1. Biochemistry Basics Flashcards
What is the first law of thermodynamics?
The law of conservation of energy. The energy of the universe is constant.
If the energy of a system decreases, than the energy of the universe (surroundings) increases, and vice versa,
What is the second law of thermodynamics?
Entropy –> the universe tends towards randomness (i.e. increased entropy)
If entropy (S) has a negative sign, what is true?
a negative entropy means that entropy has decreased, which is an unfavorable event (the universe wants increases in entropy)
What is the equation for Gibbs free energy?
ΔG = ΔH - TΔS
free energy = G
enthalpy (heat of reaction) = H
T is temperature in kelvin
S is entropy
explain exergonic and endergonic?
exergonic reaction, ΔG is negative, and the reaction is spontaneous.
endergonic reaction, ΔG is positive, and the reaction is non-spontaneous.
what are exothermic and endothermic?
exothermic, negative ΔH, release heat
endothermic, positive ΔH, require heat
how do you assign the signs (+/-) to quantities in a thermodynamic system?
signs are relative to the system NOT the surroundings.
so if the system releases heat, it is -ΔH
What is the standard free energy change?
(∆Gº and ∆Gº’)?
What is the equation for ∆Gº’?
The ∆G of a reaction also depends on the concentrations of reactants and products. To compare reactions, the
∆Gº has all R’s and P’s at 1M concentration.
Under physiological conditions, we need to further standardize because of H+ and pH. This refers to ∆Gº’.
∆Gº’ = -RTlnK’eq
Keq is the equilibrium constant for the particular reaction.
What is the formula for K’eq?
A + B –> C + D
K’eq = [C][D] / [A][B]
to the power of coefficients
if ∆Gº’ is standardized, what equation do we use to find the real ∆G of a reaction in the body?
∆G = ∆Gº’ + RTlnQ
where Q = [products] / [reactants]
∆Gº’ = -RTlnK-eq
What occurs if K’eq = 1? What occurs if Q=1?
recall, ∆Gº’ = -RTlnK’eq
if K’eq = 1, than ln(1) = 0
therefore, ∆Gº’ = 0.
recall ∆G = ∆Gº’ + RTlnQ
If Q = 1, than lnQ = 0
therefore, ∆G = ∆Gº’
What is the core difference between K and Q?
Q is the ratio of reactants and products in any given situation. K is the ratio of reactants and products at equilibrium.
What is equilibrium?
The rate of the forward and reverse reactions are equal. NOT the concentrations.
t or f, if a reaction is at equilibrium then overall concentrations stay the same.
TRUE, since the rate of reaction in both directions is equal, concentrations on each side remain what they are (but not necessarily the same [] on each side)
explain reaction shifts when…
- Q = K
- Q > K
- Q < K
- Q = K: the []’s are the same as equilibrium conditions, therefore, we are at equilibrium
- Q > K: Currently there is more product, and so there is a left shift towards reactants.
- Q < K: Currently there is more reactant, and so there is a right shift towards products.
more details on equilibrium and thermodynamics in general chemistry review.
What does a large K’eq indicate?
products / reactants. If equilibrium is achieved at a high k’eq, then products must have lower free energy than reactants.
Explain if ∆G=0.
Recall,
∆G = ∆Gº’ +RTlnQ
if ∆G = 0, than ∆Gº’ = -RTlnQ
this means, Q = K, which means we are at equilibrium.
What does spontaneous mean?
A reaction is favorable (∆G is negative). However, spontaneity says nothing about reaction rate!!
E.g. beta-decay of carbon –> this is favorable, but takes years to occur.
t or f, ∆G depends on the pathway the reaction takes and the rate of that reaction.
False! ∆G is simply a measurement of the difference in free energy between R’s and P’s. It is path-independent.
compare ∆G of oxidizing sugar in your body vs. an industrial furnace.
∆G is path-independent, and thus, is the same value in both cases. (the likely only difference is heat)
t or f, wood burning is spontaneous.
true, then why does it not occur? –> activation energy
Explain activation energy and transition states?
all reactions proceed through an unstable transition state compound. A certain level of energy is required to shove the reactants into this unstable state. This initial energy is the activation Energy (Ea).
How does Ea affect reaction rate?
If you can lower the Ea of a reaction, you speed the reaction rate up. The direction of that reaction depends on ∆G and equilibrium.
What is a catalyst?
A catalyst is something that lowers the activation energy of a reaction WITHOUT being consumed by the reaction or changing the ∆G.
How does a catalyst lower the activation energy?
it stabilizes the transition state compound. Enzymes are biological catalysts
t or f, enzymes only have a kinetic role in reactions.
True, equilibrium is not affected and therefore enzymes cannot make a reaction go in a specific direction, only faster in the given direction.
What are photoautotrophs and chemoheterotrophs?
Photoautotroph –> takes energy from sunlight and creates its own food
Chemoheterotroph –> takes energy from chemical bonds provided by others
What are three ways to identify an oxidation reaction?
LEO the lion says GER
- loss of electerons = oxidation
- loss of hydrogen = oxidation
- gain of oxygen = oxidation
What are three ways to identify a reduction reaction?
LEO the lion says GER
- gain of electrons = reduction
- gain of hydrogen = reduction
- loss of oxygen = reduction
t or f, catabolic processes are generally oxidative while anabolic processes are generally reductive.
true
we break down glucose into CO2 and ATP via oxidation
What is a bronsted base and bronsted acid?
acid - proton donor
base - proton acceptor
t or f, any species with a lone pair of electrons qualifies as bronsted base.
true, as any anion or neutral species with a lone pair of electrons is capable of bonding with H+.
What are Lewis acids and bases?
A Lewis Acid: electron pair acceptor
A Lewis Base: electron pair donator
This is the organic chemistry understanding of acids and bases.
What is a coordinate covalent bond?
a bonding reaction in which one reactant provides both of the bonding electrons. Lewis A/B reactions frequently create coordinate covalent bonds.
t or f, the more delta positive center will likely be the Lewis acid in the reaction.
true, since Lewis Acids are electron acceptors.
what is a common biological example of a coordinate covalent bond?
oxygen binding to the iron atom in the heme group of a red blood cell.
In terms of dissociation, what will a strong acid do in water?
A strong acid will completely (100%) dissociate in water. This is because strong acids want to give up their protons easily. Therefore, all of the acids will react with water to create the conjugate base.
t or f, we include water in the equilibrium expression for acids and bases.
false, we only include aqueous solutes (not liquids).
What is Ka? Interpret its values.
Ka is the K’eq of acid dissociation (and therefore, called the acid dissociation constant). A larger Ka indicates that more products are forming at equilibrium indicating a stronger acid.
What is Kb?
Kb is the K’eq of a base-ionization reaction (called the base-ionization constant). A large Kb indicates that more products are made, and therefore we have a strong base (accepting all H+ to form its conjugate acid).
What is polyprotic? What is amphoteric (amphiprotic)?
polyprotic –> an acid capable of giving up more than one hydrogen
amphiprotic –> a substance that may act as an acid or a base (H2O).
t or f, every time a polyprotic acid donates a proton, the following acid is weaker.
true, in general.
What is pH, what is its formula?
pH = -log[H+] which implies [H+] = 10^-pH
pH measures the concentration of H+ in solution on a logarithmic scale.
At room temperature, a neutral solution has a pH of 7 or a [H+] of 10^-7
What is pOH?
pOH measures the concentration of OH- in solution on a logarithmic scale.
pOH = -log[OH-] which implies [OH-] = 10^-pOH
can pH be negative?
yes, similar to pOH being over 14.
How are pH and pOH related at 25C?
pH + pOH = 14
or
[H+][OH-] = 10^-14
if the concentration of H+ goes up, then the concentration of OH- must go down. They are inversely related.
What is pKa and pKb?
p before something indicates the negative log of that something.
pKa = -log(Ka) pKb = -log(Kb)
a large pKa value indicates what?
a large Ka value indicates a strong acid, as most of the acid dissociates. Since we take the negative log of Ka, the smaller the p-value (the more negative) the stronger the acid.
the same logic applies to pKb
What is an acid/base buffer?
A solution that resists change in pH / pOH. They are typically a weak acid and its conjugate base (or a weak base and conjugate acid) existing in approximately equal concentrations (i.e. both weak acid and weak base)
What buffer system ensures our blood plasma remains around a pH of 7.4.
the carbonic acid / bicarbonate system.
CO2 + H2O –> H2CO3 (muscle creates CO2 which reacts with water to create carbonic acid)
H2CO3 + H2O –> HCO3- + H3O+ (Carbonic acid reacts with water to create bicarbonate).
Then bicarbonate constantly reacts with H+, balancing the amount of it.
What enzyme facilitates CO2 + H2O –> H2CO3
carbonic anhydraze
