Daily Newsletter

September 24, 2012 Thermodynamics

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).

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.)

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?)

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. Chemical Equlibirum

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 equilibrium play out in living systems. Use the Newsletter and our class discussions as the start point, but generate your own analogies and examples.