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BIS 2A Ireland Lecture 5 - Biology

BIS 2A Ireland Lecture 5 - Biology



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Matter and Energy in Biology

Matter and Energy

The concepts of matter and energy are essential to all scientific disciplines. The term is used 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 sciences classes, students are told that energy comes in different forms (i.e. kinetic, thermal, electrical, potential, etc.). This can sometimes make it difficult to understand exactly what energy “is”. The concept of energy is also associated with many different equations, each with different variables, but that somehow all seem to end up having units of work. Hold on! Work? I thought we were talking about energy?!

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 in some cases end up turning them off of the topics and even fields that make heavy use of these ideas. While the concepts of matter and energy are most often associated with chemistry and physics, they are nevertheless 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 help them use the concepts of matter and energy to:

  • 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 a couple of energy-related equations to learn and use in BIS2A, the main focus of the course will be on the robust development of the concepts of energy and matter and their use in the interpretation of biological phenomena.

Motivation for Learning About Matter and Energy

Discussions about matter and energy make some BIS2A students a little apprehensive. After all, aren’t these topics that belong in chemistry or physics? However, the transformations of matter and energy transfer are not phenomena reserved for the chemists and physicists or even scientists and engineers more generally. Understanding, conceptualizing, and doing some basic accounting of transformations of matter and transfers of energy are fundamental skills regardless of occupation or academic training. The scientist may need more rigorous and systematic descriptions of these transformations than the artist but both make use of these skills at various points of their personal and or professional lives. Take the following examples:

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 is based on our understanding of energy in solar radiation, the transfer of this energy with matter on the Earth, and the role and cycling of key carbon containing gases in the Earth's atmosphere. In simple terms, solar energy hits the earth and transfers energy to its surface, heating it. Some of this energy is transferred back into space. However, depending on the concentration of carbon dioxide (and other so-called greenhouse gases) different amounts of this energy may become “trapped” in the Earth’s atmosphere. Too little carbon dioxide and relatively little energy/heat is trapped - the Earth freezes and becomes inhospitable for life. Too much carbon dioxide and too much heat is trapped - the Earth overheats and becomes inhospitable for life. It stands to reason, therefore, that mechanisms (biological or other) that influence the levels of carbon dioxide in the atmosphere may be important to consider in the story of global warming and that developing a good understanding of global warming phenomena requires one to trace the flow of the carbon and oxygen (matter) through their different forms and the mechanisms by which energy is transferred to and from different components of the system.

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 be described and understood at various levels of detail: from the anatomical point of view where the system consists of muscles, skin, and bones to the molecular point of view where the system is composed of individual interacting biomolecules. At whatever level of detail, if we want to create a story describing this process we know that: (a) the description must include an accounting for what happened to the matter in the system (this includes the change in position of the molecules making up the various parts of the arm and the fuel “burned” to move it) and (b) that some fuel was burned to initiate the movement and therefore, that any description of the process must also include an accounting change in the energy of the system. In simpler terms, this is really just saying that if you want to describe a process where something has happened, you need to describe what happened to the “stuff” in the system and what happened to the energy in the system to make the process happen.

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”. Be prepared to participate!

The energy story

Overview of the energy story

Whether we know it or not, we tell stories that involve matter and energy everyday. We just don’t often use terminology associated with scientific discussions of matter and energy.

Example 1

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 that are instructive to unpack, even if they may not seem very critical to include explicitly in a casual conversation between friends over transportation choices.

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 are buried in our language, the alien's description of the morning cycling trip would be quite different than your own. What you described efficiently as "biking to campus" might be more specifically described by the alien as a change in location of a human body and its bicycle from one location (the apartment, termed position A) to a different location (the university, termed position B). The alien might be even more abstract and describe the bike trip as the movement of matter (the human body and its bike) between an initial state (at location A) to a final state (at location B). Furthermore, from the alien's standpoint, what you'd call "biking" might be more specifically described as the use of a two-wheeled tool that couples the transfer of energy from the electric fields in chemical compounds to the acceleration of the two-wheeled, tool-person combo that heats its environment. Finally, buried within the simple statement describing how we got to work is also the tacit understanding that the mass of the body and bike were conserved in the process (with some important caveats we’ll look at in future lectures) and that some energy was transfered around the system and environment to enable the movement of the body from position A to position B.

Note: possible discussion

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 “everyday” 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 were brought about.

To practice this skill in BIS2A, we will make use of something we like to call the "Energy Story." You may be asked to tell an "energy story" in class, to practice telling energy stories on your lecture study guides, and to use the concept on your exams. In this section, we focus primarily on introducing the concept of an energy story and explaining how to tell one. It is worth noting that the term "energy story" is used almost exclusively in BIS2A (and has a specific meaning in this class). This precise term will not appear in other courses at UC Davis (at least in the short term), or if it appears, is not likely to be used in the same manner. You can think of “The Energy Story” as a systematic approach to creating a statement or story describing a biological process or event. Your BIS2A instructors have given this approach a short name (energy story) so that we can all associate it with the common exercise. That way, when the instructor asks the class to tell or construct an energy story, everyone knows what is meant.

Definition 1: energy story

An energy story is a narrative describing a process or event. The critical elements of this narrative are as follows:

  1. Identify at least two states (e.g., start and end) in the process.
  2. Identify and list the matter in the system and its state at the start and end of the process.
  3. Describe the transformation of the matter that occurs during the process.
  4. Account for the “location” of energy in the system at the start and end of the process.
  5. Describe the transfer of energy that happens during the process.
  6. Identify and describe mechanism(s) responsible for mediating the transformation of matter and transfer of energy.

A complete energy story will include a description of the initial reactants and their energetic states as well as a description of the final products and their energetic states after the process or reaction is completed.

Note: possible discussion

We argue that the energy story can be used to communicate all of the useful details that are required to describe nearly any process. Can you think of a process that cannot be adequately described by an energy story? If so, describe such a process.

Example 2: energy story example

Let us suppose that we are talking about the process of driving a car from "Point A" to "Point B" (see Figure 1).

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 Marc T. Facciotti (own work)

Let's step through the Energy Story rubric:

1. Identify at least two states (e.g., start and end) in the process.

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 is done, is the nonmoving car at "Point B."

2. Identify and list the matter in the system and its state at the start and end of the process.

In this case, 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 the we are going to apply the physical law of conservation of matter. That is, in any of the processes that we will discuss, matter is neither created or destroyed. It might change form, but one should be able to account for everything at the end of a process that was there at the beginning.

At the beginning of the process, the matter in the system consists of the following:
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, the matter in the system is distributed as follows:
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; it now has less molecular oxygen, more carbon dioxide, and more water vapor.
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 that she did, at least a little). However, the driver is now in a different place.

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 some of the molecules in the fuel, which used to be in the car as a liquid, have changed forms and are now mostly in the form of carbon dioxide and water vapor (purple blob coming out of the tailpipe). Some of the oxygen molecules that used to be in the air are now also in a new place as part of the carbon dioxide and water that left the car.

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 are going to invoke the physical law of conservation of energy. That is, we stipulate that the energy in the system cannot be created or destroyed, and therefore, the energy that is in the system at the start of the process must still be there at the end of the process. It may have been redistributed, but you should be able to account for all the energy.

At the beginning of the process, the energy in the system is distributed as follows:
1. The energy is tied up in the associations between atoms that make up the matter of the car.
2. The energy is tied up in the associations between atoms that make up the fuel.
3. The energy is tied up in the associations between atoms that make up the air.
4. The energy is tied up in the associations between atoms that make up the road.
5. The energy is tied up in the associations between atoms that make up the driver.
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, the energy in the system is distributed as follows:
1. 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 particular example, it is the transfer of energy among the components of the system that is most interesting. As we mentioned, there is less energy stored in the gas tank of the car at the end of the trip, because there is now less fuel. We also know intuitively (from real-life experience) that the transfer of energy from the fuel to something else was instrumental in moving the car from "Point A" to "Point B." So, where did this energy go? Remember, it didn't just disappear. It must have moved somewhere else in the system.

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 of the energy that was in the fuel is now in the exhaust. Let's also draw from real-life experience again, and state that we know that parts of our car have gotten hot by the end of the trip (e.g., the engine, transmission, wheels/tires, exhaust, etc.). For the moment, we'll just use our intuition, and say that we understand that making something hot involves some transfer of energy. So we can reasonably postulate that some of the energy in the fuel went (directly or indirectly) into heating the car, parts of the road, and the exhaust—and thus the environment around the car. An amount of energy also went into accelerating the car from zero velocity to whatever speed it traveled at, but most of that energy eventually became heat when the car came to a stop.

This is a bit of a hand-wavy explanation, and we'll learn how to do a better job throughout the quarter. The main point is that we should be able to add all the energy of the system at the beginning of the process (in all the places it is found) and at the end of the process (in all the places it is found), and those two values should be the same.

6. Identify and describe mechanism(s) responsible for mediating the transformation of matter and transfer of energy.

Finally, it is useful to try understanding how those transformations of matter and transfers of energy might have been facilitated. For the sake of brevity, we might just say that there was a complicated mechanical device (the engine) that helped facilitate the conversion of matter and transfer of energy about the system and coupled this to the change in position of the car. Someone interested in engines would, of course, give a more detailed explanation.

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 (certainly in biology). In BIS2A, we'll use the Energy Story to get an understanding of processes as varied as biochemical reactions, DNA replication, the function of molecular motors, etc.

Important:

First: We will be working 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 of the basic concepts now.

This is important material and an important skill to develop—do not put off studying it because it doesn't "look" like "biology" to you today. The academic term moves VERY quickly, and it will be difficult to catch up later if you don't give this some thought now.

Thermodynamics

Thermodynamics is concerned with describing the changes in systems before and after a change. This usually involves a discussion about energy transfers and its dispersion within the system and its surroundings. In nearly all practical cases, these analyses require that the system and its surroundings be completely described. For instance, when discussing the heating of a pot of water on the stove, the system may includes the stove, the pot, and the water and the environment or surroundings may include everything else. Biological organisms are what are called open systems; energy is transferred between them and their surroundings.

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. In other words, there always has been, and always will be, exactly the same amount of energy in the universe.

According to the first law of thermodynamics, energy may be transferred from place to place, but it cannot be created or destroyed. Energy transfers take place around us all the time. Light bulbs transfer energy from electrical power stations into heat and photons of light. Gas stoves transfer energy stored in the bonds of chemical compounds into heat and light. (Heat, by the way, is the amount of energy transferred from one system to another because of a temperature difference.)

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 of 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 be created or destroyed. Yet, when describing an energy story of a process they often make the mistake of saying things such as "energy is produced from the transfer of electrons from atom A to atom B." While most of us will understand the point the student is trying to make, the wrong words are being used. Energy is not made or produced; it is simply transferred. To be consistent with the first law, when telling an energy story, make sure that you try to explicitly track all of the places that ALL of the energy in the system at the start of a process goes by the end of a process.

The Second Law of Thermodynamics

An important concept in physical systems is that of entropy. Entropy is related to the ways in which energy can be distributed or dispersed within the particles of a system. The Second Law of Thermodynamics states that entropy is always increasing in a system and its surroundings (that is, everything outside the system).

This idea helps explain the directionality of natural phenomena. In general, 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 dispersion of energy in a system or its surroundings increases, the ability of the energy to be directed towards work decreases.

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.

Exercise

The entropy of a system can increase when:

  1. the system gains energy;
  2. a change of state occurs from solid to liquid to gas;
  3. a mixing of substances occurs;
  4. the number of particles increases during a reaction.

possible discussion

Does the second law say that entropy is conserved?

possible discussion

Biological systems, on the surface, seem to defy the Second Law of Thermodynamics. They don't. Why?

Figure 1. An increase in disorder can happen in different ways. An ice cube melting on a hot sidewalk is one example. Here, ice is displayed as a snowflake, with organized, structured water molecules forming the snowflake. Over time, the snowflake will melt into a pool of disorganized, freely moving water molecules. (Source)

possible discussion

A fine point. Figure 1 above discusses order and disorder and shows that this is somehow related to a change in entropy (ΔS). It is common to describe entropy as a measure of order as a way to simplify the more concrete description relating entropy to the number of states in which energy can be dispersed in a system. While the idea of measuring order to define entropy has some flaws, it is sometimes a useful, if imperfect, proxy. Consider the figure above. Here, order serves as a good proxy for approximating the number of ways to distribute energy in the system. Can you describe why this is the case?

If we consider the first and second laws together, we come to a useful conclusion. Whenever energy is transferred or redistributed within a system, entropy must increase. This increase in entropy is related to how "useful" the energy is to do work. Recall again that this energy generally becomes less and less available as entropy increases.

We conclude that while all of the energy must be conserved, if the required change increases entropy, it means that some of the energy will become distributed in a way that makes it less useful for work. In many cases, particularly in biology, some of the increase in entropy can be chalked up to a transfer of energy to heat in the environment.

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 to describe where energy is in a system (perhaps how it is "stored"/distributed) and how it can be moved around in a reaction. The models we develop will not be overly detailed in the sense that they would satisfy a hard-core chemist or physicist with their level of technical detail, but we expect that they should still be technically correct and not form incorrect mental models that will make it difficult to understand the "refinements" later.

In this respect, one of the key concepts to understand is that we are going to 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 be conserved if after a transformation it is no longer the same thing (e.g. transformed)? Moreover, the second law of thermodynamics tells us that no transformation conserves all energy in a system. If energy is getting "transformed," how can it be conserved and still be consistent with the second law of thermodynamics?

So, instead, we are going to approach this issue by transferring and storing energy between different parts of a system and thus think about energy as a property that can get redistributed. That'll hopefully make the accounting of energy easier. Not that the energy "transfer" idea is, of course, completely consistent and compatible with terms like "potential energy" and "kinetic energy", as these are useful for describing how the energy is distributed between the motion of matter and the various fields (e.g. electric, gravational, etc.) in a system.

CAUTION

If we are going to 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 simply as a property of a system that can be measured and reorganized but that is neither a "thing" nor something that is at one time in one form then later in another.

Since we will often be dealing with transformations of biomolecules, we can start by thinking about where energy can be found/stored in these systems. We'll start with a couple of ideas and add more to them later.

Let us propose that one place that energy can be stored is in the motion of matter. For brevity, we'll give the energy stored in motion a name: kinetic energy. Molecules in biology are in constant motion and therefore have a certain amount of kinetic energy (energy stored in motion) associated with them.

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 is associated with the types and numbers of atoms in the molecules and their organization (the number and types of bonds between them). The discussion of exactly where the energy is stored in the molecules is beyond the scope of this class, but we can approximate it by suggesting that a good proxy is in the bonds. Different types of bonds may be associated with storing different amounts of energy. In some contexts, this type of energy storage could be labeled potential energy or chemical energy. With this view, one of the things that happens during the making and breaking of bonds in a chemical reaction is that the energy is transferred about the system into different types of bonds. In the context of an Energy Story, one could theoretically count the amount of energy stored in the bonds and motion of the reactants and the energy stored in the bonds and energy of the products.

In some cases, 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 certainly have moved into other parts of the system, stored in the motion of other molecules (warming the environment) or perhaps in the energy associated with photons of light. One good, real-life example is the chemical reaction between wood and oxygen (reactants) and it's conversion to carbon dioxide and water (products). At the beginning, the energy in the system is largely in the molecular bonds of oxygen and the wood (reactants). There is still energy left in the carbon dioxide and water (products) but less than at the beginning. We all appreciate that some of that energy was transferred to the energy in light and heat. This reaction where energy is transferred to the environment is termed exothermic. By contrast, in some reactions, energy will transfer in from the environment. These reactions are endothermic.

The transfer of energy in or out of the reaction from the environment is NOT the only thing that determines whether a reaction will be spontaneous or not. We'll discuss that soon. For the moment, it is important to get comfortable with the idea that energy can be transferred among different components of a system during a reaction and that you should be able to envision tracking it.

Chemical equilibrium—Part 1: Forward and reverse reactions

Understanding the concept of chemical equilibrium is also critical to following several of the discussions that we have in BIS2A and indeed throughout biology and the sciences. It is difficult to completely describe the concept of chemical equilibrium without reference to the energy of a system, but for the sake of simplicity, let’s try anyway and reserve the discussion of energy for another chapter. Let us, rather, begin developing our understanding of equilibrium by considering the reversible reaction below:

Hypothetical reaction #1: A hypothetical reaction involving compounds A, B and D. If we read this from left to right, we would say that A and B come together to form a larger compound: D. Reading the reaction from right to left, we would say that compound D breaks down into smaller compounds: A and B.

We first need to define what is meant by a “reversible reaction.” The term “reversible” simply means that a reaction can proceed in both directions. That is, the things on the left side of the reaction equation can react together to become the things on the right of the equation, AND the things on the right of the equation can also react together to become the things on the left side of the equation. Reactions that only proceed in one direction are called irreversible reactions.

To start our discussion of equilibrium, we begin by considering a reaction that we posit is readily reversible. In this case, it is the reaction depicted above: the imaginary formation of compound D from compounds A and B. Since it is a reversible reaction, we could also call it the decomposition of D into A and B. Let us, however, imagine an experiment in which we watch the reaction proceed from a starting point where only A and B are present.

Example #1: Left-balanced reaction

Hypothetical reaction #1: time course
Concentrationt=0t=1t=5t=10t=15t=20t=25t=30t=35t=40
[A]100908070656260606060
[B]100908070656260606060
[C]0102030453840404040

At time t = 0 (before the reaction starts), the reaction has 100 concentration units of compounds A and B and zero units of compound D. We now allow the reaction to proceed and observe the individual concentrations of the three compounds over time (t=1, 5, 10, 15, 20, 25, 30, 35, and 40 time units). As A and B react, D forms. In fact, one can see D forming from t=0 all the way to t=25. After that time, however, the concentrations of A, B and D stop changing. Once the reaction reaches the point where the concentrations of the components stop changing, we say that the reaction has reached equilibrium. Notice that the concentrations of A, B, and D are not equal at equilibrium. In fact, the reaction seems left balanced so that there is more A and B than D.

Note: Common student misconception warning

Many students fall victim to the misconception that the concentrations of a reaction’s reactants and products must be equal at equilibrium. Given that the term equilibrium sounds a lot like the word “equal,” this is not surprising. But as the experiment above tries to illustrate, this is NOT correct!

Example #2: right-balanced reaction

We can examine a second hypothetical reaction, the synthesis of compound (ce{J}) from the compounds (ce{E}) and (ce{F}).

[ ce{E +F <=> J} onumber]

Hypothetical reaction #2: A hypothetical reaction involving compounds E, F and J. If we read this from left to right, we would say that E and F come together to form a larger compound: J. Reading the reaction from right to left, we would say that compound J breaks down into smaller compounds: E and F.

The structure of hypothetical reaction #2 looks identical to that of hypothetical reaction #1, which we considered above—two things come together to make one bigger thing. We just need to assume, in this case, that E, F, and J have different properties from A, B, and D. Let’s imagine a similar experiment to the one described above and examine this data:

Hypothetical reaction #2: time course

In this case, the reaction also reaches equilibrium. This time, however, equilibrium occurs at around t=30. After that point, the concentrations of E, F, and J do not change. Note again that the concentrations of (ce{E}), (ce{F}), and (ce{J}) are not equal at equilibrium. In contrast to hypothetical reaction #1 (the ABD reaction), this time the concentration of J, the thing on the right side of the arrows, is at a higher concentration than E and F. We say that, for this reaction, equilibrium lies to the right.

Four more points need to be made at this juncture.

  • Point 1: Whether equilibrium for a reaction lies to the left or the right will be a function of the properties of the components of the reaction and the environmental conditions that the reaction is taking place in (e.g., temperature, pressure, etc.).
  • Point 2: We can also talk about equilibrium using concepts of energy, and we will do this soon, just not yet.
  • Point 3: While hypothetical reactions #1 and #2 appear to reach a point where the reaction has “stopped,” you should imagine that reactions are still happening even after equilibrium has been reached. At equilibrium the “forward” and “reverse” reactions are just happening at the same rate. That is, in example #2, at equilibrium J is forming from E and F at the same rate that it is breaking down into E and F. This explains how the concentrations of the compounds aren’t changing despite the fact that the reactions are still happening.
  • Point 4: From this description of equilibrium, we can define something we call the equilibrium constant. Typically, the constant is represented by an uppercase K and may be written as Keq. In terms of concentrations, Keq is written as the mathematical product of the reaction product concentrations (stuff on the right) divided by the mathematical product of the reactant concentrations (stuff on the left). For example, Keq,1 = [D]/[A][B], and Keq,2 = [J]/[E][F]. The square brackets "[]" indicate the “concentration of” whatever is inside the bracket.

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, of course, (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. Gibbs energy can be defined in several interconvertible ways, but a useful one in the context of biology is the enthalpy (internal energy) of a system minus the entropy of the system scaled by the temperature. The difference in free energy when a process takes place is often reported in terms of the change (Δ) of enthalpy (internal energy) denoted H, minus the temperature scaled change (Δ) in entropy, denoted S. See the equation below.

ΔG=ΔH−TΔS (1)

The Gibbs energy is often interpreted as the amount of energy available to do useful work. With a bit of hand waving, we can interpret this statement by invoking the idea presented in the section on entropy, which states the dispersion of energy (required by the Second Law) associated with a positive change in entropy somehow renders some of the energy that is transferred less useful to do work. One can say that this is reflected in part in the T∆ST∆S term of the Equation 1.

To provide a basis for fair comparisons of changes in Gibbs energy amongst different biological transformations or reactions, the free energy change of a reaction is measured under a set of common standard experimental conditions. The resulting standard free energy change of a chemical reaction is expressed as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal), when measured at a standard pH, temperature, and pressure conditions. Standard pH, temperature, and pressure conditions are generally standardized at pH 7.0, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively.It is important to note that cellular conditions vary considerably from these standard conditions, and so actual ∆G inside a cell will differ considerably from those calculated under standard conditions.

Endergonic and exergonic reactions

Any system of molecules that undergos a physical transformation/reorganizaton (aka. reaction) will have an associated change in internal energy and entropy. If we examine a single isolated reaction, in which unique reactants are converted into unique products the Gibbs energy of the system will be dependent several factors, key among which are (a) the internal energy and entropy differences associated with the molecular rearrangements and (b) the degree to which the reaction is out-of-equilibrium.

If, for the sake of simplicity we begin by considering only the contribution of the molecular transformations in the system on ∆G, we conclude that reactions with ∆G < 0, the products of the reaction have less Gibbs energy than the reactants. Since ∆G is the difference between the enthalpy and temperature-scaled entropy changes in a reaction, a net negative ∆G can arise in through changes largely of enthalpy, entropy or most often both. The left panel of Figure 1 below shows a common graphical representation of an exergonic reaction. This type of graph is called a reaction coordinate diagram. Gibbs energy is plotted on the y-axis, and the x-axis in arbitrary units shows the progress of a reaction. In the case of an exergonic reaction, the figure on the left indicates two key things: (1) the difference between the free energy of the reactants and products is negative and (2) the progress of the reaction requires some input of free energy (shown as an energy "hill" or barrier). This graph does not tell us how the energy in the system was redistributed, only that the difference between enthalpy and temperature-scaled entropy is negative. Exergonic reactions are said to occur spontaneously. Understanding which chemical reactions are spontaneous is extremely useful for biologists who are trying to understand whether a reaction is likely to "go" or not.

It is important to note that the term "spontaneous"—in the context of thermodynamics—does NOT imply anything about how fast the reaction proceeds. The change in free energy only describes the difference between beginning and end states, NOT how fast that transition takes place. This is somewhat contrary to the everyday use of the term, which usually carries the implicit understanding that something happens quickly. As an example, the oxidation/rusting of iron is a spontaneous reaction. However, an iron nail exposed to air does not rust instantly—it may take years.

A chemical reaction with a positive ∆G means that the products of the reaction have a higher free energy than the reactants (see the right panel of Figure 1). These chemical reactions are called endergonic reactions, and they are NOT spontaneous. An endergonic reaction will not take place on its own without the transfer of energy into the reaction or increase of entropy somewhere else.

Figure 1. Reaction coordinate diagrams of exergonic and endergonic reactions. Exergonic and endergonic reactions are characterized by changes in Gibbs energy. In the equilibrium state of an exergonic reaction, the Gibbs energy of the products is lower than that of the reactants. Meanwhile, the equilibrium state of an endergonic reaction in, the Gibbs energy of the products is higher than that of the reactants. Attribution: Marc T. Facciotti (own work)

The building of complex molecules, such as sugars, from simpler ones is an anabolic process and is endergonic. On the other hand, the catabolic process, such as the breaking down of sugar into simpler molecules, is generally exergonic. Like the example of rust above, while the breakdown of biomolecules is generally spontaneous, these reactions don’t necessarily occur instantaneously (quickly). Remember, the terms endergonic and exergonic only refer to the difference in Gibbs energy between the products and reactants; they don't tell you about the rate of the reaction (how fast it happens). The issue of rate will be discussed in later sections.

An important concept in the study of metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, often transferring energy into their environment in one direction and transferring energy in from the environment in the other direction. The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system will undergo chemical reactions in both directions until a state of equilibrium is reached. Equilibrium in a chemical reaction is the state in which both reactants and products are present in concentrations that have no further tendency to change with time. Usually, this state results when the forward reaction proceeds at the same rate as the reverse reaction. NOTE THIS LAST STATEMENT! Equilibrium means that the relative concentrations of reactants and products are not changing in time, BUT it does NOT mean that there is no interconversion between substrates and products—it just means that when the reactant(s) are converted to product(s) that product(s) are converted to reactant(s) at an equal rate (see Figure 2). The state of equilibrium is also one of the lowest possible free energy states for the reaction and is a state of maximal entropy.

If a reaction is kept or started far out of equilibrium this state of the system also contributes to the overall Gibbs energy of a reaction. Either a rebalancing of substrate or product concentrations (by adding or removing substrate or product) or a positive change in free energy, typically by the transfer of energy from outside the reaction, can to move a reaction to an out-of-equilibrium state. Note that in a living cell, most chemical reactions do not reach a state of equilibrium—this would require that they reach their lowest free energy state, a state that is almost by definition incompatible with life. Energy is therefore required to keep biological reactions out of their equilibrium state. In this way, living organisms are in a constant, energy-requiring, uphill battle against equilibrium and entropy. This also means that the Gibbs energy of most biological reactions as they occur in the cell must also include a contribution from this out-of-equilibrium state. The Gibbs energy of these reactions, therefore, is often different from that reported under standard conditions.

Figure 2. At equilibrium, do not think of a static, unchanging system. Instead, picture molecules moving in equal amounts from one area to another. Here, at equilibrium, molecules are still moving from left to right and right to left. The net movement however, is equal. There will still be about 15 molecules in each side of this flask once equilibrium is reached. Source: https://courses.candelalearning.com/...apter/entropy/

Chemical Equilibrium—Part 2: Gibbs Energy

In a previous section, we began a description of chemical equilibrium in the context of forward and reverse rates. Three key ideas were presented:

  1. At equilibrium, the concentrations of reactants and products in a reversible reaction are not changing in time.
  2. 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.
  3. 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. Facciotti (original work)

The figure above shows a commonly cited relationship between ∆G° and Keq:

∆Go=−RTlnKeq. (Chemical Equilibrium—Part 2.1)

Here, G° indicates the Gibbs energy under standard conditions (e.g., 1 atmosphere of pressure, 298 K). This equation describes the change in Gibbs energy for reactants converting to products in a reaction that is at equilibrium. The value of ∆G° can therefore be thought of as being intrinsic to the reactants and products themselves. ∆G° is like a potential energy difference between reactants and products. With this concept as a basis, one can also consider a reaction where the "starting" state is somewhere out of equilibrium. In this case, there may be an additional “potential” associated with the out-of-equilibrium starting state. This “added” component contributes to the ∆G of a reaction and can be effectively added to the expression for Gibbs energy as follows:

∆G=∆G°+RTlnQ, (Chemical Equilibrium—Part 2.2)

where Q is called the reaction quotient. From the standpoint of BIS2A, we will use a simple (a bit incomplete but functional) definition for

Q=[Products]st[Reactants]st (Chemical Equilibrium—Part 2.3)

at a defined non-equilibrium condition, st. One can extend this idea and calculate the Gibbs energy difference between two non-equilibrium states, provided they are properly defined and thus compute Gibbs energy changes between specifically defined out-of-equilibrium states. This last point is often relevant in reactions found in biological systems as these reactions are often found in multi-step pathways that effectively keep individual reactions in an out-of-equilibrium state.

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 be confusing because these very discussions often follow discussions of non-zero ∆G° values in the context of equilibrium (∆G° = -RTlnKeq). The nuance to point out is that ∆G° is referring to the Gibbs energy potential inherent in the chemical transformation between reactants and products alone. This is different from considering the progress of the reaction from an out-of-equilibrium state that is described by

∆G=∆Go+RTlnQ. (Chemical Equilibrium—Part 2.4)

This expression can be expanded as follows:

∆G=−RTlnKeq+RTlnQ (Chemical Equilibrium—Part 2.5)

to bring the nuance into clearer focus. In this case note that as Q approaches Keq that the reaction ∆G becomes closer to zero, ultimately reaching zero when Q = Keq. This means that the Gibbs energy of the reaction (∆G) reaches zero at equilibrium not that the potential difference between substrates and products (∆G°) reaches zero.


Active photosynthetic inhibition mediated by MPK3/MPK6 is critical to effector-triggered immunity

Affiliations Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China, Division of Biochemistry, Interdisciplinary Plant Group, and Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America

Roles Data curation, Investigation, Methodology

Affiliation Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China

Roles Data curation, Investigation

Affiliation Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China

Roles Data curation, Investigation

Affiliation Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China

Roles Data curation, Investigation

Affiliation Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China

Roles Data curation, Investigation

Affiliation Division of Biochemistry, Interdisciplinary Plant Group, and Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America

Roles Data curation, Validation

Affiliation Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China

Affiliation Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China

Roles Conceptualization, Project administration, Resources, Supervision, Writing – original draft, Writing – review & editing

Affiliation Division of Biochemistry, Interdisciplinary Plant Group, and Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America


Examples of bi-

An example of a word you may have encountered that features bi- is biannual, which can mean either “occurring twice a year” or “occurring every two years.”

Confused? You’re not alone! When it comes to indicating dates on the calendar, bi- likes to have it both ways, as it were. Learn some tips on using biannual and other tricky terms like biweekly here.

We know bi- means “twice,” but what about the -annual portion of the word? You guessed it: -annual means “yearly,” from Latin annuālis. Biannual literally translates to “twice yearly.”

What are some words that use the combining form bi-?

The following words use the equivalent forms of bi- in Latin:

What are some other forms that bi- may be commonly confused with?

There are many words that begin with the letters bi-, such as bias, that do not use the combining form bi- to denote “two.” Learn what words like bias and bilk mean at our entries for these words.


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Frequently Asked Questions

We have compiled a list of questions that are frequently asked by incoming students preparing for their first quarter at UC Davis. We strongly encouraged that you read our FAQ about prior to registering for classes. A lot of the questions that you have will be on this list. If you still have questions after reviewing the list, please contact our office.

  • Advanced Placement/ International Baccalaureate Credit
  • What if I have Advanced Placement credit?

Students are allowed to use scores of 3, 4, or 5 on Advanced Placement (AP) exams for college credit. These courses may be comparable to lower division courses and therefore can be used to satisfy major requirements, university writing requirements, and the 180 minimum unit requirement to obtain a Bachelor’s degree. However, credit received from AP Exams cannot be used to satisfy UC Davis’ General Education requirements.

To see the courses or number of units corresponding to each exam or score, please refer to the College Board Advanced Placement (AP) Examination Credit table. Please be sure to speak with the College of Agricultural and Environmental Science Dean's Office if you have questions regarding General Education Requirements.

What if I have International Baccalaureate credit?
Higher Level exams presented with scores of 5, 6, or 7 receive 8 units of college credit and sometimes may be comparable to lower division courses. Students who complete and submit the IB diploma with a score of 30 or above will receive a maximum of 30 quarter units. College credit will apply towards the minimum 180 unit requirement to obtain a Bachelor’s degree. To learn how many units can be received for an IB examination, please refer to the International Baccalaureate (IB) Higher Level Examination Credit table.

While students generally will not earn university credit for college courses or Advanced Placement (AP) transfer credits that duplicate credit already earned through IB, there are a few exceptions. Additionally, courses for which IB credit has been granted cannot be used towards fulfilling the University’s General Education Requirements. Please be sure to speak with the College of Agricultural and Environmental Science Dean's Office if you have questions regarding General Education Requirements.

What if my Advanced Placement credit does not appear in OASIS?
If Advanced Placement credit does not appear in OASIS, students should check with both College Board and the College of Agricultural and Environmental Sciences Dean’s Office to make sure their scores were both sent and received. The Dean’s Office can be contacted at [email protected] . Additionally, it is possible that the scores were sent and received, and they have yet to be processed and uploaded.

What do I do if I want to change my major?
If you are planning on changing out of your current major, please contact the College of Agricultural and Environmental Sciences Dean’s Office for more guidance on how to plan for your first quarter of classes. In order to change your major once you have started in the Fall, you will need to wait until you have completed one quarter at UC Davis and are in good academic standing.

What if ANS 001 is full?
If ANS 001 is full, you may wait list for the class during your Pass 1 Appointment . If you do not get into the course, then you may take ANS 001 next Fall. It is important that you register for another course in place of ANS 001 that you would be comfortable taking. Selecting a class that you would like to take is important so that you will not feel the need to change your registration if you are unable to get into ANS 001. Your goal is to be registered for 12-14 units in your first quarter at UC Davis. We recommend that you register for a General Education course.

What if CHE 2A is full?
You may wait list for the section of CHE 2A that works best with your schedule during your Pass 1 Appointment. Be sure to arrive on time the first day of lecture and lab. Come prepared with your PPE, lab notebook, and lab manual a few minutes early. If you cannot get into CHE 2A, you can always take it the next quarter it is offered. You can meet with an advisor to make this adjustment in your academic plan.

What if WLD 950 is full?
Students who are unable to get into WLD 950, may wait list for the course during their Pass 1 Appointment. Be certain that you have registered for an alternative course, in the place of WLD 950. We recommend that students consider taking BIS 2B, as they wait list for WLD 950. If students are still unable to get into WLD 950 for Fall, ALEKS is a great option. ALEKS Preparatory Chemistry is designed to test for individualized knowledge gaps and to fill the gaps through computerized adaptive learning software. Students take an initial assessment which the software uses to gauge your current content mastery level. Your mastery level may go up or down based on your subsequent interactions with the software. The goal of this preparatory course is to fill the "pie chart" to 100%, which is the mastery level.


What if WLD 41C is full?
Students who are unable to get into WLD 41C, may wait list for the course during their Pass 1 appointment . If they are still unable to get into WLD 41C for Fall, ALEKS is a great option. ALEKS Preparatory Chemistry is designed to test for individualized knowledge gaps and to fill the gaps through computerized adaptive learning software. Students take an initial assessment which the software uses to gauge your current content mastery level. Your mastery level may go up or down based on your subsequent interactions with the software. The goal of this preparatory course is to fill the "pie chart" to 100%, which is the mastery level.

ALEKS Preparatory Chemistry is open to all students. In this way, ALEKS Preparatory Chemistry may also be used to refresh skill sets in general chemistry or supplement one's learning of general chemistry to prepare them for the Chemistry Placement Exam.

What courses should I register for?

If you are a freshman, then you should register for CHE 2A or BIS 2B, ANS 1, and an English or General Education course. You can also take any workload or preparatory courses this quarter for chemistry or mathematics but we encourage that you keep in mind a balanced schedule. Try not to take more than two science or math courses in Fall 2021.

If you are a transfer student, you will have an opportunity to discuss your unique transfer credits and recommended first quarter schedule during your Aggie Advising appointment.

Is it possible to complete a minor while I am at UC Davis?

It is possible to complete a minor while completing your major requirements. If you do so, we recommend you do a minor that will allow you to take courses that satisfy your General Education requirements (Arts and Humanities or Social Science) to prevent having additional science courses in your overall academic plan. It is important to maintain a balance between science classes and non-science classes. Once you arrive at UC Davis, you will have the opportunity to meet with minor advisors in order to learn more about the requirements and see how your minor of interest will fit into your academic plan

What will my remote advising appointment be like?
In your advising appointment, you will be meeting with one of our four Staff Advisors (Caitlin, Emma, Janelle, or Katherine). They will help you select courses for your Fall 2021 schedule and answer any questions you may have to help prepare you to register in the coming weeks. Please review our document on how to prepare for your Aggie Advising appointment. Once you are here in the Fall, you may then schedule an in-person appointment with either a Peer Advisor or Staff Advisor to create a full academic plan.

What will we talk about in my appointment?

In your appointment, we will address any questions you may have pertaining to your Fall 2021 schedule, such as what General Education courses to select, placement exam information, any Advanced Placement or International Baccalaureate scores you may have, or any coursework you may have transferred from another institution.

What if I need to cancel my appointment?
If you need to cancel your appointment, all you need to do is visit the Online Appointment System . After cancelling, you may reschedule for another time if you’d like by using the Online Appointment System.

What is Zoom?
Zoom is an online remote conferencing service that can be used for online meetings. We will be using Zoom for your Aggie Advising appointment. Zoom will allow us to have a video conference, share screens, and plan out your first quarter schedule. Here is a video on how to join a meeting via Zoom.

What if my internet stops working?
Zoom allows for you to phone into the meeting as well from any mobile phone (cell phone or land line). Please see the Zoom invite you received for options on how to dial in.

What if I did not pass the Chemistry Placement Test?
Students who did not receive a passing score of 24 or above on the Chemistry Placement Exam are encouraged to either register for Workload Chemistry (WLD 41C) or take the ALEKS Preparatory Chemistry course in order to prepare to retake the exam. Please note that taking either of these will not satisfy the Chemistry Placement Requirement scoring a 24 or above on the Chemistry Placement Exam is the only way to qualify for CHE 2A. Additionally, if students are unable to pass the exam on their second attempt, they will need to submit an online petition to the Department of Chemistry.

The Animal Science Advising Center also encourages students to refer to the online Chemistry resources found on Libretexts to help supplement their preparation for the exam.

What if I did not pass the Math Placement Test?
The Math Placement Exam is offered every quarter over two separate testing sessions. Students may only take the exam once per session. There are multiple options for students who did not pass the Math Placement Exam to prepare for another attempt. These options include enrolling in Workload Course (WLD 55M), another college-level mathematics course (MAT B or MAT C), or utilizing the practice questions provided by the Math Department online . To determine the best course of action, students should consult with an advisor.

What is the Entry Level Writing Requirement?
The Entry Level Writing Requirement (ELWR) is a requirement for all students enrolled in a UC School. The ELWR serves to ensure that all first-year students have college-level proficiency in writing. Satisfaction of the ELWR is a prerequisite to the English Composition and Writing Experience Courses that are required for graduation. Students can have fulfilled the ELWR prior to coming to UC Davis if they completed the following:

Standardized Testing Scores
- 30 or better on the ACT, English Language Arts, or
-63 or better on the ACT English exam + the ACT Reading exam or
- 680 or better on the SAT, Evidence-Based Reading and Writing (beginning with Fall 2018 admits)*
OR
AP or IB Test Scores
- 3 or above on either Advanced Placement Examination in English (Language and Composition or Literature and Composition) or
- 5 or above on an International Baccalaureate Higher Level English A: Literature exam (formerly known as Higher Level English A1 exam) or
- 6 or above on an International Baccalaureate Standard Level English A: Literature exam (formerly known as Standard Level English A1 exam) or
- 5 or above on an International Baccalaureate Higher Level English A: Language and Literature exam or
- 6 or above on an International Baccalaureate Standard Level English A: Language and Literature exam
OR
Transferable Courses
Credit earned before entering UCD can be transferred to fulfill the ELWR if there is a grade of C or higher in an acceptable 3 semester-unit or 4 quarter-unit English composition course. If you are transferring credit from a California community college, the course must be listed in Area UC-E under "UC Transfer Admission Eligibility Courses" on http://www.assist.org/ and must be completed before you enter into UCD. English composition courses completed at both in-state and out of-state institutions are evaluated by Admissions for ELWR fulfillment.

What if I don’t get into the classes I want?
If you do not get into the classes that you want, we recommend you either wait list for those courses or we can help you update your academic plan. Make sure you are registered for a minimum of 12 units, wait listed units do not count as you are not enrolled.

What is a wait list?
If a class is full and closed, students can place themselves on a wait list using Schedule Builder and wait lists are established on a first-come, first-serve basis. During the academic terms, wait lists begin during Pass 2 registration appointments and end after the last day to add classes, the 12th day of instruction .

The units of a wait listed course count towards the maximum units allowed during registration periods. However, the units of a wait listed course do not count when determining eligibility for financial aid. Students must be enrolled in 12 or more units for financial aid to disburse in full. By adding yourself to the wait list, you are letting the department know that you would like to take the class. Wait list policies are different for each department that the class is in. For example, ANS courses would fall under the Department of Animal Science.

How do wait lists work?
When you wait list for a course you are assigned a number on that wait list. As people drop the course, you will move up the wait list.

How many units should I register for?
You should be registered for at least 12 units in order to be considered as a full time student. You also need 12 units to receive financial aid. Again, wait list units do not count .

What if I am at 10-11 units? What can I register for?
If you are at 10-11 units, then we recommend you register for additional courses such as an ANS 49 class or a First-Year Seminar in order to reach a minimum of 12 units for full time status.

What is a Pass Time?

Registration takes place during two intervals called “Passes.” Undergraduate students are assigned a registration appointment time during each of the two passes. Each registration appointment time is a four-hour window. Undergraduate students can enroll in up to 17 units during Pass One, 19 units during Pass Two, and 28.5 units during Schedule Adjustment.

What if I miss my Pass Time?
Your Pass Time is four hours long from your assigned time noted on your Schedule Builder. If you happen to miss that registration window you can register during Open Hours. Open Registration is a time after hours and on weekends that allow students to edit their schedules and enroll in additional courses (given the unit cap).

What if I am a freshman and took college courses during high school?
If you took college-level courses in high school, we recommend that you avoid taking classes with similar course titles for your first quarter at UC Davis. After the Fall quarter begins, you may make an appointment with an advisor in our office to evaluate your transfer coursework.

Will my courses be evaluated before I register?
Yes, the Staff Advisors will be reviewing the transcripts that you have submitted to UC Davis prior to your meeting.

What if I am waiting on my transcript from Spring or Summer?
Please follow the directions you receive from the UC Davis Admissions Office but please have an unofficial copy to your transcript on hand for your remote advising appointment for your Staff Advisor to view.

What if I did not pass a class in Spring or Summer?
We recommend that you contact the UC Davis Office of Admissions as soon as possible as this can impact your status with UC Davis.

What if I got a grade in a course at Community College that I would like to repeat at UC Davis?
Any course that you received a C- or higher in cannot be repeated at UC Davis. While it is possible to repeat a course that you received a D-, D, or D+ in at UC Davis, there may be issues with illegal repeats (https://registrar.ucdavis.edu/records/grades/repeat-illegal). Please talk to your Staff Advisor about this to receive information about next steps. If it is a course you received an F in, then you can retake that course here at UC Davis.

What is an Intersegmental General Education Transfer Curriculum (IGETC) certificate?
An IGETC certificate fulfills your College General Education requirement and possibly the College English requirement as well. If you have questions concerning your IGETC or College requirements, please contact the College of Agricultural and Environmental Science Dean’s Office .

How do I know if I have IGETC?
In the Fall, the College of Agricultural and Environmental Science Dean’s Office will evaluate every transfer student’s record by the end of November. You will receive a notification through the Message Center on whether UC Davis has received your IGETC, if you have a partial IGETC, or if your IGETC has not been received. Further details will be provided in this message.

What if my Official IGETC has not been submitted?

Please contact your Community College as soon as possible to have your IGETC submitted to UC Davis.

May I complete my IGETC requirements at UC Davis?
If you have a partial IGETC, the College of Agricultural and Environmental Science Dean’s Office will reach out to you and let you know what requirements you have left to fulfill at UC Davis. If you did not fulfill an IGETC, please check in with the CAES Dean’s Office during Fall 2021 to discuss your General Education Requirements.


Conclusions

We present a novel computational framework to study the evolution of regulatory networks in representative species of the rapid adaptive radiations of East African cichlids. Using six tissues from five species, our approach identified tissue-specific gene expression divergence between the five cichlid species that is likely associated with gene regulatory changes. As a case study, we focus on a well-studied trait—the visual system—for which we identified regulatory variation at TFBSs and demonstrate how the functional disruption of TFBSs abrogates binding of key regulators and, thus, can drive GRN evolution. Our approach revealed hundreds of novel potential regulatory regions and regulators of the five cichlid genomes, many of which have been previously associated with evolutionary traits. In conclusion, we show that regulatory network evolution can be driven by discrete changes at regulatory binding sites, and network rewiring events are likely to be a contributing source to evolutionary innovations in radiating cichlid species. This approach, with further functional validations, has the potential to identify novel genes linked to other evolutionary traits in cichlids and other evolutionary systems.


Why Choose This Course

The BSc Chemistry of Pharmaceutical Compounds (CPC) is the only course in Ireland to cover both the chemistry and biology underpinning the pharmaceutical industry.

In addition, CPC is the only undergraduate course in chemistry that offers an organised placement scheme in the pharmaceutical industry. Feedback on the placements from both students and companies is excellent.

CPC is the only course on which industry experts present on key technical and economic aspects of the industry.

CPC is on the Auto-Qual list of the Teaching Council for eligibility to apply for PDE for teaching of Biology and Chemistry.

Placement or Study Abroad Information

BSc Chemistry of Pharmaceutical Compounds industrial placements have included sites in the UK and in the Netherlands, although most placements are in Ireland.

Skills and Careers Information

On this course you will gain skills in the synthesis and analysis of pharmaceuticals using chemical and biochemical technologies. The laboratory skills you will acquire include synthesis, chromatography (e.g. HPLC) and spectroscopy (e.g. NMR).

You will also learn presentation skills such as document and poster preparation, oral presentation and interview skills. Problem solving skills are developed in interactive group problem-solving sessions.

CPC is a pathway to careers in:

  • pharmaceutical process support and development
  • new process development
  • supply-chain management
  • HR and financial management
  • drug discovery research

The pharmaceutical industry in Ireland is a major employer of CPC graduates. Graduates of this course are also working in leading research and development sites outside Ireland.


Contents

The first evidence for the existence of a gene encoding a DNA repair enzyme involved in breast cancer susceptibility was provided by Mary-Claire King's laboratory at UC Berkeley in 1990. [22] Four years later, after an international race to find it, [23] the gene was cloned in 1994 by scientists at University of Utah, National Institute of Environmental Health Sciences (NIEHS) and Myriad Genetics. [18] [24]

The human BRCA1 gene is located on the long (q) arm of chromosome 17 at region 2 band 1, from base pair 41,196,312 to base pair 41,277,500 (Build GRCh37/hg19) (map). [25] BRCA1 orthologs have been identified in most vertebrates for which complete genome data are available. [6]

The BRCA1 protein contains the following domains: [26]

The human BRCA1 protein consists of four major protein domains the Znf C3HC4- RING domain, the BRCA1 serine domain and two BRCT domains. These domains encode approximately 27% of BRCA1 protein. There are six known isoforms of BRCA1, [28] with isoforms 1 and 2 comprising 1863 amino acids each. [ citation needed ]

BRCA1 is unrelated to BRCA2, i.e. they are not homologs or paralogs. [10]

Zinc ring finger domain Edit

The RING motif, a Zn finger found in eukaryotic peptides, is 40–60 amino acids long and consists of eight conserved metal-binding residues, two quartets of cysteine or histidine residues that coordinate two zinc atoms. [30] This motif contains a short anti-parallel beta-sheet, two zinc-binding loops and a central alpha helix in a small domain. This RING domain interacts with associated proteins, including BARD1, which also contains a RING motif, to form a heterodimer. The BRCA1 RING motif is flanked by alpha helices formed by residues 8–22 and 81–96 of the BRCA1 protein. It interacts with a homologous region in BARD1 also consisting of a RING finger flanked by two alpha-helices formed from residues 36–48 and 101–116. These four helices combine to form a heterodimerization interface and stabilize the BRCA1-BARD1 heterodimer complex. Additional stabilization is achieved by interactions between adjacent residues in the flanking region and hydrophobic interactions. The BARD1/BRCA1 interaction is disrupted by tumorigenic amino acid substitutions in BRCA1, implying that the formation of a stable complex between these proteins may be an essential aspect of BRCA1 tumor suppression. [30]

The ring domain is an important element of ubiquitin E3 ligases, which catalyze protein ubiquitination. Ubiquitin is a small regulatory protein found in all tissues that direct proteins to compartments within the cell. BRCA1 polypeptides, in particular, Lys-48-linked polyubiquitin chains are dispersed throughout the resting cell nucleus, but at the start of DNA replication, they gather in restrained groups that also contain BRCA2 and BARD1. BARD1 is thought to be involved in the recognition and binding of protein targets for ubiquitination. [31] It attaches to proteins and labels them for destruction. Ubiquitination occurs via the BRCA1 fusion protein and is abolished by zinc chelation. [30] The enzyme activity of the fusion protein is dependent on the proper folding of the ring domain. [ citation needed ]

Serine cluster domain Edit

BRCA1 serine cluster domain (SCD) spans amino acids 1280–1524. A portion of the domain is located in exons 11–13. High rates of mutation occur in exons 11–13. Reported phosphorylation sites of BRCA1 are concentrated in the SCD, where they are phosphorylated by ATM/ATR kinases both in vitro and in vivo. ATM/ATR are kinases activated by DNA damage. Mutation of serine residues may affect localization of BRCA1 to sites of DNA damage and DNA damage response function. [29]

BRCT domains Edit

The dual repeat BRCT domain of the BRCA1 protein is an elongated structure approximately 70 Å long and 30–35 Å wide. [32] The 85–95 amino acid domains in BRCT can be found as single modules or as multiple tandem repeats containing two domains. [33] Both of these possibilities can occur in a single protein in a variety of different conformations. [32] The C-terminal BRCT region of the BRCA1 protein is essential for repair of DNA, transcription regulation and tumor suppressor function. [34] In BRCA1 the dual tandem repeat BRCT domains are arranged in a head-to-tail-fashion in the three-dimensional structure, burying 1600 Å of hydrophobic, solvent-accessible surface area in the interface. These all contribute to the tightly packed knob-in-hole structure that comprises the interface. These homologous domains interact to control cellular responses to DNA damage. A missense mutation at the interface of these two proteins can perturb the cell cycle, resulting a greater risk of developing cancer. [ citation needed ]

BRCA1 is part of a complex that repairs double-strand breaks in DNA. The strands of the DNA double helix are continuously breaking as they become damaged. Sometimes only one strand is broken, sometimes both strands are broken simultaneously. DNA cross-linking agents are an important source of chromosome/DNA damage. Double-strand breaks occur as intermediates after the crosslinks are removed, and indeed, biallelic mutations in BRCA1 have been identified to be responsible for Fanconi Anemia, Complementation Group S, [35] a genetic disease associated with hypersensitivity to DNA crosslinking agents. BRCA1 is part of a protein complex that repairs DNA when both strands are broken. When this happens, it is difficult for the repair mechanism to "know" how to replace the correct DNA sequence, and there are multiple ways to attempt the repair. The double-strand repair mechanism in which BRCA1 participates is homology-directed repair, where the repair proteins copy the identical sequence from the intact sister chromatid. [36]

In the nucleus of many types of normal cells, the BRCA1 protein interacts with RAD51 during repair of DNA double-strand breaks. [37] These breaks can be caused by natural radiation or other exposures, but also occur when chromosomes exchange genetic material (homologous recombination, e.g., "crossing over" during meiosis). The BRCA2 protein, which has a function similar to that of BRCA1, also interacts with the RAD51 protein. By influencing DNA damage repair, these three proteins play a role in maintaining the stability of the human genome. [ citation needed ]

BRCA1 is also involved in another type of DNA repair, termed mismatch repair. BRCA1 interacts with the DNA mismatch repair protein MSH2. [38] MSH2, MSH6, PARP and some other proteins involved in single-strand repair are reported to be elevated in BRCA1-deficient mammary tumors. [39]

A protein called valosin-containing protein (VCP, also known as p97) plays a role to recruit BRCA1 to the damaged DNA sites. After ionizing radiation, VCP is recruited to DNA lesions and cooperates with the ubiquitin ligase RNF8 to orchestrate assembly of signaling complexes for efficient DSB repair. [40] BRCA1 interacts with VCP. [41] BRCA1 also interacts with c-Myc, and other proteins that are critical to maintain genome stability. [42]

BRCA1 directly binds to DNA, with higher affinity for branched DNA structures. This ability to bind to DNA contributes to its ability to inhibit the nuclease activity of the MRN complex as well as the nuclease activity of Mre11 alone. [43] This may explain a role for BRCA1 to promote lower fidelity DNA repair by non-homologous end joining (NHEJ). [44] BRCA1 also colocalizes with γ-H2AX (histone H2AX phosphorylated on serine-139) in DNA double-strand break repair foci, indicating it may play a role in recruiting repair factors. [17] [45]

Formaldehyde and acetaldehyde are common environmental sources of DNA cross links that often require repairs mediated by BRCA1 containing pathways. [46]

This DNA repair function is essential mice with loss-of-function mutations in both BRCA1 alleles are not viable, and as of 2015 only two adults were known to have loss-of-function mutations in both alleles both had congenital or developmental issues, and both had cancer. One was presumed to have survived to adulthood because one of the BRCA1 mutations was hypomorphic. [47]

Transcription Edit

BRCA1 was shown to co-purify with the human RNA Polymerase II holoenzyme in HeLa extracts, implying it is a component of the holoenzyme. [48] Later research, however, contradicted this assumption, instead showing that the predominant complex including BRCA1 in HeLa cells is a 2 megadalton complex containing SWI/SNF. [49] SWI/SNF is a chromatin remodeling complex. Artificial tethering of BRCA1 to chromatin was shown to decondense heterochromatin, though the SWI/SNF interacting domain was not necessary for this role. [45] BRCA1 interacts with the NELF-B (COBRA1) subunit of the NELF complex. [45]

Certain variations of the BRCA1 gene lead to an increased risk for breast cancer as part of a hereditary breast–ovarian cancer syndrome. Researchers have identified hundreds of mutations in the BRCA1 gene, many of which are associated with an increased risk of cancer. Females with an abnormal BRCA1 or BRCA2 gene have up to an 80% risk of developing breast cancer by age 90 increased risk of developing ovarian cancer is about 55% for females with BRCA1 mutations and about 25% for females with BRCA2 mutations. [50]

These mutations can be changes in one or a small number of DNA base pairs (the building-blocks of DNA), and can be identified with PCR and DNA sequencing. [ citation needed ]

In some cases, large segments of DNA are rearranged. Those large segments, also called large rearrangements, can be a deletion or a duplication of one or several exons in the gene. Classical methods for mutation detection (sequencing) are unable to reveal these types of mutation. [51] Other methods have been proposed: traditional quantitative PCR, [52] multiplex ligation-dependent probe amplification (MLPA), [53] and Quantitative Multiplex PCR of Short Fluorescent Fragments (QMPSF). [54] Newer methods have also been recently proposed: heteroduplex analysis (HDA) by multi-capillary electrophoresis or also dedicated oligonucleotides array based on comparative genomic hybridization (array-CGH). [55]

Some results suggest that hypermethylation of the BRCA1 promoter, which has been reported in some cancers, could be considered as an inactivating mechanism for BRCA1 expression. [56]

A mutated BRCA1 gene usually makes a protein that does not function properly. Researchers believe that the defective BRCA1 protein is unable to help fix DNA damage leading to mutations in other genes. These mutations can accumulate and may allow cells to grow and divide uncontrollably to form a tumor. Thus, BRCA1 inactivating mutations lead to a predisposition for cancer. [ citation needed ]

BRCA1 mRNA 3' UTR can be bound by an miRNA, Mir-17 microRNA. It has been suggested that variations in this miRNA along with Mir-30 microRNA could confer susceptibility to breast cancer. [57]

In addition to breast cancer, mutations in the BRCA1 gene also increase the risk of ovarian and prostate cancers. Moreover, precancerous lesions (dysplasia) within the Fallopian tube have been linked to BRCA1 gene mutations. Pathogenic mutations anywhere in a model pathway containing BRCA1 and BRCA2 greatly increase risks for a subset of leukemias and lymphomas. [14]

Women who have inherited a defective BRCA1 or BRCA2 gene are at a greatly elevated risk to develop breast and ovarian cancer. Their risk of developing breast and/or ovarian cancer is so high, and so specific to those cancers, that many mutation carriers choose to have prophylactic surgery. There has been much conjecture to explain such apparently striking tissue specificity. Major determinants of where BRCA1/2 hereditary cancers occur are related to tissue specificity of the cancer pathogen, the agent that causes chronic inflammation or the carcinogen. The target tissue may have receptors for the pathogen, may become selectively exposed to an inflammatory process or to a carcinogen. An innate genomic deficit in a tumor suppressor gene impairs normal responses and exacerbates the susceptibility to disease in organ targets. This theory also fits data for several tumor suppressors beyond BRCA1 or BRCA2. A major advantage of this model is that it suggests there may be some options in addition to prophylactic surgery. [58]

BRCA1 expression is reduced or undetectable in the majority of high grade, ductal breast cancers. [59] It has long been noted that loss of BRCA1 activity, either by germ-line mutations or by down-regulation of gene expression, leads to tumor formation in specific target tissues. In particular, decreased BRCA1 expression contributes to both sporadic and inherited breast tumor progression. [60] Reduced expression of BRCA1 is tumorigenic because it plays an important role in the repair of DNA damages, especially double-strand breaks, by the potentially error-free pathway of homologous recombination. [61] Since cells that lack the BRCA1 protein tend to repair DNA damages by alternative more error-prone mechanisms, the reduction or silencing of this protein generates mutations and gross chromosomal rearrangements that can lead to progression to breast cancer. [61]

Similarly, BRCA1 expression is low in the majority (55%) of sporadic epithelial ovarian cancers (EOCs) where EOCs are the most common type of ovarian cancer, representing approximately 90% of ovarian cancers. [62] In serous ovarian carcinomas, a sub-category constituting about 2/3 of EOCs, low BRCA1 expression occurs in more than 50% of cases. [63] Bowtell [64] reviewed the literature indicating that deficient homologous recombination repair caused by BRCA1 deficiency is tumorigenic. In particular this deficiency initiates a cascade of molecular events that sculpt the evolution of high-grade serous ovarian cancer and dictate its response to therapy. Especially noted was that BRCA1 deficiency could be the cause of tumorigenesis whether due to BRCA1 mutation or any other event that causes a deficiency of BRCA1 expression.

Mutation of BRCA1 in breast and ovarian cancer Edit

Only about 3%–8% of all women with breast cancer carry a mutation in BRCA1 or BRCA2. [65] Similarly, BRCA1 mutations are only seen in about 18% of ovarian cancers (13% germline mutations and 5% somatic mutations). [66]

Thus, while BRCA1 expression is low in the majority of these cancers, BRCA1 mutation is not a major cause of reduced expression. Certain latent viruses, which are frequently detected in breast cancer tumors, can decrease the expression of the BRCA1 gene and cause the development of breast tumors. [67]

BRCA1 promoter hypermethylation in breast and ovarian cancer Edit

BRCA1 promoter hypermethylation was present in only 13% of unselected primary breast carcinomas. [68] Similarly, BRCA1 promoter hypermethylation was present in only 5% to 15% of EOC cases. [62]

Thus, while BRCA1 expression is low in these cancers, BRCA1 promoter methylation is only a minor cause of reduced expression.

MicroRNA repression of BRCA1 in breast cancers Edit

There are a number of specific microRNAs, when overexpressed, that directly reduce expression of specific DNA repair proteins (see MicroRNA section DNA repair and cancer) In the case of breast cancer, microRNA-182 (miR-182) specifically targets BRCA1. [69] Breast cancers can be classified based on receptor status or histology, with triple-negative breast cancer (15%–25% of breast cancers), HER2+ (15%–30% of breast cancers), ER+/PR+ (about 70% of breast cancers), and Invasive lobular carcinoma (about 5%–10% of invasive breast cancer). All four types of breast cancer were found to have an average of about 100-fold increase in miR-182, compared to normal breast tissue. [70] In breast cancer cell lines, there is an inverse correlation of BRCA1 protein levels with miR-182 expression. [69] Thus it appears that much of the reduction or absence of BRCA1 in high grade ductal breast cancers may be due to over-expressed miR-182.

In addition to miR-182, a pair of almost identical microRNAs, miR-146a and miR-146b-5p, also repress BRCA1 expression. These two microRNAs are over-expressed in triple-negative tumors and their over-expression results in BRCA1 inactivation. [71] Thus, miR-146a and/or miR-146b-5p may also contribute to reduced expression of BRCA1 in these triple-negative breast cancers.

MicroRNA repression of BRCA1 in ovarian cancers Edit

In both serous tubal intraepithelial carcinoma (the precursor lesion to high grade serous ovarian carcinoma (HG-SOC)), and in HG-SOC itself, miR-182 is overexpressed in about 70% of cases. [72] In cells with over-expressed miR-182, BRCA1 remained low, even after exposure to ionizing radiation (which normally raises BRCA1 expression). [72] Thus much of the reduced or absent BRCA1 in HG-SOC may be due to over-expressed miR-182.

Another microRNA known to reduce expression of BRCA1 in ovarian cancer cells is miR-9. [62] Among 58 tumors from patients with stage IIIC or stage IV serous ovarian cancers (HG-SOG), an inverse correlation was found between expressions of miR-9 and BRCA1, [62] so that increased miR-9 may also contribute to reduced expression of BRCA1 in these ovarian cancers.

Deficiency of BRCA1 expression is likely tumorigenic Edit

DNA damage appears to be the primary underlying cause of cancer, [73] and deficiencies in DNA repair appears to underlie many forms of cancer. [74] If DNA repair is deficient, DNA damage tends to accumulate. Such excess DNA damage may increase mutational errors during DNA replication due to error-prone translesion synthesis. Excess DNA damage may also increase epigenetic alterations due to errors during DNA repair. [75] [76] Such mutations and epigenetic alterations may give rise to cancer. The frequent microRNA-induced deficiency of BRCA1 in breast and ovarian cancers likely contribute to the progression of those cancers.

All germ-line BRCA1 mutations identified to date have been inherited, suggesting the possibility of a large “founder” effect in which a certain mutation is common to a well-defined population group and can, in theory, be traced back to a common ancestor. Given the complexity of mutation screening for BRCA1, these common mutations may simplify the methods required for mutation screening in certain populations. Analysis of mutations that occur with high frequency also permits the study of their clinical expression. [77] Examples of manifestations of a founder effect are seen among Ashkenazi Jews. Three mutations in BRCA1 have been reported to account for the majority of Ashkenazi Jewish patients with inherited BRCA1-related breast and/or ovarian cancer: 185delAG, 188del11 and 5382insC in the BRCA1 gene. [78] [79] In fact, it has been shown that if a Jewish woman does not carry a BRCA1 185delAG, BRCA1 5382insC founder mutation, it is highly unlikely that a different BRCA1 mutation will be found. [80] Additional examples of founder mutations in BRCA1 are given in Table 1 (mainly derived from [77] ).

Population or subgroup BRCA1 mutation(s) [81] Reference(s)
African-Americans 943ins10, M1775R [82]
Afrikaners E881X, 1374delC [83] [84]
Ashkenazi Jewish 185delAG, 188del11, 5382insC [78] [79]
Austrians 2795delA, C61G, 5382insC, Q1806stop [85]
Belgians 2804delAA, IVS5+3A>G [86] [87]
Dutch Exon 2 deletion, exon 13 deletion, 2804delAA [86] [88] [89]
Finns 3745delT, IVS11-2A>G [90] [91]
French 3600del11, G1710X [92]
French Canadians C4446T [93]
Germans 5382insC, 4184del4 [94] [95]
Greeks 5382insC [96]
Hungarians 300T>G, 5382insC, 185delAG [97]
Italians 5083del19 [98]
Japanese L63X, Q934X [99]
Native North Americans 1510insG, 1506A>G [100]
Northern Irish 2800delAA [101]
Norwegians 816delGT, 1135insA, 1675delA, 3347delAG [102] [103]
Pakistanis 2080insA, 3889delAG, 4184del4, 4284delAG, IVS14-1A>G [104]
Polish 300T>G, 5382insC, C61G, 4153delA [105] [106]
Russians 5382insC, 4153delA [107]
Scottish 2800delAA [101] [108]
Spanish R71G [109] [110]
Swedish Q563X, 3171ins5, 1201del11, 2594delC [82] [111]

As women age, reproductive performance declines, leading to menopause. This decline is tied to a reduction in the number of ovarian follicles. Although about 1 million oocytes are present at birth in the human ovary, only about 500 (about 0.05%) of these ovulate. The decline in ovarian reserve appears to occur at a constantly increasing rate with age, [112] and leads to nearly complete exhaustion of the reserve by about age 52. As ovarian reserve and fertility decline with age, there is also a parallel increase in pregnancy failure and meiotic errors, resulting in chromosomally abnormal conceptions. [113]

Women with a germ-line BRCA1 mutation appear to have a diminished oocyte reserve and decreased fertility compared to normally aging women. [114] Furthermore, women with an inherited BRCA1 mutation undergo menopause prematurely. [115] Since BRCA1 is a key DNA repair protein, these findings suggest that naturally occurring DNA damages in oocytes are repaired less efficiently in women with a BRCA1 defect, and that this repair inefficiency leads to early reproductive failure. [114]

As noted above, the BRCA1 protein plays a key role in homologous recombinational repair. This is the only known cellular process that can accurately repair DNA double-strand breaks. DNA double-strand breaks accumulate with age in humans and mice in primordial follicles. [116] Primordial follicles contain oocytes that are at an intermediate (prophase I) stage of meiosis. Meiosis is the general process in eukaryotic organisms by which germ cells are formed, and it is likely an adaptation for removing DNA damages, especially double-strand breaks, from germ line DNA. [ citation needed ] (Also see article Meiosis). Homologous recombinational repair employing BRCA1 is especially promoted during meiosis. It was found that expression of four key genes necessary for homologous recombinational repair of DNA double-strand breaks (BRCA1, MRE11, RAD51 and ATM) decline with age in the oocytes of humans and mice, [116] leading to the hypothesis that DNA double-strand break repair is necessary for the maintenance of oocyte reserve and that a decline in efficiency of repair with age plays a role in ovarian aging.

Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. At diagnosis, almost 70% of persons with NSCLC have locally advanced or metastatic disease. Persons with NSCLC are often treated with therapeutic platinum compounds (e.g. cisplatin, carboplatin or oxaliplatin) that cause inter-strand cross-links in DNA. Among individuals with NSCLC, low expression of BRCA1 in the primary tumor correlated with improved survival after platinum-containing chemotherapy. [117] [118] This correlation implies that low BRCA1 in cancer, and the consequent low level of DNA repair, causes vulnerability of cancer to treatment by the DNA cross-linking agents. High BRCA1 may protect cancer cells by acting in a pathway that removes the damages in DNA introduced by the platinum drugs. Thus the level of BRCA1 expression is a potentially important tool for tailoring chemotherapy in lung cancer management. [117] [118]

Level of BRCA1 expression is also relevant to ovarian cancer treatment. Patients having sporadic ovarian cancer who were treated with platinum drugs had longer median survival times if their BRCA1 expression was low compared to patients with higher BRCA1 expression (46 compared to 33 months). [119]

A patent application for the isolated BRCA1 gene and cancer promoting mutations discussed above, as well as methods to diagnose the likelihood of getting breast cancer, was filed by the University of Utah, National Institute of Environmental Health Sciences (NIEHS) and Myriad Genetics in 1994 [18] over the next year, Myriad, (in collaboration with investigators at Endo Recherche, Inc., HSC Research & Development Limited Partnership, and University of Pennsylvania), isolated and sequenced the BRCA2 gene and identified key mutations, and the first BRCA2 patent was filed in the U.S. by Myriad and other institutions in 1995. [19] Myriad is the exclusive licensee of these patents and has enforced them in the US against clinical diagnostic labs. [21] This business model led from Myriad being a startup in 1994 to being a publicly traded company with 1200 employees and about $500M in annual revenue in 2012 [20] it also led to controversy over high prices and the inability to get second opinions from other diagnostic labs, which in turn led to the landmark Association for Molecular Pathology v. Myriad Genetics lawsuit. [21] [120] The patents began to expire in 2014.

According to an article published in the journal, Genetic Medicine, in 2010, "The patent story outside the United States is more complicated. For example, patents have been obtained but the patents are being ignored by provincial health systems in Canada. In Australia and the UK, Myriad’s licensee permitted use by health systems but announced a change of plans in August 2008. Only a single mutation has been patented in Myriad’s lone European-wide patent, although some patents remain under review of an opposition proceeding. In effect, the United States is the only jurisdiction where Myriad’s strong patent position has conferred sole-provider status." [121] [122] Peter Meldrum, CEO of Myriad Genetics, has acknowledged that Myriad has "other competitive advantages that may make such [patent] enforcement unnecessary" in Europe. [123]

As with any gene, finding variation in BRCA1 is not hard. The real value comes from understanding what the clinical consequences of any particular variant are. Myriad has a large, proprietary database of such genotype-phenotype correlations. In response, parallel open-source databases are being developed.

Legal decisions surrounding the BRCA1 and BRCA2 patents will affect the field of genetic testing in general. [124] A June 2013 article, in Association for Molecular Pathology v. Myriad Genetics (No. 12-398), quoted the US Supreme Court's unanimous ruling that, "A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated," invalidating Myriad's patents on the BRCA1 and BRCA2 genes. However, the Court also held that manipulation of a gene to create something not found in nature could still be eligible for patent protection. [125] The Federal Court of Australia came to the opposite conclusion, upholding the validity of an Australian Myriad Genetics patent over the BRCA1 gene in February 2013. [126] The Federal Court also rejected an appeal in September 2014. [127] Yvonne D’Arcy won her case against US-based biotech company Myriad Genetics in the High Court of Australia. In their unanimous decision on October 7, 2015, the "high court found that an isolated nucleic acid, coding for a BRCA1 protein, with specific variations from the norm that are indicative of susceptibility to breast cancer and ovarian cancer was not a 'patentable invention.'" [128]


Abstract

The O,P-type phosphinophenol ligands 1ac were found to readily react with 1 equiv of AlMe3 to afford in high yields the corresponding Al chelate complexes <η 2="">2-4-R′-6-R-C6H2O)>AlMe2, 2ac (R = Me, R′ = H, 2a R = Ph, R′ = H, 2b R = t Bu, R′ = Me, 2c). The bis-adduct Al methyl complexes <η 2="">2-4-R′-6-R-C6H2O)>2AlMe (R = Ph, R′ = H, 3b R = t Bu, R′ = Me, 3c) also formed quantitatively upon reaction of phosphinophenols 1b,c with 0.5 equiv of AlMe3. Both the mono- and bis-adduct Al methyl species 2ac and 3b,c are stable monomeric species whether in solution or in the solid state and remain stable in coordinating solvents such as thf. In contrast, the bis-adduct Al methyl complex 3c undergoes a ligand exchange reaction in the presence of an alcohol source ( i PrOH, BnOH) to generate the homoleptic tris-adduct Al complex <η 2="">2-4-Me-6- t Bu-C6H3O)>3Al (5c), as determined from X-ray crystallographic studies. Both the mono- and bis-adduct Al methyl species 2b,c and 3b,c react fast with B(C6F5)3 via a methide abstraction reaction to afford the stable and well-defined Al cationic species <η 2="">2-6-Ph-C6H3O)>Al(Me)(THF) + (6b,c + ) and <η 2="">2-4-R′-6-R-C6H3O)>2Al + (7b,c + ), respectively, which were found to be highly active in propylene oxide polymerization to afford atactic poly(propylene oxide). These cations also readily initiate the ring-opening polymerization of ε-caprolactone via successive ring-opening insertions of the monomer into the Al−O phenoxide bond of the phosphinophenolate chelating ligand to exclusively afford linear poly(ε-caprolactone) capped, at the ester end, with a (phosphino oxide)phenolate group, as deduced from NMR and MALDI-TOF data. In these cationic systems, the PO − chelating moiety may thus act as both a supporting ligand and an initiating group for the ROP of ε-CL.


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