2020_Winter_Bis2a_Facciotti_Lecture_06
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Learning Objectives Associated with 2020_Winter_Bis2a_Facciotti_Lecture_06
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Matter and Energy in Biology
Matter and Energy
The concepts of matter and energy are essential to all scientific disciplines. Yet, while ubiquitous and fundamental, these concepts are often among the most confounding for students. Take the concept of energy. We use the term in a variety of contexts in everyday life:
- “Can we move the couch tomorrow? I don’t have the energy.”
- “Hey dude! Turn the light off. We need to conserve energy.”
- “This is a great energy drink.”
In some science classes, students are told that energy comes in different forms (i.e. kinetic, thermal,
Given all the different contexts and sometimes seemingly contradictory treatments and definitions, it’s easy to understand why these topics seem challenging for many students and sometimes end up turning them off of the topics and even fields that heavily use these ideas. While the concepts of matter and energy are most often associated with chemistry and physics, they are central ideas in biology and we don’t hide from this in BIS2A. In this respect, our instructional goals are to help students develop a framework that
- successfully describe biological reactions and transformations;
- create models and hypotheses for “how things work” in biology that explicitly include matter and energy
and; - be scientifically correct and transfer these ideas to new problems
as well as other disciplines.
While there may be
Motivation for Learning About Matter and Energy
Discussions about matter and energy make some BIS2A students a little apprehensive.
Example 1: Matter and Energy Transformation in Global Warming
Let us for a moment consider a topic that affects us all, global warming. At its core lies a relatively simple model that
Example 2: Muscle Contraction
Let us now consider a more personal example, the flexing of an arm starting from an extended position and ending in a flexed position. Like most processes, this one can
We can't possibly cover all examples of matter and energy transfer in BIS2A. But, we will explore these issues often and practice describing transformations that happen in Nature with a structured and explicit attention to what is happening to the matter and energy in a system as it changes. We will do this exercise across different structural levels in biology, from the molecular level (like a single chemical reaction) to more large-scale and abstracted models like nutrient cycling in the environment. We will practice this skill by using a pedagogical tool we call “The Energy Story
Thermodynamics
Thermodynamics
The First Law of Thermodynamics
The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant.
According to the first law of thermodynamics, energy may
Plants perform one of the most biologically useful energy transfers on earth: they transfer energy in the photons of sunlight into the chemical bonds of organic molecules. In every one of these cases, energy is neither made nor destroyed, and we must try to account for all the energy when we examine some of these reactions.
The First Law and the Energy Story
The first law of thermodynamics is deceptively simple. Students often understand that energy cannot
The Second Law of Thermodynamics
An important concept in physical systems is entropy. Entropy relates to how energy can
This idea helps explain the directionality of natural phenomena. The notion is that the directionality comes from the tendency for energy in a system to move towards a state of maximal dispersion. The Second Law, therefore, implies that in any transformation, we should look for an overall increase in entropy (or dispersion of energy), somewhere. As the dispersion of energy in a system or its surroundings increases, the ability of the energy to
We associate the four scenarios below with
a. the system gains energy;
b. a change of state occurs from solid to liquid to gas;
c. a mixing of substances occurs;
d.
Possible NB Discussion Point
Justify or refute the following statement: "Biological systems are an exception to the Second Law of Thermodynamics, since
Figure 1. An increase in disorder can happen in different ways. An ice cube melting on a hot sidewalk is one example. Here, ice
If we consider the first and second laws together, we come to a useful conclusion. Whenever energy
Keep in mind: you will find many examples in which the entropy of a system decreases locally. However, according to the Second Law, the entropy of the entire universe can never decrease. This must mean that there is an equal or greater increase in entropy somewhere else in the surroundings (most likely in a closely connected system) that compensates for the local decrease.
We conclude that while all
The Energy Story
Overview of the energy story
Whether we know it, we tell stories that involve matter and energy every day. We just rarely use terminology associated with scientific discussions of matter and energy.
Example
The setup: a simple statement with implicit details
You tell your roommate a story about how you got to campus by saying, "I biked to campus today." In this simple statement are several assumptions
An outsider's reinterpretation of the process
To illustrate this, imagine an external observer, such as an alien being watching the comings and goings of humans on Earth. Without the benefit of knowing much of the implied meanings and reasonable assumptions that
Note: Details are important. What if you owned a fully electric bike, and the person you were talking with didn’t know that? What important details might this change about the “every day” story you told that the more detailed description would have cleared up? How would the alien’s story have changed? In what scenarios might these changes be relevant?
As this simple story illustrates, irrespective of many factors, the act of creating a full description of a process includes some accounting of what happened to the matter, what happened to the energy, and almost always some description of a mechanism that describes how changes in matter and energy of a system
Definition: Energy story
An energy story is a narrative describing a process or event. The critical elements of this narrative are
- Identify at least two states (e.g., start and end)
in the process . - Identify and list the matter in the system and its state at the start and end of the process.
- Describe the transformation of the matter that occurs during the process.
- Account for the “location” of energy in the system at the start and end of the process.
- Describe the transfer of energy that happens during the process.
- Identify and describe the mechanism
( s) responsible for mediating the transformation of matter and transfer of energy.
A complete energy story will
Possible NB Discussion Point
We argue that the energy story can
Example 2:
Let us suppose that we are talking about
Figure 1: This is a schematic of a car moving from a starting position, "Point A," to an end point, "Point B." The blue rectangle depicted in the back of the car represents the level of the gasoline; the purple, squiggly line near the exhaust pipe represents the exhaust; squiggly blue lines on top of the car represent sound vibrations; and the red shading represents areas that are hotter than at the start. Source: created by
Let's step through the Energy Story rubric:
1. Identify at least two states (e.g., start and end)
In this example, we can easily identify two states. The first state is the nonmoving car at "Point A," the start of the trip. The second state, after the process
2. Identify and list the matter in the system and its state at the start and end of the process.
Here, we first note that the "system" includes everything in the figure—the car, the road, the air around the car, etc.
It is important to understand that we will apply the physical law of conservation of matter. In any of the processes that we will discuss, matter is neither created nor destroyed. It might change form, but one should be able to account for everything at the end of a process
At the beginning of the process, the matter in the system
1. The car and all the stuff in it
2. The fuel in the car (a special thing in the car)
3. The air (including oxygen) around the car.
4. The road
5. The driver
At the end of the process,
1. The car and all the stuff in it is in a new place (let's assume, aside from the fuel and position, that nothing else changed).
2. There is less fuel in the car, and it too is in a new place.
3. The air has changed;
4. The road did not change (let's assume it didn't change—other than a few pebbles that moved around).
5. The driver did not change (let's assume she didn't change—though we'll see by the end of the term
3. Describe the transformation of the matter that occurs during the process.
What happened to the matter in this process? Thanks to a lot of simplifying assumptions, we see that two big things happened. First, the car and its driver changed positions—they went from "Point A" to "Point B." Second, we note that
4. Account for the “location” of energy in the system at the start and end of the process.
It is again important to understand that we
At the beginning of the process,
1. The energy
2. The energy
3. The energy
4. The energy
5. The energy
6. For all the things above, we can also say that there is energy in the molecular motions of the atoms that make up the stuff.
At the end of the process,
1. The energy
2. The energy
3. The energy
4. The energy
5. The energy
6. For all the things above, we can also say that there is energy in the molecular motions of the atoms that make up the stuff.
This is interesting in some sense, because the lists are about the same. We know that the amount of energy stored in the car has decreased, because there is less fuel. Something must have happened.
5. Describe the transfer of energy that happens during the process.
In this
Well, we know that there is more carbon dioxide and water vapor in the system after the process. There is energy in the associations between those atoms (atoms that used to be in the fuel and air). So some energy
This is a bit of a hand-wavy explanation, and we'll learn how to do a better job throughout the quarter.
6. Identify and describe
Finally, it is useful to try understanding how those transformations of matter and transfers of energy might have
In this example, we made a bunch of simplifying assumptions to highlight the process and to focus on the transformation of the fuel. But that's fine. The more you understand about the processes, the finer details you can add. Note that you can use the Energy Story rubric for describing your understanding (or looking for holes in your understanding) of nearly any process (
First: We will work on many examples of the energy story throughout the course—do not feel that you need to have mastery over this topic today.
Second: While it is tempting to think all this is superfluous or not germane to your study of biology in BIS2A, let this serve as a reminder that your instructors (those creating the course midterm and final assessments) view it as core material. We will revisit this topic often throughout the course but need you to get familiar with some basic concepts now.
This is
Energy
Energy is a central concept in all sciences. Energy is a property of a system. While it can
There are plenty of examples where we use the concept of energy in our everyday lives to describe processes. A bicyclist can bike to get to campus for class. The act of moving herself and her bicycle from point A to point B can
How we will approach conceptualizing energy
In
Energy sources
Ultimately, the source of energy for many processes occurring on the Earth's surface comes from solar radiation. But as we will see, biology has been
Energy in chemical reactions
Chemical reactions involve a redistribution of energy within the reacting chemicals and with their environment. So, like it or not, we need to develop some models that can help us describe where energy is in a system (perhaps how it is "stored"/distributed) and how it can
In this respect, one of the key concepts to understand is that we will think about energy being transferred between parts of a system rather than referring thinking too much about it as being transformed. The distinction between "transfer" and "transform" is important because the latter gives the impression that energy is a property that exists in different forms, that it gets reshaped somehow. The common use of the term "transform" in relation to energy is understandable as different phenomena associated with the concept of energy physically "look" different to us. However, one potential problem with using the "transform" language is that it is sometimes difficult to reconcile with the idea that energy is being conserved (according to the first law of thermodynamics) if it is constantly changing form. How can the entity of energy
CAUTION
If we think about transferring energy from one part of a system to another, we also need to be careful about NOT treating energy like a substance that moves like a fluid or "thing." Rather, we need to appreciate energy as a property of a system that can
Since we will often deal with transformations of biomolecules, we can start by thinking about where energy can
Let us propose that one place that energy can
Let us also propose that there is a certain amount of energy stored in the biomolecules themselves and that the amount of energy stored in those molecules
Sometimes, you might find that when you add up the energy stored in the products and the energy stored in the reactants that these sums are not equal. If the energy in the reactants is greater than that in the products, where did this energy go? It had to get transferred to something else. Some will
The transfer of energy in or out of the reaction from the environment is NOT the only thing that determines
Free Energy
If we want to describe transformations, it is useful to have a measure of (a) how much energy is in a system, (b) the dispersal of that energy within the system and (c) how these factors change between the start and end of a process. The concept of free energy, often referred to as Gibbs energy or Gibbs enthalpy (abbreviated with the letter G), in some sense, does just that. We can define Gibbs energy in several interconvertible ways, but a useful one in biology is the enthalpy (internal energy) of a system minus the entropy of the system scaled by the temperature.
ΔG=ΔH−TΔS
We often interpret
To provide a basis for fair comparisons of changes in Gibbs energy amongst different biological transformations or reactions,
Chemical Equilibrium—Part 2: Gibbs Energy
In a previous section, we began a description of chemical equilibrium in
- At equilibrium, the concentrations of reactants and products in a reversible reaction are not changing in time.
- A reversible reaction at equilibrium is not static—reactants and products continue to
interconvert at equilibrium, but the rates of the forward and reverse reactions are the same. - We
were NOT going to fall into a common student trap of assuming that chemical equilibrium means that the concentrations of reactants and products are equal at equilibrium.
Here we extend our discussion and put the concept of equilibrium into the context of Gibbs energy, also reinforcing the Energy Story exercise of considering the "Before/Start" and "After/End" states of a reaction (including the inherent passage of time).
Figure 1. Reaction coordinate diagram for a generic exergonic reversible reaction. Equations relating Gibbs energy and the equilibrium constant: R = 8.314 J mol-1 K-1 or 0.008314 kJ mol-1 K-1; T is temperature in Kelvin. Attribution:
The figure above shows a commonly cited relationship between ∆G° and
∆G° = -RT ln Keq
∆G = ∆G° + RT ln Q
Q = [Products] ÷ [Reactants]
This takes us to a point of confusion for some. In many biology books, the discussion of equilibrium includes not only the discussion of forward and reverse reaction rates but also a statement that ∆G = 0 at equilibrium. This can
∆G = ∆G° + RT ln Q
∆G = -RT ln Keq + RT ln Q