Thermodynamics Flashcards
What is thermodynamics?
Thermodynamics is the study of heat and energy and how it relates to the matter of the universe.
Thermodynamics involves the energy associated with reactions at equilibrium.
What are kinetics?
Kinetics describes the rate(s) at which a reaction moves towards equilibrium.
What is ‘Free Energy’?
Free energy is a thermodynamic quantity equivalent to the capacity of a system to do work.
What does the 1st Law of Thermodynamics state?
The 1st Law of Thermodynamics states that the total energy in a system is constant and can be transformed from one form to another.
Energy can neither be created or destroyed.
What does the 2nd Law of Thermodynamics state?
The 2nd Law of Thermodynamics states that the entropy of an isolated system never decreases because isolated systems tend towards equilibrium.
In other words, the entropy of the universe increases with every physical process that occurs.
What does the term ‘entropy’ refer to?
Entropy refers to the level of disorder / randomness in a system.
What is enthalpy?
Enthalpy is a measure of the total energy of a thermodynamic system.
This relates to the amount of heat in a system.
Most biochemical systems involve very little changes in enthalpy.
What is the enthalpy equation?
delta H = delta E + P delta V + V delta P
Most biochemical systems have a constant Volume and Pressure
delta H = delta E
What are ‘standard conditions’?
The standard conditions are:
- A temperature of 25 °C or 298 K
- A pressure of 1 atm
- A concentration of 1.0 M
What does the equilibrium constant measure?
Keq is a measure of the concentrations of reactant and product when the chemical reaction has reached equilibrium.
How do free energy and equilibrium relate to one another?
The equilibrium constant is a measure of the ratio of product concentrations to reactant concentrations at equilibrium
Standard free energy is a measure of the avaliable energy in the products and reactants
These two measures come together to describe Gibbs Free Energy
What is the Gibs Free Energy equation?
G = H - TS
If there is a isothermal rxn, the equation becomes delta G = delta H - T delta S
When will a reaction proceed to the right? That is, when will a reaction be spontaneous?
A reaction will only be spontaneous when the delta G < 0; this is a spontaneous reaction
When will a reaction be nonspontaneous? That is, when will a reaction favor the reactants?
If delta G > 0, a reaction will be nonspontaneous and favor reactants.
This is not a favorable reaction
What is the equation that relates Gibbs Free Energy to the equilibrium constant?
delta G = - RT ln Keq
Keq = exp (- delta G / RT)
How do delta G and delta Go’ relate?
delta Go’ is for reactants at standard conditions (298 K, 1.0 M, and 1 atm)
Most biochemical rxn’s are not at standard conditions however
To calculate the free energy of rxn’s in this state, use the following equation:
delta G = delta Go’ + RT ln ([C][D] / [A][B])
How do spontaniety and free energy relate to one another?
If a rxn is spontaneous, delta Go = 0, then Keq = 1
However
If delta Go’ < 0, then Keq > 1. The rxn is exergonic and spontaneous. This is a favorable rxn that results in more products than reactants.
But
If delta Go’ > 0, then Keq < 1. The rxn is endergonic and requires an energy input. Non spontaneous and an unfavorable rxn. More reactants than products.
How can an unfavorable rxn be driven to completion?
Unfavorable reactions can be linked to favorable reactions (One thet releases energy).
These are called ‘Coupled’ reactions.
What is catabolism?
Catabolism is the breaking down of products.
What is anabolism?
This is the building up of molecules.
What molecule that is derived from catabolic rxns can be used to drive reactions?
ATP; Adenosine Triphosphate
ATP contains two high-energy phosphate bonds that can be hydrolyzed to release energy
Any reaction that has a delta Go < + 30 kj / mol, can be coupled to ATP hydrolysis to drive the rxn
What are some other high energy compounds that contain high energy phosphates?
Creatin phosphate
Phosphoenolpyruvate (PEP)
1,3-Bisphosphoglycerate (1,3-BPG)
What are the most important substrates in oxidation - reduction reactions in aerobic organisms?
NAD+ and NADP+
The nicotinamide ring is positively charged
The chemical difference between the two molecules is in the phosphorylation of the 2’ phosphate group of the ribose
NAD+ usually associated with catabolic rxns and NADP+ is usually associated with anabolic rxns
Picture showing oxidation-reduction of NAD+ to NADH.
Reduction occurs on the nicotinamide ring and the ring no longer carries a net + charge.
Picture showing oxidation - reduction of NADP+ to NADPH.
Reduction occurs on the nicotinamide ring and the ring no longer carries a net + charge.
What are other redox reaction participants?
FAD and FMN
Flavin group is based on riboflavin
These are alternate participants in redox rxn’s
They tightly but noncovalently bind to their enzymes
FADH2 is a weaker reducing agent than NADH
Picture of FAD / FADH2 undergoing redox.
NOTE: Remember that FADH2 is a weaker reducing agent than NADH!
Picture of FMN / FMNH2 redox reaction.
How can Coenzyme A participate in biochemical rxn’s?
Coenzyme A has a reactive sulfhydrl at one end of the molecule.
It can form thioesters with acetate and other comounds.
Picture of Coenzyme A.
CoA carries acyl groups.
What are B vitamins involved in relating to metabolism?
The B vitamins participate in a variety of rxn’s including redox reactions, aldehyde transfers, and acyl group transfers.
This is not an all-inclusive list.
What does a deficiency of the B vitamin Niacin lead to?
A deficiency in Niacin can lead to pellagra, dermatitis, diarrhea, and dementia.
Many diets are low in vitamin contant but humans can synthesize nicotinamide from tryptophan. However, tryptophan is often in short dietary supply.
What does a thiamine deficiency lead to?
Thiamine deficiency can lead to Beriberi.
The primary symptoms of this disease impact the nervous system and muscles
White rice is missing thiamine but brown rice hulls are rich in it
What does a deficiency in Cobalamin (B12) lead to?
B12 deficiency leads to pernicious anemia
Symptoms are weakness, fatigue, pallor, palpatations, and dizziness
Animal meats are sources of B12
What does Ascorbate (Vit C) deficiency lead to?
This deficiency leads to impaired collagen formation (Scurvy)
What are the types of chemical reactions involved in metabolism?
Redox
ATP-dependent ligation (Covalent bond making)
Isomerization
Group transfers of functional groups
Hydrolytic cleavage
Addition or removal of functional groups
Picture of Succinate to Fumarate and Malate to Oxaloacetate.
Succinate + FAD —> Fumarate + FADH2
Malate + NAD+ —>Oxaloacetate + NADH + H+
Picture of Pyruvate to Oxaloacetate reaction.
Picture of citrate to isocitrate.
Picture of glucose to glucose 6-phosphate.
