Special Newsletter: Gibbs Free Energy and Transition State Energy

Special Newsletter
Gibbs Free Energy and Transition State Energy

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This goal of this newsletter is to help students navigate the complexity of Gibbs Free Energy (ΔG) and help avoid confusion about Gibbs Free Energy and Transition State Energy (Energy of Activation).

Gibbs Free Energy (ΔG) is a thermodynamics concept, and describes the thermodynamic potential of a system.  It measures the "work" that can be obtained from a system, for us a chemical reaction, if that system is held at constant temperature and pressure.  The goal is to determine whether a given reaction is spontaneous in the direction written, i.e., whether the reaction will proceed in the given direction without the input of energy.

Mathematically, Gibbs Free Energy is described as:
ΔG=ΔH−TΔS

Where:

• ΔG  The change in Free Energy
• ΔH  The change in Enthalpy
• ΔS   The change in Entropy

In biochemistry, the change in Enthalpy (ΔH) is the same as the change in internal energy.  Remember that ΔG is calculated based on a set of given conditions:  we are at constant temperature and pressure, and all variables have been taken into account (such as the solvent of the system).  If you change anything, you change the system, and thus the ΔG.

Gibbs free energy is a measure ONLY of the difference in free energy of the products and reactants, and does not tell us about the rate of the reaction.  It only tells us whether the reaction is Exergonic or Endergonic.

• ΔG < 0   Exergonic:  The reaction is considered spontaneous in the direction written.
• ΔG = 0   The system is in equilibrium
• ΔG >0    Endergonic:  To carry out this reaction as written, there needs to be an addition of free energy (NOTE: this means that the reverse reaction is spontaneous).

Transition State Energy is not Gibbs Free Energy.
Gibbs Free Energy does not describe the path of transformation or the mechanism of transformation.  It does not describe the rate of transformation.  It only describes whether the reaction is spontaneous, non-spontaneous or at equilibrium.

The breakdown of the dissacharide sucrose to glucose and fructose has a ΔG of -5.5 kcal/mol.  This is a spontaneous (Exergonic) reaction in terms of ΔG.  Yet you can store sucrose in your kitchen and it remains sucrose.  There is no spontaneous degradation into monosaccharides.  Why?

Sucrose is a stable molecule.  In order to force the breakdown (catabolism) of sucrose, we need to destabilize the molecule.  This destabilization is the transition state of the reaction, and in a closed system, requires the input of energy.  This is termed the Activation Energy of the reaction (you will also hear this described as the Transition State Energy).  If we were to look at our breakdown of sucrose, we would see the following:

Sucrose   ⇄    Transition State   →   Glucose + Fructose

The energy of the transition state is noted as either E_a or ΔG^‡.  These two expression are from different formula for calculating activation energy. ΔG^‡ is used in a formula that relates activation energy to Gibbs Free Energy (the Eyring equation).  In either case, the expression describe transition state energy (aka, activation energy).

In biochemistry, enzymes are used to reduce the activation energy (just like catalysts are used in chemistry).  Catalysts and Enzymes reduce the activation energy ΔG^‡; they do not alter Gibbs Free Energy (ΔG).  This is a critical concept!

Transition state deals with the rate of the reaction.  By lowering the activation energy (transition state energy), you increase the rate of the reaction.  In essence, you are making the reaction more likely to happen.  But the enzyme does not change Gibbs Free Energy.

Original Image from ChemWiki,
http://chemwiki.ucdavis.edu/@api/deki/files/10017/fREE_eNERgY_cHART.jpg?size=bestfit&width=471&height=294&revision=1

Take home message:

Gibbs Free Energy (ΔG) describes whether a reaction is exergonic or endergonic.  It does not describe rate, and neither enzymes or catalysts will alter ΔG.

Activation Energy (ΔG^‡) does not alter ΔG; it does not determine whether a reaction is spontaneous or non-spontaneous. Activation energy does help determine the rate of the reaction.

Daily Newsletter: September 23, 2013 - Thermodyanmics

Daily Newsletter

September 24, 2012 Thermodynamics

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Remember that modern molecular biology is based on chemistry. 
What makes up cells?  
Chemicals. You have water, ions, proteins, carbohydrates, lipids, nucleic acids, and other compounds. Together, all of these chemicals make up what we see as the cell; but remember, the cell is greater than the sum of its chemical parts. It is the interaction of these chemical parts that makes the cell unique.
Biologists look at the chemistry of the cell from a different perspective, or lens, than chemists. In order to understand each individual chemical reaction, chemists will isolate a specific reaction, measure it, manipulate it, and report on it. Our knowledge of biochemistry and molecular pathways are all based on this reductionist perspective (reductionism - simplifying complex systems to component parts for study). Biologists take the information on these parts and attempt to visualize the whole from the individual parts. Due to this, we have to look at how the perspective of biologists differs from that of chemists when we start discussing cellular energetics and chemistry.
Today you are asked to reflect upon the topics of thermodynamics and equilibrium as they pertain to biology. These are topics originally introduced in chemistry, so you may want to go back to your chemistry books to refresh your memory. While biochemists may use these concepts unaltered from their original meaning in chemistry, most biologists look at these two concepts from a slightly different perspective.

The Laws of Theromodynamics: (the two important ones for biology are in bold).
0. If two systems are in thermal equilibrium with a third system, they must be in thermal equilibrium with each other.
(seems obvious to us know; sometimes shows up in biology).

1. Energy can neither be created nor destroyed, but can be changed from one form to another. (First Law)
• We are constantly moving energy around in living systems.
• The most obvious example of this will be the conversion of Light Energy to Chemical Energy in the production of Glucose.
• Examle: Phototrophs are organisms that can convert light energy to chemical energy.
• Example: Motile organisms (such as animals) can convert chemical energy into mechanical energy.
• Example: Luminescent organisms can convert chemical energy into light energy.
• Example: Heterotrophic organisms can convert one type of chemical energy into a different type of chemical energy. (Remember the First Law includes the conversion of Chemical Energy into a different "form" of Chemical Energy.)
2. In all energy exchanges, if no energy enters or leaves the system, the potential energy of the state will always be less than that of the initial state. (Second Law)
• This is big for biology, but not often discussed.
• You will remember this as the law of Entropy.
• Every time we experience an energy exchange, some of that energy is used, but the rest is lost due to entropy.
• Let's say you eat a muffin: Only a fraction of the chemical energy in the muffin will be harvested as useful energy by your cells. The rest is lost to entropy.
• Heat is a common disorganization of energy, i.e., entropy; but we don't want to over heat cells. (How do we get around this?)
3. All processes cease as temperature approaches absolute zero. (not generally a concern to biologists).

Later in the week, we will discuss redox reactions, but for now I want to put this concept into your heads: One of the most critical energy exchanges in biology will be the production of reducing potential.

The second law of homeostasis plays a role in homeostasis. With the second law, we know that energetically, we can never break even. Every time that we undergo a chemical reaction, we loose energy. This loss is generally going to be as heat, which is also not good for a cell (too much heat, and the cell boils). So we have be as efficient as possible knowing that we are always loosing energy. How does this play out?

• Plants take in sunlight, and make glucose.
• The sunlight is high energy.
• The glucose is going to have to have less energy because we used photons to excite electrons (an energy change).
• Animals eat plants.
• We catabolize the glucose for energy (reducing potential).
• Do we get 100% of the energy in glucose? NO.
• Animals build biomass (make proteins, lipids, etc... as needed for life).
• The energy we got from glucose is further lost when we make new biochemicals.
• We constantly need energy to keep rebuilding ourselves.
• We constantly need energy inputs to maintain homeostasis.

So why is the second law so important? To answer this question, we need to look at chemical equilibrium. You will recall this concept from chemistry, and it deals with reactions. On the right is an image of an Iron Thiocyanate reaction that was produced by the BBC. It shows the forward and reverse reactions. As you will remember, at a given set of conditions (such as a constant temperature and pressure) you can expect to see an equilibrium reached in which you will have some quantity of substrate and product. While the forward and reverse reactions will continue to occur, there will be a fairly constant quantity of substrate and product.
You may recall that one way to influence the equilibrium is to either add more substrate or remove the product. The removal of product is important for biologists, and sets up a very important condition.
In metabolic pathways, the product of one reaction becomes the substrate for the next reaction. We are constantly taking products to the next reaction. There is a constant flow, at least while an organism is alive, moving product to become the substrate of the next reaction. In biology, it is not about a single reaction, it is always about a series of reactions. This is a critical point! A chemist may look at a single reaction, but a biologist must look at the overall set of reactions if they are to understand the organism.
So, an organism is constantly alterating the equalibirum of a given reaction by taking the product and using it as a substrate in another reaction. We will also see that organisms are constantly acquiring energy and "building block". As such, organisms never acheive the equilibrium a chemist would see in a test tube, and we constantly acquire energy to avoid entropy (consider starvation where you have no new inputs of energy, what happens to the system?).

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Daily Challenge

Today you are tasked with describing in your own words how the laws of thermodynamics and equilibrium play out in living systems. Use the Newsletter and our class discussions as the start point, but generate your own analogies and examples. 

Daily Newsletter: September 24, 2012 - Thermodynamics

Daily Newsletter

September 24, 2012 Thermodynamics

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Modern biology is based on chemistry. What makes up cells? Chemicals. You have water, ions, proteins, carbohydrates, lipids, nucleic acids, and other compounds. Together, all of these chemicals make up what we see as the cell; but remember, the cell is greater than the sum of its chemical parts. It is the interaction of these chemical parts that makes the cell unique.
Biologists look at the chemistry of the cell from a different perspective, or lens, than chemists. In order to understand each individual chemical reaction, chemists will isolate a specific reaction, measure it, manipulate it, and report on it. Our knowledge of biochemistry and molecular pathways are all based on this reductionist perspective (reductionism - simplifying complex systems to component parts for study). Biologists take the information on these parts and attempt to visualize the whole from the individual parts. Due to this, we have to look at how the perspective of biologists differs from that of chemists when we start discussing cellular energetics and chemistry.
Today you are asked to reflect upon the topics of thermodynamics and equilibrium as they pertain to biology. These are topics originally introduced in chemistry, so you may want to go back to your chemistry books to refresh your memory. While biochemists may use these concepts unaltered from their original meaning in chemistry, most biologists look at these two concepts from a slightly different perspective.

The Laws of Theromodynamics: (the two important ones for biology are in bold).
0. If two systems are in thermal equilibrium with a third system, they must be in thermal equilibrium with each other.
(seems obvious to us know; sometimes shows up in biology).

1. Energy can neither be created nor destroyed, but can be changed from one form to another. (First Law)
• We are constantly moving energy around in living systems.
• The most obvious example of this will be the conversion of Light Energy to Chemical Energy in the production of Glucose.
• Examle: Phototrophs are organisms that can convert light energy to chemical energy.
• Example: Motile organisms (such as animals) can convert chemical energy into mechanical energy.
• Example: Luminescent organisms can convert chemical energy into light energy.
• Example: Heterotrophic organisms can convert one type of chemical energy into a different type of chemical energy. (Remember the First Law includes the conversion of Chemical Energy into a different "form" of Chemical Energy.)
2. In all energy exchanges, if no energy enters or leaves the system, the potential energy of the state will always be less than that of the initial state. (Second Law)
• This is big for biology, but not often discussed.
• You will remember this as the law of Entropy.
• Every time we experience an energy exchange, some of that energy is used, but the rest is lost due to entropy.
• Let's say you eat a muffin: Only a fraction of the chemical energy in the muffin will be harvested as useful energy by your cells. The rest is lost to entropy.
• Heat is a common disorganization of energy, i.e., entropy; but we don't want to over heat cells. (How do we get around this?)
3. All processes cease as temperature approaches absolute zero. (not generally a concern to biologists).

Later in the week, we will discuss redox reactions, but for now I want to put this concept into your heads: One of the most critical energy exchanges in biology will be the production of reducing potential.

The second law of homeostasis plays a role in homeostasis. With the second law, we know that energetically, we can never break even. Every time that we undergo a chemical reaction, we loose energy. This loss is generally going to be as heat, which is also not good for a cell (too much heat, and the cell boils). So we have be as efficient as possible knowing that we are always loosing energy. How does this play out?

• Plants take in sunlight, and make glucose.
• The sunlight is high energy.
• The glucose is going to have to have less energy because we used photons to excite electrons (an energy change).
• Animals eat plants.
• We catabolize the glucose for energy (reducing potential).
• Do we get 100% of the energy in glucose? NO.
• Animals build biomass (make proteins, lipids, etc... as needed for life).
• The energy we got from glucose is further lost when we make new biochemicals.
• We constantly need energy to keep rebuilding ourselves.
• We constantly need energy inputs to maintain homeostasis.

So why is the second law so important? To answer this question, we need to look at chemical equilibrium. You will recall this concept from chemistry, and it deals with reactions. On the right is an image of an Iron Thiocyanate reaction that was produced by the BBC. It shows the forward and reverse reactions. As you will remember, at a given set of conditions (such as a constant temperature and pressure) you can expect to see an equilibrium reached in which you will have some quantity of substrate and product. While the forward and reverse reactions will continue to occur, there will be a fairly constant quantity of substrate and product.
You may recall that one way to influence the equilibrium is to either add more substrate or remove the product. The removal of product is important for biologists, and sets up a very important condition.
In metabolic pathways, the product of one reaction becomes the substrate for the next reaction. We are constantly taking products to the next reaction. There is a constant flow, at least while an organism is alive, moving product to become the substrate of the next reaction. In biology, it is not about a single reaction, it is always about a series of reactions. This is a critical point! A chemist may look at a single reaction, but a biologist must look at the overall set of reactions if they are to understand the organism.
So, an organism is constantly alterating the equalibirum of a given reaction by taking the product and using it as a substrate in another reaction. We will also see that organisms are constantly acquiring energy and "building block". As such, organisms never acheive the equilibrium a chemist would see in a test tube, and we constantly acquire energy to avoid entropy (consider starvation where you have no new inputs of energy, what happens to the system?).

---

Daily Challenge

 Today you are tasked with describing in your own words how the laws of thermodynamics and eqiulibrium play out in living systems. Use the above a a jumping off point, but build your own discussion, examples or analogies.

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