Biochemistry: Thermodynamics and Kinetics

Question 1

The second law of thermodynamics states…

Law of conservation of energy

Answer 1

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

Question 2

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

Answer 2

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

Question 3

Something that is non spontaneous requires…

Answer 3

Energy input

Question 4

What equation would we use for calculating ΔG for a reaction in the body?

Answer 4

ΔG = ΔGº’ + RTlnQ

where Q = [C][D]/[A][B] (this is similar to Keq equation but there you would use concentrations at equilibrium)

Question 5

What does Keq tell you versus Q?

Answer 5

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.

Question 6

When Keq is large this means…

When Q is large this means …

Answer 6

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

Question 7

Two factors determine whether a reaction is spontaneous:

Answer 7

a) The intrinsic properties of reactants and products

b) The concentrations of reactants and products (RTlnQ)

Question 8

If something is spontaneous this means nothing about rate of reaction
Thermodynamics only tells you…
A thermodynamically favorable reaction is…

Answer 8

Where a system starts and finishes but nothing about the path traveled to get there

Spontaneous

Question 9

Chemical kinetics is…

Answer 9

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

Question 10

What does catalyst do to transiton state? What does it do to delta G? Do enzymes have a thermodynamic or kinetic role?

Answer 10

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

Question 11

Oxidation

Reduction

Answer 11

Oxidation = loss of e-s
Reduction = gain of e-s

Question 12

Important: 3 different ways to recognize oxidation reactions

Answer 12

1) gain of oxygen atoms
2) loss of hydrogen atom
3) loss of electrons

Question 13

Important: 3 different ways of recognizing reduction reactions

Answer 13

1) loss of oxygen
2) gain of hydrogen atom
3) gain of electrons

Question 14

How can you visualize if something is oxidation or reduction? ex. disulfide bond

Answer 14

Ex. For forming of disulfide bond see H’s disappear so it’s an oxidation

Question 15

What does oxidative catabolism mean in terms of extracting energy from glucose

Answer 15

We break down glucose by oxidizing it

Question 16

Bronsted Lowry Acid/Base definition

Lewis acids and what kind of bond it forms
Example of lewis acid/base pair

Answer 16

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

Question 17

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…

Answer 17

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

Question 18

Polyprotic

Answer 18

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

Question 19

Amphoteric

Answer 19

When a substance can act as an acid or a base

Ex. HCO3-

Question 20

Equation for pH and pOH

Answer 20

pH= - Log[H+]
so [H+] = 10^-pH

pOH = -log[OH-] and [OH-] = 10^-pOH

Question 21

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)?

Answer 21

Since [H+] = 10^-pH

then the pH is -1

Question 22

Equation that combines pH and pOH

Answer 22

pH + pOH = 14

since [H+][OH-] = 14

Question 23

pKa and pKb equations

Answer 23

pKa = -logKa
pKb = -logKb

Question 24

Get buffer when you have…

Answer 24

roughly equal amounts of weak acid and conjugate base or weak base and conjugate acid

Question 25

What is the most important buffer system in our blood plasm (and on MCAT)
Write the two chemical equations for it:

Answer 25

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)

Question 26

What would happen to pKa of a acidic Glu residue if you replace the nearby neutral Ile residue with positively charged Lys residue?

Answer 26

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

Question 27

The most basic functional group is the one with the ____ pKa

Answer 27

highest

Question 28

The higher the Ka (____ the pKa), the ___the acid

The higher the Kb (____ the pKa), the ___the base

Answer 28

The higher the Ka (lower the pKa), the stronger the acid

The higher the Kb (lower the pKb), the stronger the base

Question 29

The higher the Ka (____ the pKa), the ___the acid

The higher the Kb (____ the pKa), the ___the base

Answer 29

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

Question 30

What does a negative entropy mean? Neg enthalpy?

Answer 30

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

Question 31

What is another word for heat of formation?

Answer 31

Heat of formation is ΔH change in enthalpy

Question 32

What is the phase of F2, I2, and Br2 in standard state?

Answer 32

Liquids and then…

Br2 is LIQUID IN STANDARD STATE so Hfº is not 0!!