SS3 Script Molecular Motion

Molecular Motion

MOLECULAR MOVEMENT. This lecture brings together a number of topics loosely connected by their relationship between energy and molecular movement. It does not line up well with any particular section of the text, but it’s a collection of recurrent themes. We will revisit some of this in the metabolism lecture. I will warn you that the lecture will present some biophysics equations. I would encourage you to think about the concepts rather than memorize the details.

FORMS OF ENERGY. There are multiple different types of energy, so let’s begin with some definitions. Kinetic energy refers to the energy associated with movement. In the case of biology, an example might be the way a motor protein uses chemical energy to move its cargo along a microtubule. Thermal energy is the kinetic energy that arises from molecular movement. A pot of water is perceived as warm because of the movement of the water molecules in the pot. When you jump in warm water, it feels warm because thermal energy from the movement of water molecules is transferred to the molecules in your skin. Temperature is a measurement of kinetic energy, and heat is the transfer of thermal energy between objects. The potential energy of an object is the energy that is stored in the object due to its relative position. Perhaps the most important form of potential energy in this course is chemical energy. That’s the potential energy trapped in organic molecule, associated with the chemical bonds. This is the energy that is available to be released through chemical reactions.

ENERGY AND THERMODYNAMICS. The study of energy and its transformations is known as thermodynamics. Two basic terms in thermodynamics are system and surroundings. System refers to the matter that’s being studied, where everything else is the surroundings. So, in this figure on the screen, this brown bear may be our system and everything around it is surroundings. There are four laws of thermodynamics, but we will only touch on two of them in this lecture. The first law of thermodynamics states that energy can be transferred and transformed, but it cannot be created or destroyed. In this figure, the chemical energy of the organic molecules in the fish is collected by the bear, which converts into kinetic energy as it runs. The second law of thermodynamics states that every energy transformation results in an increase in entropy in the universe. Entropy is a measure of disorder in the universe. Another way of thinking about it is how spread out the energy is. So, if all energy in the universe were equally spreadout, we would be at maximal entropy. So looking again at this figure on the screen, the chemical energy that’s stored or organized in this fish is lost to the environment through the form of heat while the bear runs. So, you have a dissipation of the energy that increases entropy in the universe.

MOLECULAR MOVEMENT. When looking at a molecule, there are four kinds of movement that has effects on biology. Rotation is a molecule spinning in space around all 3 axes. Vibration is where one atom moves closer and further from a point in space. The atoms also move in space. Each of these movements focuses on a single molecule. The last category, Brownian motion, is when a molecule moves relative to other molecules.

MOLECULAR MOVEMENT AND TEMPERATURE. As mentioned previously, temperature is a measure of the kinetic energy of molecules in shared space. It is related to the internal and lateral movement of molecules. When heat is transferred to this space, then the additional thermal energy increases the movement of the molecules. This movement also has a force associated with it. I’m sure you recall the famous Noble gas law shown here. If you have a balloon and increase temperature, T, the balloon either expands in volume (V) or increases in pressure (P) if the volume is fixed. This ability to change pressure or volume is a force. Many of the processes we talk about involve harnessing the force associated with the tendency of molecules to disperse.

SPECIFIC HEAT. Molecules have an inherent ability to translate thermal energy into molecular movement. Mathematically, this is reflected in that entity’s specific heat. In other words, how much heat do you need to transfer to an object before you see a 1 degree change in temperature. Objects with a high specific heat are able to absorb a lot of heat without much of a change in temperature. As you learn in our water lecture, water has an exceptionally high specific heat, which has profound implications for our planet and the organisms that live on it.

REACTIVITY I want to take a bit of time to illustrate energy states using a very simple scenario – molecule of a salt, NaCl cartooned a small Na ion and a larger Cl ion. The approach is a bit different than the text, so hopefully it complements that discussion using a different perspective. The three states here are examples of conditions that may apply to the molecule with different energy state. As you know, when you add salt to water, it dissolves. When it sits in your salt shaker, there is not a lot of molecular movement and it is fairly stable or inert. But if you add it to water, then more molecular movement is possible. A given molecule will vibrate, putting stress on the bonds that connect the sodium and chloride atoms. If there is a lot of movement, that stress creates a higher energy state. It is possible that the molecule will experience so much internal stress that the bond connecting Na and Cl will break, releasing the two ions and releasing energy. So here, I have 3 arrangements of those atoms: low energy when the atoms aren’t moving much, higher energy when the bonds have reached the breaking point, and less energy when the ions have separated. On this graph, I show just 3 states but in reality, there are many more states and this graph could be represented as a collection of points, each representing a discrete energy level.

REACTIVITY: FOLLOWING THE REACTION OVER TIME. Rather than compare molecules in different energy states, you can also focus on the energy changes following a single molecule over time as it changes energy states. Going from left to right, the molecule begins with its lowest energy, then secures enough energy from the environment to reach the peak reactivity, before dissociating into Na and Cl at lower energy states. The ability to reach this peak depends on the available energy. So temperature increases this reaction rate by transferring thermal energy from the water to the NaCl, which enables more of the molecules to reach the energy state needed to dissociate.

REACTIVITY: ACTIVATION ENERGY Here we use this same graph to illustrate some other properties. The amount of energy needed for a molecule to go from its lowest energy state to this transition state is called the activation energy, or E subscript A. After the ionic bond breaks, the two ions have a lower energy. The intact molecule has a chemical energy and the separated ions have chemical energy. The difference in energy between the start and the end of the reaction is the change in free energy, or delta G. In this reaction, note that the intact molecules have more energy than the individual ions, and as a result there is a net release of energy in this reaction.

FREE ENERGY: Reactions have a characteristic change in energy between where you start and where you end. In those where the product has lower free energy, the reaction has a negative delta G and is called exergonic. Where the reaction leads to products with greater energy than the substrates, the reaction has a positive delta G and is called endergonic. Exergonic reactions can occur spontaneously but endergonic reactions need some sort of energy input to proceed. Note that a given reaction will be endergonic going in one direction and exergonic in the opposite direction.

TRANSLATION AND BROWNIAN MOTION. The previous few slides dealt with internal movement of molecules and the implications of that to reactions. Now we will talk a bit about lateral movement of molecules and what that means for biology. Recall that translation is a molecule moving in space, and Brownian motion is molecules moving in space relative to each other. You are probably aware of what diffusion is in a general sense, but the way to think about it is that it is a consequence of Brownian motion of molecules. For a given solution, a higher temperature means more molecular movement and a greater rate of diffusion. The Fick equation shown here is a mathematical representation of the rate of diffusion, J. The rate of diffusion from one point to another depends on the concentration gradient, dC/dx. But it also depends on how easily the molecule can diffuse – the diffusion coefficient- and that value is itself dependent on temperature.

CONCENTRATION. A very important concept in biology is chemical concentration and its important that you understand the implications. A mole is a number of particles, and molarity is the expression of the number of molecules in a given volume, typically moles per liter. In this course, most of the discussions around concentration are in mM, but you should in general be able to convert between the various SI units of molarity. You probably realize that when you add 1 mole of NaCl into a liter, you will get a 1M solution of NaCl. But since one NaCl gives rise to 2 particles, you 2 moles of particles per liter. When focused on a specific chemical, you use molarity, but when discussing solutes in general, the meaningful measure is osmolarity. So a 1 M solution of NaCl would have an osmolarity of about 2 OsM. The osmotic properties of a solution are important in understanding how various solutions affect cell volume, so let’s explore this in a bit more detail.

OSMOLARITY AND OSMOTIC PRESSURE. Here we have a beaker of water, with a barrier in the middle separating the two halves. On one side, we add salt, which dissociates into Na and Cl. What happens next depends on how that barrier behaves, more specifically what molecules can permeate through it. Here, there are pores big enough to let Na, Cl and H20 move freely. Over time, the Na and Cl would diffuse throughout the solution. This would be faster at higher temperature because of the greater Brownian motion.

OSMOLARITY AND OSMOTIC PRESSURE. Here, we have the same situation but with a membrane possessing different properties. This membrane is semipermeable, able to let H2O move freely but it prevents Na and Cl from moving. In this case, there will be energy associated with the molecular movement of the Na and Cl on one side, and water will move in a way that equalizes to the extent possible how many molecules it bumps into. Since there are more solutes on the left, water will tend to move from the right to the left. This increases the volume on the left as water moves, but at some point the force pushing water through the membrane will be matched by the force of gravity preventing the volume from growing taller. This force is the osmotic pressure. In comparing these two scenarios, the outcome in terms of water movement depends entirely on what the membrane allows to cross. In living cells, the nature of membranes differ, and as a result we have to incorporate those differences when thinking about how osmolarity and permeability interact to affect water movement in and out of cells.

THE IMPROTANCE OF OSMOLARITY AND TONICITY. Recall the distinction between molarity and osmolarity. These are properties of a solution, and any solution will have a characteristic osmolarity and molarity regardless of whether it is in a beaker or in your bloodstream. Tonicity is more of a biological concept, and it depends on how osmolarity affects cells. A cell sits in a solution, and interacts with that solution in ways that are influenced by the gradients as well as the permeability. In other words, tonicity describes the effects of osmotic gradients on a cell. We will explore this more in our cell membrane lectures.

PLANTS VS ANIMALS. But there are important differences between plants and animals in their relationship with osmolarity. Animal cells are somewhat fragile balloons that need to ensure osmotic gradients don’t cause a cell to swell or shrink. Plant cells conversely are built to ensure that there is an inward osmotic force. Cell swelling is restricted by the presence of a cell wall. The ability of a plant to stay upright depends on this force. One of the cool distinctions between animals and plants is in how their physiology differs in service of their osmotic properties, all because plant cells have cell walls but animal cells do not.