closed- Only energy can enter and leave the system to the surroundings
Isolated - Neither matter nor energy can be transferred from system to the surroundings
What is the 1 law of thermodynamics
The sum of energies in a system and its surroundings is a constant as energy cant be created or destroyed only tranferred as different energy forms
Energy transfer as work energy
Work is a process in order to lift a weight and when it is perfomed energy is transferred to the surroundings
Work = Force x Distance - where Force = mass x acceleration
Energy tranfer as hesat energy
Q= M x C x Delta T
A hot system in contact with a colder surrounding will sponteneously get colder but the opposute will not happen
What are the energy changes during a reaction
This is called the enthalpy of the reaction
Enthalpy = H = U + pV
Change of enthalpy = Delta U + Delta pV
This simplify relations between measurement of energy and measurable quantity
DeltaH= Delta U + pDeltaV = Delta work + Delta q + pDeltaV
So at constant pressure
DeltaH = -pDeltaV + delta Q + pDeltaV = Delta q
This means Delta q = enthalpy change
What are endothermic and exothermic reaction
Endothermic have a + Delta H so more energy enter the system that leaves it
Exothermic have a -Delta H so more energy leave the system than enters is
How to measuure enthalpy change
Use a Bomb calorimeter due an exothermic reaxction will increase temp so can then use
q=mcDeltaT
Then Delta H = q/n
What is the 2nd law of thermodynamics
In an isolated system the entropy can omly ever increase and so a hot system in a cold surrounding wil only gte colder and at the same time the surrounding will get hotter, camt happen other way round
What is a change in entropy
Change of entropy is proportional to the heat transferred from the system to the surroundings
Delta S = DeltaQ/T
at equlibrium Delta S = Delta q/T
However due to Delta Q = Delta H
Then entropy = Delta H / T
What is the enbtropy of exothermic and endothermic reactions
In an exothermic reaction the entropy will decrease but surroundings entropy will increase
In an endothermic reaction the entropy of the system wil increase but trhe entropy of the surroudnings will decrease
What is the entropy change for a spontaeneous reaction
The entropy has to increase for a reaction to be spontaneous and has to be in btoh the system and the surroundings
What are the quantities that describe a system
A macrostate = Temperature, Volume , Pressure
A microstate = Kinetic energy, force and mainly the number of configurations of all the particles in the system
A macrostate can be described as a collection of microstates
What can entropy be defined as
The number of microstates in a system
S= Kb x ln(Microstate number )
Kb= Boltzmann constant
What are the microstate rules
For an isolated system in thermla equilibrium all microstates are equaly likel;y to happen
The equilobrium state is thet state in the system with the most microstates
What is the origin of the hydrophobic effect
Obsevred tendency of non-polar substances to aggragtes in aqueous solution
It is used to stabilise the phospholipid bilayer and also will drive proteins to fold inot 3 dimensioanl structure so they can function
How is protein folding driven by hydrophobic effect
It is driven by hydrophobic collapse and so the hydrophobic sdie chains are buried in the 3d structure
The unfolded state has many different conformation so large entropy compared to the folded state
How does the mixing of substances show observations
Entropy wil favour the mixing of substances as there are more ways to arrange the molecules so a greater entropy
The enthalpy of the mixing is determined by the intercation between the molecules
= Gain enthalpy of A bonding to B and lose enthalpy of A bonding to A and B bonding to B
What are the intermoleculsr forces that give rise to enthalpies of intercation
Ion- dipole, H bond, Dipole - dipole, Ion inducved dipole, Dipo,e induced dipole and disersion forces
They can all do work or can gain work from them
What is the structure of water
In a solution of water each molecule will have 4 neighbourghs so a tetrahedral bonding shape
There will be 2 hydrogen bonds formed
How mnay microstates does water
We can arrange the molecules of the water in the tetrahedral bonding shspe in 6 different ways to maintain 2 hydorgne bonds to be formed
This means 6 microstates
If replace a water molecule in the solution with a methyl group then does not allow formation of hydrogne bonds so only 3 microstates can be formed for the central water molecule
= 3 microstates
How to calculate delta S using microstates
Can use entropy in water - entropy in other environment
Delta S = Kb x (ln microstate in water - ln microstate of other enviornment)
How does hydrophobic effect cause phospholipid assembly
It will minimise the exposure of hydrovarbon chains to the water so then maximise the entropy of water in the presence of phospholipid
What is Gibbs Free energy
The energy from a reaction that is availble to generate work
DeltaG= DeltaH - TdeltaS
What does Delta G need to be for spontaneous reaction
For a reaction to be spontaneous then Delta G needs to be a negative number as the gibbrs energy of the product is less then the gibbs free energy of the reactants
What is law of mass action
At equilibrium the concentration of reactants and products are related by Q which= Kc the equilibrium constant
Kc= [Product]/[Reactants]
If Kc larger than Q then reaction proceed left to right favoruing the products
If Q larger than Kc then reactiom favours the reactants and go right to left
What is the connection between Delta G and concentrations
For Q =[A]/[B]
Then at - delta G = A is greater than B
Id Delta G= 0 then at equilibrium
If Delta G is + then B is greater than A so
Connection between Delta G and Kc
Delta G = Delta Go(Gibbs free energy) + RT ln(Q)
At equilobrium the Delta G (standard state ) and Q=KC
So Delta G = -RT kn(Kc)
Delta G = reaction mixtured in standard states
What is life and control
Life - The properties that distinguish the living organisms from dead organaims and inaminate objects
Control- The turning on or off of specific genes, cellular pathwasys or the function of enzymes
What is ligand binding
This occurs when thing intercat with each other in bioloigical systems with receptors, it is controlled by weak non-covalent interaction between the molecuels
What are the characteristics of a binding equlibrium
Kinetics - The rate at which soemthing appears or disappears
Affinity - The stregnth of the intermolecular forces between the ligand the protein receptor
What is the association complex
As the protein receptor and the ligand associate together to get a constant
= [Complex]/ [receptor]x[ligand]
What is the dissociation constant
The inverse of the association constant so a constant for when the ligand and protein unbind from each other
[Protein receptor] x [ Ligand ] / [ Complex ]
What are the binding free energies for association and dissociation
For association = Delta G = -RT x ln(Ka)
For Dissociation = Delta G = +RT x ln(kd)
How to determine the Kd using binding assays
Detect a radio labelled lignad
Mix with the unradiolabelled ligand that is chemically indentical to it
Add a sampole and reach the equlibrium in the system
Seperate the bonded ligand from the unbound lingand and measure the total boud with liquid scintillation counter
What does different values of Kd mean
Ligands with a low Kd will be tightly bound to the protein and Ligand with a high Kd will bind weakly to the protein receptor
When ligand = 4 x Kd then 80% of the receptor are occupied
When liagnd = 9 x Kd then 90% of the receptors are occupied
Takes 99 x Kd to fill all the receptors
What is the formula for the fraction of bound ligand
[ Bound receptor ] / [Free and bound receptors ]
What are the law of mass assumption used for ligand binding calculations
All receptors are equallty accessible to ligands - they are not
All receptors are either free or bound to the ligand - Ignore state of partial bound in model
Neither ligand or receptor are altered in binding
Binding is reversible
What is the ligand binding curve
Must be measured at constant temperature and is a regular hyperabola shape
Deviation from the curve due to multiple binding sites or different affinities or allosteric regulation