A1 (Temperature):

- 0th law of thermodynamics states that if two systems and in thermal equilibrium with a
third, they are all in thermal equilibrium with each other
- Utrans is the translational kinetic energy of the internal energy
- Speed of the molecule and average kinetic energy of the molecule are important \

A2 (Work and Heat):

- First law of thermodynamics states that energy is conserved
- Steady State: elastic collisions ( no energy trasfer to the wall. There is normal bouncing on atoms
to the piston wall. Ex. +mv=-mv)
- Expansion: inelastic collisions (energy is transferred from particles to the wall and the particles
lose kinetic energy and is formed into ordered energy/ work done by the piston).
- U=q+w in a closed system but u=0 in an isolated system
- If work is positive, work is performed on the system

A3 (Isotherms):
- Ideal gases use pv=nrt
- deltaU= 0 in isotherms
- Thus, qT=-wT

B1 (Entropy):
- Second law of thermodynamics states that the overall entropy never decreases. In an isolated
system the entropy increases but in a reversible process it remains constant.
- Delta S is greater than or equal to zero
- Entropy of a system is independent of path and a state variable, meaning that it is not inclusive
of the path entropy takes (reversible (Ssurr= 0) or irreversible (Suni = 0))
- Third law of thermodynamics states that the entropy of any pure, perfect crystal is zero at 0K.
- Cp and Cv are always positive and thus S rises with T.
- DeltaCp= Cp products -Cp reactants

B2 (Free Energy)
- Gibbs free energy describes the free energy at constant pressure and temperature.
- Helmholtz Free energy describes free energy at constant volume and temperature.
 - Expansion work is pressure-volume work, and non-expansion work is anything else (electrical,
friction, motional, etc.). Thus, there is constant temperature and pressure and delta G= w rev
- Delta G= 0 for phase changes at equilibrium as the T and P is constant.

B3 (Fundamental Relations):
- Chemical Potential is the change in driving force towards equilibrium resulting from a change in
composition of a mixture at constant P,T.

B4 (Pure Phases):
- A phase change at equilibrium and constant temperature and pressure has a Gibbs free energy
of 0
- The red line divides the solid and gas phases, represents sublimation (solid to gas) and
deposition (gas to solid). The green line divides the solid and liquid phases and represents
melting (solid to liquid) and freezing (liquid to solid). The blue divides the liquid and gas
phases, represents vaporization (liquid to gas) and condensation (gas to liquid).
- Triple point – the point on a phase diagram at which the three states
of matter: gas, liquid, and solid coexist
- Critical point – the point on a phase diagram at which the substance
is indistinguishable between liquid and gaseous states
- Fusion(melting) (or freezing) curve – the curve on a phase
diagram which represents the transition between liquid and solid
states
- Vaporization (or condensation) curve – the curve on a phase
diagram which represents the transition between gaseous and liquid
states
- Sublimation (or deposition) curve – the curve on a phase diagram
which represents the transition between gaseous and solid states
- Clapeyron’s equation describes the solid-liquid equilibria
- Activity and Equilibrium constant are not limited to ideal gasses
- Activity of ideal gasses are just its partial pressure while for real gasses, there is an
activity coefficient. For solids and liquids, the activity is equal to 1.
- The van’t Hoff equation describes the temperature dependence of K.
- Clausius-Clapeyron equation describes the heat of vaporization and vapor pressure.
B5 (Binary Phases):
- The phase rule states that F = C − P + 2. Thus, for a one-component system with one
phase, the number of degrees of freedom is two, and any temperature and pressure,
within limits, can be attained. With one component and two phases—liquid and vapour,
for example—only one degree of freedom exists, and there is one pressure for each
temperature. For one component and three phases (e.g., ice floating in water with water
vapour above it, in a closed container), there is no degree of freedom, and temperature
and pressure are both fixed at what is called the triple point (see phase diagram).
- Entropy of mixing is only with two different species
- The sum rule considers a constant T and P to find the entropy of mixing two ideal gasses.
Under these conditions, delta U and delta H are equal to 0
 - A solid or gas in equilibrium with solution is a pure solute. Increasing or decreasing
solubility is dependent on entropy

- All solids and liquids have a vapor pressure, and this pressure is constant regardless of
how much of the substance is present.
- Raoult's Law (Pa=XaPa) only applies under ideal conditions in an
ideal solution.
- If you look review the concepts of colligative properties, you will
find that adding a solute lowers vapor pressure because the
additional solute particles will fill the gaps between the solvent
particles and take up space.
- Henry’s Law: An equivalent way of stating the law is that the
solubility of a gas in a liquid is directly proportional to the partial
pressure of the gas above the liquid. This law only applies to the
solute of dilute solutions.

B6 (Colligative Properties):
- Colligative Properties are the properties of solutions that rely only
on the number(concentration) of the solute particles, and not on
the identity/type of solute particles, in an ideal solution
- Colligative properties are helpful when characterizing the nature
of a solute after it is dissolved in a solvent.

- The boiling points of solutions are all higher than that of the pure
solvent. Difference between the boiling points of the pure solvent and
the solution is proportional to the concentration of the solute particles:
ΔTb=Tb(solution)−Tb(solvent)=Kb×m(1)(1)ΔTb=Tb(solution)
−Tb(solvent)=Kb×m, where ΔTbΔTb is the boiling point
elevation, KbKb is the boiling point elevation constant, and m is the
molality (mol/kg solvent) of the solute.

- Freezing point is reached when the chemical potential of the pure

liquid solvent reaches that of the pure solid solvent. Again, since
we are dealing with mixtures with decreased chemical potential,
we expect the freezing point to change. Unlike the boiling point,
the chemical potential of the impure solvent requires a colder
temperature for it to reach the chemical potential of the pure
solid solvent. Therefore, a freezing point depression is
observed
 - Semipermiable membranes do not let the solute pass through
(Think of the sugar example). A solvent will move to the side that
is more concentrated to try to make each side more similar!
Since there is a flow of solvents, the height of each side changes,
which is osmotic pressure.

B7 (Real Solutions):

- Solvent standard states are defining a pure component as standard state

- Solute standard state defines a 1M solution as standard state
- This biochemical standard state is defined as pH 7, 298 K, 1 atmosphere
pressure, and unit concentrations for chemicals other than water or
protons.
- Small uncharged molecules have an activity coefficient of 1.
 - The solubility of proteins usually increases slightly in the presence of salt,
referred to as "salting in". However, at high concentrations of salt, the
solubility of the proteins drop sharply and proteins can precipitate out,
referred to as "salting out".

B8 (Chemical Equilibria):

C1(Molecular Motion):
- a formula describing the statistical distribution of particles in a system among different
energy levels. The number of particles in a given energy level is proportional to exp.
( − E / kT ), where E is the energy of the level, k is Boltzmann's constant, and T is the
absolute temperature.
- An example of steady state can be found a bathtub with the drain open and
water being added. If water is leaving the tub at the same rate that water is
being added, the state variable volume will be constant over time.
- mean free path is the average distance over which a moving particle (such
as an atom, a molecule, or a photon) travels before substantially changing
its direction or energy (or, in a specific context, other properties), typically as a
result of one or more successive collisions with other particles.
- Mean free path is dependent on the ration of volume/N and T/P not one individual. For ex. If
you expand the area of the tube, the number of moles will also increase, meaning it is not
exactly dependent on volume.
- Brownian motion is the random motion of particles suspended in a fluid (a
liquid or a gas) resulting from their collision with the fast-moving atoms or
molecules in the gas or liquid
-

- Boltzmann distribution describes the distribution of molecular energies in a gas at

constant T.
- Discrete level imply the atom has an energy level that can be one of a distinct
number of levels. it can not be between these levels. This is like a car have
discrete gears. it can be in neutral, reverse, first, second etc, but not in between
these gears
 - The partition function describes the weighted average number of occupied states at temp
T.

C2 (Diffusion):
- Diffusion can be described as the random movement of particles
through space, usually due to a concentration gradient. Diffusion
is a spontaneous process and is a result of the random thermal
motions between two particles. The diffusion coefficient ( D) can
be solved for with Fick’s laws of diffusion, which are broken up
into two laws.
- The first law can only be applied to systems in which the
conditions remain the same— in other words, if the flux coming
into the system equals the flux going out. Fick’s second law is
more applicable to physical science and other systems that are
changing. This second law is applied to systems in which the
condition are not steady, or the solution in not equal throughout.
- The dependence of the diffusion coefficient on the viscosity can
be modeled by the Stokes-Einstein relationwhere a is the radius of
the molecule and η is the coefficient of viscosity and is defined by:
η=ηoeEa/RT. This equation demonstrates the dependence of viscosity
on temperature.
- Ostwalk viscometer measures the time for liquid level to drop from A to B. Fluids must
be Newtonian.
- Specific Velocity: a measure of the resistance to flow of a fluid, expressed as
the ratio of the absolute viscosity of the fluid to that of a reference
fluid (usually water in the case of liquids)
- The intrinsic viscosity, also known as the limiting viscosity number or the
Staudinger index, (2) is defined as the ratio of the increase in the relative
viscosity by the polymeric solute to its concentration in the limit of infinite
dilution

C3 (Sedimentation):
- Boundary sedimentation is sedimentation of macromolecules in a
homogeneous solution. (a) Begin with a homogeneous solution of
macromolecules. (b) As the solution is spun in the ultracentrifuge and
macromolecules move down the centrifugal field, a solution-solvent boundary is
generated.
- As concentration increases, the distance from the center of rotation also
increases

C4 (Electric Fields):
-
 - An electrical double layer exists at the interface between an electrode and its surrounding
electrolyte. This double layer is formed as ions from the solution "stick to" the surface of
the electrode. Charges in the electrode are separated from the charges of these ions.
- The cell-surface charge is assessed by measuring their electrokinetic potential (zeta
potential), which characterizes the electrical double-layer potential on the cell surface.
- The slip plane is the plane defined by the distance at which the structure with its
chemically bound water and ions moves in bulk through the solution. It is the plane at
which the zeta potential is valid. The zeta potential is the “modified” or “effective”
surface charge.
- Migration of compounds in gel electrophoresis is characterized by terminal velocity (u).
The electrophoretic mobility is the terminal velocity scaled to the field.

C5 (Biomolecules):
- Clustering non-polar groups increases the entropy of a water which is the driving force
for the separation of water and oil.
- Folding of proteins occurs due to H-Bonding, van der Waals, hydrophilic/hydrophobic
interactions, and coulombic interactions.
- Nucleotides consist of phosphates, sugars, and a base
- DNA is destabilized by the interactions of the phosphate with sodium ions. K is not
dependant on [Na+], thus the stability of the complex will depend on ion concentration.
- DNA double strands are not just dependant on the number of bases. But the
thermodynamic interactions as well as seen by the thermodynamic parameters of double
strands.
- DNA sequences are recognized via. radioactive labelling of complementary target
sequences.
- Gin-8.1, Hin=0.8 and Sin=-23.4kJ/mol
- As probe conc. Goes up, so does the melting temperature
- As target conc goes up, the melting temp remains the same
- If the probe contains a single base mismatch, the melting temp will decrease
- Lower salt concentration decreases the stability of the complex and decreases Tm

C6 (Ligand Binding):
- The Langmuir adsorption model explains adsorption by assuming an adsorbate behaves
as an ideal gas at isotherma lconditions. According to the model, adsorption and desorption
are reversible processes.
 - The hill plot is used to determine this type of binding

C7 (Surfaces):
- Surface tension is described by the units of force per length (N/m or gamma)as described
by young’s equation
- The Gibbs adsorption isotherm for multicomponent systems is an equation used to relate
the changes in concentration of a component in contact with a surface with changes in the
surface tension, which results in a corresponding change in surface energy.
 - We can assume the pressure of a surface using Langmuir films assuming no solubility in
subphase
- Surface tension depends on the droplet size. Pure water has the highest surface tension.
- Surface tension is inversely proportional to temperature.
- The most common examples of amphiphilic chemicals are soaps, detergents, and
surfactants [1,2]. Their special structures lead to relatively high solubility in both polar
solvents like water and a large variety of nonpolar solvents. Amphiphilic molecules may
form aggregates or micelles in water.
- Micelles contain hydrophobic tails and a hydrophilic head.
- The CMC (critical micelle concentration) is the concentration of a surfactant in a bulk
phase, above which aggregates of surfactant molecules, so-called micelles, start to form.
The CMC is an important characteristic for surfactants.
- In adsorption of adsorbate on adsorbent, the interior of the adsorbent, where
concentration of adsorbate is less as compared to the concentration of adsorbate on the
surface is known as the Bulk Phase.
- Surfactants are substances that reduce surface tension of a liquid in contact with another
gas or solid. Ex. Detergents and soaps
- An emulsifier or emulsifying agent is a compound or substance that acts as a stabilizer
for emulsions, preventing liquids that ordinarily don't mix from separating. Useful in
foods, cosmetics, paint, and oil dispersants. But they may be toxic to the environment.

C8(Membranes):
- Lipid Bilayers have tails pointing in whereas soap bubbles have the tail pointing out.
- Na+ - K+ pumps via. membrane bound protein occur through an ATP-Driven process.
- All components in a membrane strive for a inside= a outside.
- The Gibbs–Donnan effect (also known as the Donnan's effect, Donnan law, Donnan
equilibrium, or Gibbs–Donnan equilibrium) is a name for the behaviour of charged
particles near a semi-permeable membrane that sometimes fail to distribute evenly across
the two sides of the membrane.

D1 (Rate Laws):
D2 (Reaction Mechanisms):
- Parallel or competing reactions When a reactant gives two products (desired, and
undesired) simultaneously with different rate constant then this is called a parallel
reaction.
- The initial rate of a reaction is the instantaneous rate at the start of the reaction (i.e., when
t = 0). The initial rate is equal to the negative of the slope of the curve of reactant
concentration versus time at t = 0.
- The “clock reaction” is a reaction famous for its dramatic colorless-to-blue color change
and is often used in chemistry courses to explore the rate at which reactions take place.
The color change occurs when I2 reacts with starch to form a dark blue iodine/starch
complex.
- The pre-equilibrium approximation of a complex reaction mechanism implies that a slow
reaction follows a fast equilibrium reaction.

D3 (Transition States):
- The Arrhenius plot describes the activation energy in a plait describing the temperature
dependence of k. The rate constant is exponentially dependant on temperature.
 - The transition state is the local minimum with respect to some coordinates of the
potential energy surface.
- Collision theory suggests that In order to effectively initiate a reaction, collisions must be
sufficiently energetic (kinetic energy) to break chemical bonds; this energy is known as
the activation energy.
- Transition-state theory, also called activated-complex theory or theory of absolute
reaction rates, treatment of chemical reactions and other processes that regards them as
proceeding by a continuous change in the relative positions and potential energies of the
constituent atoms and molecules.
- The Born-Oppenheimer Approximation is the assumption that the electronic motion and
the nuclear motion in molecules can be separated. It leads to a molecular wave function
in terms of electron positions and nuclear positions. This approximation makes it possible
to separate the motion of the nuclei and the motion of the electrons.
- The potential energy surface concept can be used to theoretically explore properties of
structures composed of atoms, for example, finding the minimum energy shape of a
molecule or computing the rates of a chemical reaction.

D4 (Catalysis):
-

- The Haber process, also called the Haber–Bosch process, is an artificial nitrogen fixation
process and is the main industrial procedure for the production of ammonia today.
- Poisons lower catalytic activity by site blocking and stearic effects
- Promoters enhance catalytic activity by modifications of electronic structure
 - Dissociative chemisorption is one of the simplest surface chemical reactions, which
undergoes the dissociation of a gas-phase molecule upon its collision with a surface,
leading to chemisorbed products
- The Lennard-Jones potential is a simplified model that yet describes the essential features
of interactions between simple atoms and molecules: Two interacting particles repel each
other at very close distance, attract each other at moderate distance, and do not interact at
infinite distance, see figure 1.
- The Langmuir isotherm describes the maximum amount of gas that a shale can hold at a
specified pressure and temperature. Several factors may result in a shale holding less than
the maximum amount of gas as represented by the isotherm. Such shales are termed
undersaturated.

D5 (Enzyme Kinetics):
- Absorbance/Product vs time slopes can provide the rates required to plot a michaelis-
menten graph with substrate concentration.
- The Lineweaver-Burk compresses values at high [S], whereas the Eadie-Hofstee spreads
values at high [S].
- Two substrates can compete in a parallel reaction with va/vb kinetics
- Parallel reactions to inactive form EI have the same Vmax but different Km.
- For non-competitive inhibition, there is poisoning of the active site, where only Vmax is
affected by deactivation not Km in its simplest form. But it is possible to affect Vmax
and modify still active enzyme to change Km as well.
- Allosteric effectors (promoters) and Allosteric inhibitors (Poison) exist
- Enzyme subunits exist in one of two conformations, tensed (T) or relaxed (R), and those
relaxed subunits bind substrate more readily than those in the tense state. The two models
differ most in their assumptions about subunit interaction and the pre-existence of both
states.
- The allosteric effects are found by finding equilibrium between a relaxed (good fit) and a
tense (poor fit) form of the enzyme. If L=0, it resembles the Mechaelis-Menten, and no
allosteric effect and the tense form does not exist. But if there is a large L, there is S-
shaped dependence and a large allosteric effect.

- Kr for relaxed form and Kt for tense form.

D6 (Fast Reactions):
- Flow instruments are rapid mixing devices used to study the chemical kinetics of fast
reactions in solution
- The continuous flow method was used first in 1923 to study the binding of O2 to
haemoglobin. This is for reactions that took place in the milliseconds. If the distance
between the point at which the reaction is initiated and the product detector is known,
then the time interval can be found from the flow rate.
- The stopped flow approach is by far the most common means of studying fast solution-
phase reactions over time intervals of down to a fraction of a millisecond. The basic
stopped-flow apparatus consists of two or more coupled syringes that rapidly inject the
reactants into a small mixing chamber and then through an observation cell that can be
coupled to instruments that measure absorption, fluorescence, light scattering, or other
optical or electrical properties of the solution. As the solution flows through the cell, it
empties into a stopping syringe that, when filled, strikes a backstop that abruptly stops the
flow. The volume that the stopping syringe can accept is adjusted so that the mixture in
the cell has just become uniform and has reached a steady state; at this point, recording of
the cell measurement begins and its change is followed.
 - To monitor reactions, take place in less than a millisecond, we can use the following:

- Relaxation kinetics are always 1st order.

D7 (Autocatalysis):
- Autocatalysis is a reaction yielding a product that increases the rate of reaction itself,
most often by producing more of one of the starting materials than it consumes.
- Output is not proportional to input
 - This oscillation was observed through the Berlushov-Zhabotinsky reaction: Can exhibit
both temporal and spatial patterns.
- The Belousov-Zhabotinsky reaction, or BZ reaction for short, is a family of oscillatory
chemical reactions first discovered by Russian chemist Boris Belousov in the 1950s and
then later analyzed by Russian-American chemist Anatol Zhabotinsky in the 1960s. One
of the common variations of this reaction is essentially an oxidation of malonic acid
(𝐶𝐻2(𝐶𝑂𝑂𝐻)2CH2(COOH)2) by an acidified bromate solution, yet this process
shows nonlinear oscillatory behavior or a substantial length of time before eventually
reaching chemical equilibrium. The actual chemical mechanism is quite complex,
involving about 30 different chemicals. Moreover, if this chemical solution is put into a
shallow petri dish, the chemical oscillation starts in different phases at different locations.
Interplay between the reaction and the diffusion of the chemicals over the space will
result in the self-organization of dynamic traveling waves

D8 (Diffusion Control):
- Diffusion Controlled (k3≫k2k3≫k2): If the activation energy of the A+B reaction is
very small or if escape of molecules from the {AB} cage is difficult, the kinetics will be
dominated by k1, and thus by the activation energy of diffusion. Such a process is said to
be diffusion controlled. Reactions in aqueous solution in which Ea > 20 kJ/mol are likely
to fall into this category.
- Heart beats and heart attacks were identified through ECG with a rabbit heart with tracer
dyes and a numerical model. Spiral waves with shorter wavelengths were the killers
(arrhythmia)
- Turing proposed a model wherein two homogeneously distributed substances (P and S)
interact to produce stable patterns during morphogenesis. These patterns represent
regional differences in the concentrations of the two substances. Their interactions would
produce an ordered structure out of random chaos.
[Link]
Evolutionary_Developmental_Biology_(Rivera)/07%3A_Patterning/
7.1%3A_Turing_Patterns_to_Generate_Stripes_and_Spots

- Therefore, fast activator diffusion and slow inhibitor diffusion will lead to travelling
waves but slow activator diffusion and fast inhibitor diffusion are required for turning
patterns.
- Turing patterns also require rapid response of the inhibitor to the activator concentration
(the inhibitor removal has to be faster than activator removal). Thus, turing patterns
require both short-ranged activation and long-ranged activation.