Chapter 4: Biochemistry Flashcards
What are the 2 relevant forms of energy in chemsitry?
heat energy (movement of molecules) and potential energy (energy stored in chemical bonds)
1st law of thermodynamics
the law of conservation of energy; states that the energy in the universe is constant
(implies that when energy of a system decreases, energy of sorroudings increases and vice vers)
2nd law of thermondynamics
disorder (entropy) of the universe tends to increase, can also be said as spontaneous reactions tend to increase the disorder of the universe
Gibbs Free Energy
- ΔG = ΔH – TΔS (H = enthalpy, which is heat or thermodynamic potential)
a) ΔG > 0 → needs heat, nonspontaneous
b) ΔG - ΔH = ΔE – PΔV (E = bond energy)
ΔH = enthalpy
ΔG increases when ΔH increases
ΔG increases when ΔS decreases
ΔG > 0
A positive ΔG is endergonic
ΔG
A negative ΔG is exergonic
ΔH
exothermic and release heat
ΔH > 0
endothermic and require an imput of heat
Standard Gibbs free energy
- ΔGº → all at 1 M concentration
- ΔGº’ → 1 M concentration and @ pH 7
- ΔGº’ = -RtlnK’eq (R = gas constant, Keq = ratio of products to reactants at equilibrium)
a) Keq = [C]eq[D]eq/[A]eq[B]eq - Remember: spontaneity says nothing about the reaction rate!
Equillibrium
defined as the point where the rate of reaction in one direction equals the rate of reaction in the other
Q
ratio of products to reactants in any given set up
<span>K</span>eq
ratio at equillibrium
How can ΔG be negative if ΔGº’ is positive (which indicates that the reaction is unfavorable at standard conditions)?
The reaction may be favorable (ΔG
Does Keq indicate the rate at which a reaction will proceed?
Keq indicates only the relative concentration once equillibrium is reached, not the reaction rate (how fast equillibrium is reached)
When Keq is large, which has lower free energy: products or reactants?
A large Keq means that more products are present at equillibrium. Remember that equillibrium tends toward the lowest energy state. Hence, when Keq is large, products have lower free energy than reactants.
When Q is large, which has lower free energy: products or reactants?
The size of Q says nothing about the properties of the reactants and products. Q is calculated from whatever the initial concentrations happen to be. It is Keq that says something about the nature of reactants and products since it describes their concentrations after equillibrium has been reached.
Which direction, forward or backward, will be favored in a reaction if ΔG = 0?
If ΔG = 0 then neither the forward nor the reverse reaction is favored. Q = Keq and when this is true we are by definition at equillibrium. Understand and memorize the following: When ΔG = 0, you are at equillibrium: forward reaction equals back reaction and the net concentrations of reactants and products do not change.
Spontaneous means that a reaction may proceed without additional energy input BUT it says nothing about what?
It says nothing about the rate of a reaction
Thermodynamics will tells you where
a system starts and finishes but nothing about the path traveled to get there. The difference in free energy in a reaction is only a function of the nature of the reactants and products. Therefore ΔG does not depend on the pathway a reaction takes or the rate of reaction, it is only a measurement of the difference in free energy between reactants and products.
How does the ΔG for a reaction burning sugar in a furnace compare to the ΔG when sugar is broken down in a human?
The ΔG is the same in both cases. ΔG does not depend on the pathway only on the different energies of the reactants and products.
All reaction proceed through a transient intermediate that is unstable and takes a great deal of energy to produce. The energy required to produce the transient intermediate state is called the …….. ?
activation energy , this is the barrier that prevents many reactions from proceeding even though the ΔG for the reaction may be negative. It is the activation energy that determines the kinetics of the reaction.
Chemical Kinetics
the study of reaction rates
How would the rate of a spontaneous reaction be affected if the activation energy were lowered?
The rate would be increased
Transition State
The transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate. It exists for a very short time either moving forward to form productor breaking back down into reactants
Catalyst
A catalyst lowers the Ea of a reaction without changing the ΔG. The catalyst lowers the Ea by stabilizing the transition state, making existence less thermodynamically unfavorable.
It is also important to note that a catalyst is not consumed in the reaction, it is regenerated with each reaction cycle
Enzymes are _________
catalysts, they increase the rate of a reaction by lowering the reactions activation energy but they do not affect ΔG between reactants and products. As catalysts, enzymes have a kinetic role, not a thermodynamic one.
Will enzymes alter the concentrations of reagents at equillibrium?
No, it will only affect the rate at which reactants and products reach equillibrium.
Hydrolase
hydrolyzes chemical bonds
Isomerase
rearranges bonds within a molecule to form an isomer
Ligase
forms a chemical bond
Lyase
breaks chemical bonds by means other than onxidation or hydrolysis
Kinase
transfers a phosphate group to a molecule from a high energy carrier such as ATP
Oxidoreductase
runs redox reactions
Polymerase
polymerization (adding of nucleotides to leading strand of DNA by DNA polymerase 3)
Phosphatase
removes a phosphate group from a molecule
Phosphorylase
transfers a phosphate group to a molecule from inorganic phosphate
Protease
hydrolyzes peptide bonds
Enzymes increase the rate of what type of reactions?
reactions that have a negative ΔG. These reactions would occur on their own without an ezyme but far more slowly than with one
Thermodynamically unfavorable reaction in the cell can be driven forward by what?
reaction coupling, in reaction coupling, one very favorable reaction is used to drive an unfavorbale one. This is possible because free energy changes are additive.
What is the favorable reaction that the cell can use to drive unfavorable reactions?
ATP Hydrolysis
kinetics and activation energy summary
A. Kinetics: the study of reaction rates
B. Activation energy (Ea): energy required to produce a transient intermediate (denoted ‡)
- ↑ Ea = slower rxn rate
- The energy for bob to apply for a job is higher than Bob with or without a job
C. Catalysts (enzymes) will lower Ea but will not affect ΔG!!
D. Because enzymes lower Ea, they increase the rate at which favorable rxns occur!
- Ea is lower with catalyst than without, but notice ΔG does not change!
- ΔG represents net change of energy from reactants to products
E. ATP as energy source: useful for reactions with + ΔG
- Reaction coupling: a favorable rxn is used to drive an unfavorable rxn by combining 2 together
- ATP hydrolysis drives unfavorable reactions
- Note that reaction coupling will alter total free energy, making an unfavorable rxn proceed!
Kinetics Diagram
Understand this diagram
Enzymes
Enzymes lower the activation E of a rxn making it easier for the substrate to reach the transition state.
- Enzymes increase the rate of a rxn (how fast equilib is reached), but do not alter the position of the equilibrium;
- Do not affect the overall free E or enthalpy of a rxn;
- Are not altered or consumed in the course of a rxn; thus, small amt required.
- Enzymes are pH and T sensitive; ranges of optimal activity.
- may consist of a single polypeptide chain, or several subunits in quaternary structure (globular)
Enzyme Specificity
Enzymes are designed to work only on a specific substrate or group of closely related substrates
Enzyme prefix
End in -ase