Thermodynamics

Question 1

What is thermodynamics?

Answer 1

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.

Question 2

What are kinetics?

Answer 2

Kinetics describes the rate(s) at which a reaction moves towards equilibrium.

Question 3

What is ‘Free Energy’?

Answer 3

Free energy is a thermodynamic quantity equivalent to the capacity of a system to do work.

Question 4

What does the 1st Law of Thermodynamics state?

Answer 4

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.

Question 5

What does the 2nd Law of Thermodynamics state?

Answer 5

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.

Question 6

What does the term ‘entropy’ refer to?

Answer 6

Entropy refers to the level of disorder / randomness in a system.

Question 7

What is enthalpy?

Answer 7

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.

Question 8

What is the enthalpy equation?

Answer 8

delta H = delta E + P delta V + V delta P

Most biochemical systems have a constant Volume and Pressure

delta H = delta E

Question 9

What are ‘standard conditions’?

Answer 9

The standard conditions are:

• A temperature of 25 °C or 298 K
• A pressure of 1 atm
• A concentration of 1.0 M

Question 10

What does the equilibrium constant measure?

Answer 10

Keq is a measure of the concentrations of reactant and product when the chemical reaction has reached equilibrium.

Question 11

How do free energy and equilibrium relate to one another?

Answer 11

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

Question 12

What is the Gibs Free Energy equation?

Answer 12

G = H - TS

If there is a isothermal rxn, the equation becomes delta G = delta H - T delta S

Question 13

When will a reaction proceed to the right? That is, when will a reaction be spontaneous?

Answer 13

A reaction will only be spontaneous when the delta G < 0; this is a spontaneous reaction

Question 14

When will a reaction be nonspontaneous? That is, when will a reaction favor the reactants?

Answer 14

If delta G > 0, a reaction will be nonspontaneous and favor reactants.

This is not a favorable reaction

Question 15

What is the equation that relates Gibbs Free Energy to the equilibrium constant?

Answer 15

delta G = - RT ln K_eq

K_eq = exp (- delta G / RT)

Question 16

How do delta G and delta G^o’ relate?

Answer 16

delta G^o’ 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 G^o’ + RT ln ([C][D] / [A][B])

Question 17

How do spontaniety and free energy relate to one another?

Answer 17

If a rxn is spontaneous, delta G^o = 0, then K_eq = 1

However

If delta G^o’ < 0, then K_eq > 1. The rxn is exergonic and spontaneous. This is a favorable rxn that results in more products than reactants.

But

If delta G^o’ > 0, then K_eq < 1. The rxn is endergonic and requires an energy input. Non spontaneous and an unfavorable rxn. More reactants than products.

Question 18

How can an unfavorable rxn be driven to completion?

Answer 18

Unfavorable reactions can be linked to favorable reactions (One thet releases energy).

These are called ‘Coupled’ reactions.

Question 19

What is catabolism?

Answer 19

Catabolism is the breaking down of products.

Question 20

What is anabolism?

Answer 20

This is the building up of molecules.

Question 21

What molecule that is derived from catabolic rxns can be used to drive reactions?

Answer 21

ATP; Adenosine Triphosphate

ATP contains two high-energy phosphate bonds that can be hydrolyzed to release energy

Any reaction that has a delta G^o < + 30 kj / mol, can be coupled to ATP hydrolysis to drive the rxn

Question 22

What are some other high energy compounds that contain high energy phosphates?

Answer 22

Creatin phosphate

Phosphoenolpyruvate (PEP)

1,3-Bisphosphoglycerate (1,3-BPG)

Question 23

What are the most important substrates in oxidation - reduction reactions in aerobic organisms?

Answer 23

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

Question 24

Picture showing oxidation-reduction of NAD⁺ to NADH.

Answer 24

Reduction occurs on the nicotinamide ring and the ring no longer carries a net + charge.

Question 25

Picture showing oxidation - reduction of NADP⁺ to NADPH.

Answer 25

Reduction occurs on the nicotinamide ring and the ring no longer carries a net + charge.

Question 26

What are other redox reaction participants?

Answer 26

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

Question 27

Picture of FAD / FADH₂ undergoing redox.

Answer 27

NOTE: Remember that FADH₂ is a weaker reducing agent than NADH!

Question 28

Picture of FMN / FMNH₂ redox reaction.

Answer 28

Question 29

How can Coenzyme A participate in biochemical rxn’s?

Answer 29

Coenzyme A has a reactive sulfhydrl at one end of the molecule.

It can form thioesters with acetate and other comounds.

Question 30

Picture of Coenzyme A.

Answer 30

CoA carries acyl groups.

Question 31

What are B vitamins involved in relating to metabolism?

Answer 31

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.

Question 32

What does a deficiency of the B vitamin Niacin lead to?

Answer 32

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.

Question 33

What does a thiamine deficiency lead to?

Answer 33

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

Question 34

What does a deficiency in Cobalamin (B12) lead to?

Answer 34

B12 deficiency leads to pernicious anemia

Symptoms are weakness, fatigue, pallor, palpatations, and dizziness

Animal meats are sources of B12

Question 35

What does Ascorbate (Vit C) deficiency lead to?

Answer 35

This deficiency leads to impaired collagen formation (Scurvy)

Question 36

What are the types of chemical reactions involved in metabolism?

Answer 36

Redox

ATP-dependent ligation (Covalent bond making)

Isomerization

Group transfers of functional groups

Hydrolytic cleavage

Addition or removal of functional groups

Question 37

Picture of Succinate to Fumarate and Malate to Oxaloacetate.

Answer 37

Succinate + FAD —> Fumarate + FADH₂

Malate + NAD⁺ —>Oxaloacetate + NADH + H⁺

Question 38

Picture of Pyruvate to Oxaloacetate reaction.

Answer 38

Question 39

Picture of citrate to isocitrate.

Answer 39

Question 40

Picture of glucose to glucose 6-phosphate.

Answer 40