Biochemistry: Thermodynamics and Kinetics Flashcards
The second law of thermodynamics states…
Law of conservation of energy
The second law of thermodynamics states entropy (disorder) of the universe tends to increase
Spontaneous reactions tend to increase disorder of the universe
Law of conservation of energy
states that energy of the universe is constant so if energy of system decreases then energy of rest of the universe (surroundings) increases and vice versa
Equation for Gibbs free energy and change in enthalpy
What is considered spontaneous?
Under standard conditions, pure elements in their natural phase have ____ and ____ of zero
Also, _______ of simple, chemically pure elements is zero at 0.0K
ΔG = ΔH -TΔS
ΔS -> change in entropy
ΔH = ΔE - PΔV
E -> bond energy of products or reactants in a system
P -> pressure
V -> volume BUT if cellular rxns occur in liquid phase so no change in volume SO
ΔH =ΔE
The change in Gibbs free energy of a reaction determines whether the reaction is favorable (spontaneous, ΔG negative, exergonic) or unfavorable (nonspontaneous, ΔG pos, endergonic)
A negative ΔH means the reaction is exothermic
Under standard conditions, pure elements in their natural phase have Hfº and Gfº of zero
-> Note that the standard Gibbs free energy of formation of an element in its standard is zero (ΔGƒ° = 0) because, at 298.15 K and atmospheric pressure, the element in its standard state already exists, no change has to take place.
Only the entropy of simple, chemically pure elements is zero at 0.0K
Something that is non spontaneous requires…
Energy input
What equation would we use for calculating ΔG for a reaction in the body?
ΔG = ΔGº’ + RTlnQ
where Q = [C][D]/[A][B] (this is similar to Keq equation but there you would use concentrations at equilibrium)
What does Keq tell you versus Q?
A large Keq means that more products are present at equilibrium. It is Keq that says something about the nature of reactants and products, since it describes their concentrations after equilibrium is reached
The size of Q says nothing about properties of the reactants and products. Q is calculated from whatever initial concentrations happen to be. Can’t tell if prod or reactants have lower free energy.
When Keq is large this means…
When Q is large this means …
Keq -> means more products present at equilibrium
Q -> Says nothing about properties of reactants or products bc Q is calc with whatever the natural present concentrations happen to be then
Two factors determine whether a reaction is spontaneous:
a) The intrinsic properties of reactants and products
b) The concentrations of reactants and products (RTlnQ)
If something is spontaneous this means nothing about rate of reaction
Thermodynamics only tells you…
A thermodynamically favorable reaction is…
Where a system starts and finishes but nothing about the path traveled to get there
Spontaneous
Chemical kinetics is…
Study of reaction rates
All reactions proceed through transition state that is unstable and takes a great deal of energy to produce
Need certain amount of energy to produce transition state - need to have activation energy
What does catalyst do to transiton state? What does it do to delta G? Do enzymes have a thermodynamic or kinetic role?
Catalyst lowers the transition state by stabilizing the transiton state
The catalyst is not consumed, it is regenerated
Does NOTHING to delta G
Enzymes have a kinetic role not a thermodynamic one
A rxn that would take 100 years to reach equilibrium without an enzyme may occur in just seconds with an enzyme
Oxidation
Reduction
Oxidation = loss of e-s Reduction = gain of e-s
Important: 3 different ways to recognize oxidation reactions
1) gain of oxygen atoms
2) loss of hydrogen atom
3) loss of electrons
Important: 3 different ways of recognizing reduction reactions
1) loss of oxygen
2) gain of hydrogen atom
3) gain of electrons
How can you visualize if something is oxidation or reduction? ex. disulfide bond
Ex. For forming of disulfide bond see H’s disappear so it’s an oxidation
What does oxidative catabolism mean in terms of extracting energy from glucose
We break down glucose by oxidizing it
Bronsted Lowry Acid/Base definition
Lewis acids and what kind of bond it forms
Example of lewis acid/base pair
a) Acids proton donors
Bases proton acceptors
b) lewis acids electron acceptors
lewis bases electron donors
electrons involved in coordinate covalent bond
Ex. Binding of oxygen atom to iron atom in a heme group
Oxygen is donating pair of electrons so it is a lewis base
Equilibrium expression for acid base chemistry and for base chemistry
What does Ka and Kb stand for?
The larger the Ka value, the…
The larger the Kb value, the…
Ka = [H30+][A-]/[HA] Kb = [HB+][OH-]/[B] Ka -> acid-ionization/acid dissociation kb-> Base-ionization/ base-dissociation ... the stronger the acid ... the stronger the base
Polyprotic
When something has more than one proton to donate Carbonic acid (H2CO3) is said to be polyprotic The conjugate base of H2CO3 is HCO3- which also has an ionizable proton
Amphoteric
When a substance can act as an acid or a base
Ex. HCO3-
Equation for pH and pOH
pH= - Log[H+]
so [H+] = 10^-pH
pOH = -log[OH-] and [OH-] = 10^-pOH
Some strong acids or bases extend the traditional pH scale of 0 - 14
For example, what is the pH of a 10M solutiom of HCl (It will fully dissociate)?
Since [H+] = 10^-pH
then the pH is -1
Equation that combines pH and pOH
pH + pOH = 14
since [H+][OH-] = 14
pKa and pKb equations
pKa = -logKa pKb = -logKb
Get buffer when you have…
roughly equal amounts of weak acid and conjugate base or weak base and conjugate acid
What is the most important buffer system in our blood plasm (and on MCAT)
Write the two chemical equations for it:
Bicarbonate buffer system
This buffer consists of carbonic acid (H2CO3) and its conjugate base, bicarbonate (HCO3-)
H2CO3 -> HCO3- + H+ (lactic acid produces H+ so le chat can push rxn in left direction)
H20 + CO2 -> H2CO3 (cell resp produces CO2)
What would happen to pKa of a acidic Glu residue if you replace the nearby neutral Ile residue with positively charged Lys residue?
The pKa would decrease (more acidic) bc it would be more stabilized in its deprotonated, negatively charged state and bc it would be more stable, it is more likely to give up its proton
The most basic functional group is the one with the ____ pKa
highest
The higher the Ka (____ the pKa), the ___the acid
The higher the Kb (____ the pKa), the ___the base
The higher the Ka (lower the pKa), the stronger the acid
The higher the Kb (lower the pKb), the stronger the base
The higher the Ka (____ the pKa), the ___the acid
The higher the Kb (____ the pKa), the ___the base
The higher the Ka (lower the pKa), the stronger the acid
pKa = -logKa
The higher the Kb (lower the pKb), the stronger the base
pKb = -logKb
What does a negative entropy mean? Neg enthalpy?
Negative ΔS (entropy) means something becoming less disordered (increase in order)
Positive ΔS means something becoming more disordered
A negative ΔH enthalpy - products in the reaction have lower energy compared to the reactants, so the reaction has lost energy and released it as heat, making it exothermic.
A positive ΔH implies that products in reaction have higher energy compared to reactants, so the reaction has gained energy and absorbs it as heat so it is endothermic
What is another word for heat of formation?
Heat of formation is ΔH change in enthalpy
What is the phase of F2, I2, and Br2 in standard state?
Liquids and then…
Br2 is LIQUID IN STANDARD STATE so Hfº is not 0!!
