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Thermodynamics Review - Biology

Thermodynamics Review - Biology



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Thermodynamics Review

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 has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight into the chemical energy stored within organic molecules (). Some examples of energy transformations are shown in Figure.

The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge very well. Chemical energy stored within organic molecules such as sugars and fats is transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the beating motion of cilia or flagella, contracting muscle fibers to create movement, and reproduction.

Shown are two examples of energy being transferred from one system to another and transformed from one form to another. Humans can convert the chemical energy in food, like this ice cream cone, into kinetic energy (the energy of movement to ride a bicycle). Plants can convert electromagnetic radiation (light energy) from the sun into chemical energy. (credit “ice cream”: modification of work by D. Sharon Pruitt credit “kids on bikes”: modification of work by Michelle Riggen-Ransom credit “leaf”: modification of work by Cory Zanker)


Nonequilibrium Thermodynamics in Cell Biology: Extending Equilibrium Formalism to Cover Living Systems

We discuss new developments in the nonequilibrium dynamics and thermodynamics of living systems, giving a few examples to demonstrate the importance of nonequilibrium thermodynamics for understanding biological dynamics and functions. We study single-molecule enzyme dynamics, in which the nonequilibrium thermodynamic and dynamic driving forces of chemical potential and flux are crucial for the emergence of non-Michaelis-Menten kinetics. We explore single-gene expression dynamics, in which nonequilibrium dissipation can suppress fluctuations. We investigate the cell cycle and identify the nutrition supply as the energy input that sustains the stability, speed, and coherence of cell cycle oscillation, from which the different vital phases of the cell cycle emerge. We examine neural decision-making processes and find the trade-offs among speed, accuracy, and thermodynamic costs that are important for neural function. Lastly, we consider the thermodynamic cost for specificity in cellular signaling and adaptation.


The thermodynamics of DNA structural motifs

DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.


A look at ligand binding thermodynamics in drug discovery

Drug discovery is a challenging endeavor requiring the interplay of many different research areas. Gathering information on ligand binding thermodynamics may help considerably in reducing the risk within a high uncertainty scenario, allowing early rejection of flawed compounds and pushing forward optimal candidates. In particular, the free energy, the enthalpy, and the entropy of binding provide fundamental information on the intermolecular forces driving such interaction. Areas covered: The authors review the current status and recent developments in the application of ligand binding thermodynamics in drug discovery. The thermodynamic binding profile (Gibbs energy, enthalpy, and entropy of binding) can be used for lead selection and optimization (binding enthalpy, selectivity, and adaptability). Expert opinion: Binding thermodynamics provides fundamental information on the forces driving the formation of the drug-target complex. It has been widely accepted that binding thermodynamics may be used as a decision criterion along the ligand optimization process in drug discovery and development. In particular, the binding enthalpy may be used as a guide when selecting and optimizing compounds over a set of potential candidates. However, this has been recently called into question by arguing certain difficulties and in the light of certain experimental examples.

Keywords: Binding adaptability Gibbs energy binding affinity binding selectivity enthalpy entropy isothermal titration calorimetry ligand binding ligand optimization lipophilic efficiency thermodynamics.


Thermodynamics Review - Biology

Let us briefly review some fundamentals of thermodynamics. All organisms require energy to persist and to replace themselves, and the ultimate source of practically all Earth's energy is the Sun. One can think of our Sun as "feeding" the earth via its radiant energy. But 99 percent or more of this incident solar radiation goes unused by organisms and is lost as heat and heat of evaporation only about 1 percent is actually captured by plants in photosynthesis and stored as chemical energy. Moreover, energy available from sunlight varies widely over the earth's surface both in space and in time.

Physics and chemistry have produced two basic laws of thermodynamics that are obeyed by all forms of matter and energy, including living organisms.

The first law is that of "conservation of matter and energy," which states that matter and energy cannot be created or destroyed. Matter and energy can be transformed, and energy can be converted from one form into another, but the total of the equivalent amounts of both must always remain constant. Light can be changed into heat, kinetic energy, and/or potential energy. Whenever energy is converted from one form into another, some of it is given off as heat, which is the most random form of energy. Indeed, the only energy conversion that is 100 percent efficient is conversion to heat, or burning. Aliquots of dried organisms can be burned in "bomb calorimeters" to determine how much energy is stored in their tissues. Energy can be measured in a variety of different units such as ergs and joules, but heat energy or calories is the common denominator.

The second law of thermodynamics states that energy of all sorts, whether it be light, potential, chemical, kinetic, or whatever, tends to change itself spontaneously into a more dispersed, random, or less organized, form. This law is sometimes stated as "entropy increases" -- entropy being random, unavailable energy. Suppose you heat a skillet to cook an egg, and after finishing you leave it on the stove. At first, heat energy is concentrated near the skillet, which is, relative to the rest of the room, hot and quite nonrandom. But by the next morning the skillet has cooled to air temperature, and the heat energy has radiated throughout the room. That heat energy is now dispersed and unavailable for cooking the system of the skillet, the room, and the heat has gone toward equilibrium, become more random, and entropy has increased. Unless an outside source of energy such as a stove, with fuel or electricity, is continually at work to maintain a non-equilibrium state, dispersion of heat results in a random equilibrium state. The same is true for all kinds of energy. According to this law, our solar system and presumably the entire universe should theoretically become a completely random overdispersed array of molecules and heat in the far distant future.

Life has sometimes been called "reverse entropy" (negentropy) because organisms maintain complex organized non-random states compared to their surroundings. But they must obey the second law just as any other system of matter and energy all organisms must work continually to build and maintain nonrandom assemblages of matter and energy locally. This process requires energy, and organisms use the energy of the decaying sun (which, of course, also obeys the second law of thermodynamics and tends toward decreasing concentration of energy -- A Cosmic Perspective) to "oppose" the second law within their own tissues by concentrating energy in their own bodies. Wherever there is a live plant or animal, there must be an energy source. Without a continued influx of energy, no organism can survive for very long. Again, this "reverse entropy" occurs only within each organism, and the overall energy relations of the entire solar system are in accord with the second law of thermodynamics, with the overall system continually becoming more and more random.

Almost all life on Earth depends on photo-synthesis, the capture of solar energy by plants. Remnants of ancient photosynthetic prokaryotes (bacteria-like organisms) long ago became incorporated into eukaryotic cells of all higher plants. Known as chloro-plasts, these tiny green engines house chlorophyll and other molecular machinery that enables plants to convert solar energy into the chemical energy on which all life on Earth depends.

Only a small fraction of the plant food on land is actually harvested by animals most products of primary production are consumed by decomposers. Transfer of energy from one trophic level to the next higher trophic level is defined as ecological efficiency. Such efficiencies of transfer of energy from one trophic level to the next are low, generally only about 5 to 10 percent.

Consider complex networks of interacting species such as those that occur in natural ecological communities. Are these "designed" for orderly and efficient function? Is there a natural "balance of nature?" Although it may be tempting, it is dangerously misleading to view entire ecosystems as having been "designed" for orderly and efficient function. Natural selection does not operate for the "good of the species" but works by differential reproductive success of individual organisms. Antagonistic interactions at the level of individuals and populations are widespread: for example, these include competition, predation, and parasitism. Even the two parties engaged in a mutualism experience conflicts of interest because costs and benefits differ for each participant. Such negative interactions must frequently impair some aspects of ecosystem performance.

Natural selection operating on individual prey organisms favors escape ability, which in turn reduces the rate of flow of matter and energy through that trophic level, decreasing ecological efficiency but simultaneously increasing community stability. In contrast, predators evolve so as to be better able to capture their prey, which increases the efficiency of flow of energy through trophic levels but reduces a system's stability.

In the coevolution of a predator and its prey, to avoid extinction, the prey must remain a step ahead of its predator. As a corollary, community-level properties of ecological efficiency and community stability may in fact be inversely related because natural selection operates at the level of individual predators and prey. Moreover, the apparent constancy and observed low levels of ecological efficiency are probably a result of this compromise that must be reached between prey and their predators.


Free Response

Imagine an elaborate ant farm with tunnels and passageways through the sand where ants live in a large community. Now imagine that an earthquake shook the ground and demolished the ant farm. In which of these two scenarios, before or after the earthquake, was the ant farm system in a state of higher or lower entropy?

The ant farm had lower entropy before the earthquake because it was a highly ordered system. After the earthquake, the system became much more disordered and had higher entropy.

Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving. Explain how the second law of thermodynamics applies to these two scenarios.

While cooking, food is heating up on the stove, but not all of the heat goes to cooking the food, some of it is lost as heat energy to the surrounding air, increasing entropy. While driving, cars burn gasoline to run the engine and move the car. This reaction is not completely efficient, as some energy during this process is lost as heat energy, which is why the hood and the components underneath it heat up while the engine is turned on. The tires also heat up because of friction with the pavement, which is additional energy loss. This energy transfer, like all others, also increases entropy.


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Obesity & the First Law of Thermodynamics

Obesity is the costliest preventable health problem in the United States. Understanding and applying the first law of thermodynamics will help students prevent and treat this all-too-common problem.

Failure to understand the first law of thermodynamics impairs our nation’s health. Students need to learn that obesity is caused simply by consuming more calories than the body expends. People offer many excuses for obesity: hormone imbalance, slow metabolism, genetics, big bones, willpower deficiency, limited access to healthy foods, poverty, and fear of looking too thin. Biologists also contribute to the complexity of obesity by discovering new hormones and signaling pathways involved in the regulation of body weight. Obesity is fundamentally, however, about calories in versus calories out. With obesity come significant health risks, including heart disease, hypertension, sleep apnea, and arthritis. Two thirds of adults in the United States are overweight (body mass index [BMI] > 25), and almost half of these overweight adults are obese (BMI > 30). Despite the above excuses, most people who are overweight are aware of their weight and want to shed pounds. It is incumbent on science teachers to bring physics into the biology class and combat excuses with the first law of thermodynamics. A simple exercise for students who have a good understanding of the first law is to apply it in as many ways as possible to the energy balance in the body.

The first law of thermodynamics states that energy is conserved, or that energy in closed systems cannot be created or destroyed. A beautiful introduction is given by Richard Feynman (1995) in the book Six Easy Pieces, in the chapter on conservation of energy. The conservation of indestructible children’s toy blocks, and the intuitive formulation of equations to account for missing blocks, is a wonderful analogy for the unit of energy used with nutrition, the Calorie. Once growth is completed, any excess energy not needed to maintain body temperature, cellular work, and body movements is converted to fat. Eating less than is needed for body metabolism leads to the breakdown of this body fat for energy. This body-fat storage of excess food intake represents the first refrigerator and was an adaptation when food sources were unpredictable. In developed countries today, where food is plentiful, easily accessed, and easily digested, this human refrigerator is often overstocked.

Students should be familiar with the energy unit used in nutrition. I will not use the SI units for energy and weight in this article, because the Calorie is used instead of the joule, and the pound instead of the kilogram, in most of the labeling and dieting literature to which students are exposed. The capitol “C” calorie used in nutrition is the equivalent of 1000 small “c” calories used in the physical sciences. Some quick conversions are useful. A pound of fat on the human body contains 3500 Calories. A 12-ounce can of soda has about 150 Calories. One can of soda a day, for 1 year, is equivalent to eating six 5-pound bags of table sugar over the year, and, if that one can a day is ingested in excess of Calories needed, results in the storage of 16 pounds of fat. If an adult is 5 feet 4 inches tall, to go from a healthy normal BMI of 25 at 145 pounds to a BMI of 40 at a weight of 232 pounds, in the morbidly obese range, entails the ingestion of 3500 Calories per pound of fat times the extra 87 pounds, or 304,500 Calories. A 20-year-old would only have to have eaten 42 Calories a day more than the body needed over his or her lifetime to achieve this excess weight. That’s the Calorie amount in only 4 ounces of soda. As should be clear, it’s all about the Calorie. One can understand student misconceptions about energy by examining cans of popular drinks, like Monster Energy Lo-Carb, which has only 20 Calories in the 16-ounce can and 160 mg of caffeine. Another is 5 Hour Energy Drink, often sold at fitness centers, that sells for $2 for a 2-ounce bottle and has caffeine but only 4 Calories (there is also an oxymoronic Calorie-free 5 Hour Energy Drink!). If a 1-mile run burns up 100 Calories, then that 4-Calorie 5 Hour Energy drink will supply the energy for only the first 200 feet.

Students should be able to apply this information, and what they have heard about dieting and obesity, to come up with a scientific approach to weight loss. Table 1 outlines five approaches to legal and safe weight loss using the first law of thermodynamics as a framework. These will be discussed in order.

Five approaches to legal and safe weight loss.

Approaches . How .
Decrease input Eat less food: habits, social groups Bariatric surgery: restrictive Appetite-suppressing drugs: lorcaserin phentermine/topiramate (both FDA approved 2012)
Decrease food absorption Bariatric surgery: malabsorptive Malabsorptive drugs Carbohydrates: Acarbose Fats: Orlistat, bile acid sequestrants Cholesterol: Ezetimibe Change gut flora?
Increase excretion Glycosuria: potential drugs to inhibit renal reabsorption of glucose
Convert calories to heat Eat ice Activate brown fat cold, exercise
Increase output Move
Approaches . How .
Decrease input Eat less food: habits, social groups Bariatric surgery: restrictive Appetite-suppressing drugs: lorcaserin phentermine/topiramate (both FDA approved 2012)
Decrease food absorption Bariatric surgery: malabsorptive Malabsorptive drugs Carbohydrates: Acarbose Fats: Orlistat, bile acid sequestrants Cholesterol: Ezetimibe Change gut flora?
Increase excretion Glycosuria: potential drugs to inhibit renal reabsorption of glucose
Convert calories to heat Eat ice Activate brown fat cold, exercise
Increase output Move

Fewer Calories going into the closed system of the body is one obvious solution. This takes some willpower, because the body thinks it is starving rather than dieting and sends strong signals to eat. Simple habits like only eating at the table and using smaller plates will help. Forming social ties to thinner people also may help (Christakis & Fowler, 2007). Surgery for obesity is of three types: restrictive surgery that makes the stomach smaller so that satiety is reached sooner malabsorptive types that link up the intestines so that most of the digesting and absorbing surface of the small intestine is bypassed and a combination of both (Karmali et al., 2010). It is the restrictive type that results in decreased oral intake, because satiety is reached earlier. Two drugs were approved in 2012 to suppress the appetite by effects on the central nervous system, but after a year the median weight loss is only 10% for the better of the two drugs (Colman et al., 2012).

Once food enters the mouth, there are several strategies to prevent absorption. Malabsorptive type bariatric surgeries are mentioned above. No matter how much is ingested, the intestinal enzymes are bypassed so that digestion is minimized. Nutrients are passed into the stool. Intentional drug-mediated malabsorption is also possible (Powell et al., 2011). Acarbose is an oral drug that inhibits the intestinal enzyme alpha glucosidase, which releases glucose from polysaccharides, thus decreasing the digestion and absorption of carbohydrates. Orlistat (sold by prescription as Xenical and over the counter as Alli) inhibits pancreatic lipase, thus decreasing digestion and absorption of fats. Bile acid sequestrants like cholestyramine bind bile, thus diminishing its emulsifying effect and decreasing fat absorption. Ezetimibe specifically prevents the absorption of cholesterol by binding to a critical cholesterol receptor on the brush border of the intestine, and so it is used primarily for treatment of hypercholesterolemia, but it also would have a small effect on weight loss. As of yet, there are no intestinal peptidase inhibitors used therapeutically. There is some evidence that the bacterial ecology of the intestine influences the absorption of nutrients, so that one potential treatment could be an alteration of the flora to cause less efficient absorption (Tilg et al., 2009). All these malabsorptive strategies are expensive and associated with side effects, including bloating, gas, and vitamin deficiencies. Students can discuss the ethics of taking medications or having surgery to decrease food absorption in the United States when Third World countries are struggling with basic nutrition and health needs.

Normally, any glucose in the glomerular filtrate in the kidneys is reabsorbed, leaving little or no glucose in the final urine product. Families have been found that have a mutation in a renal sodium–glucose co-transporter gene that codes for a protein called SGLT2 (Calado et al., 2006). These phenotypes tend to lose glucose in the urine and also tend to be thin. In 2009, the FDA declined to approve a drug for diabetes, called dapaglifozin, which was an inhibitor of SGLT2, because it was linked to bladder cancers and genital yeast infections. This is an open avenue of research, because SGLT2 inhibitors block

25% of renal glucose reabsorption, which amounts to

70 g of glucose and 280 Calories per day (Chao, 2011).

Students can review their physical science courses by figuring out how much weight they would lose by eating a given amount of ice every day. The heat of fusion of ice is 80 calories (small “c”) per gram. The specific heat of water is 1 calorie per gram. Students can do the calculations to determine that eating 66 pounds of ice at zero degrees Celsius, and converting it to body-temperature water would require

3500 Calories, which is the energy equivalent of 1 pound of fat.

Brown fat is a histological type of fat that is primarily used in thermoregulation rather than energy storage. UCP1 (uncoupling protein 1) is a protein activated in brown fat cells that allows hydrogen ions to pass through the inner mitochondrial membrane without generating ATP in the process. The potential energy stored in the chemiosmotic gradient is wasted as heat. Adrenaline and thyroxine are hormones that cause activation of uncoupling protein, but long-term use of these two hormones has negative health effects in the absence of a deficiency. Brown fat can be activated by regular exercise and by a cold environment (Celi, 2009). Turning down the thermostat in the house and exercising can both activate brown fat and help with weight loss. These steps are good for the body and good for the environment. There is an interesting benign tumor of brown fat cells, called a hibernoma, which is often associated with heat intolerance, night sweats, and leanness (Furlong et al., 2001).

Energy in food can be converted to the energy of motion through work and exercise. As described above, muscular activity not only burns through the energy in yellow fat deposits, but it also activates brown fat so that energy is burned as heat even after the physical activity. There are online calculators for determination of Calorie expenditure for a given type of exercise.

Obesity needs to be seen as a problem of energy balance rather than as a character defect. Approaching the topic in a scientific way will help students avoid making excuses and develop simple strategies, like eating less and exercising more, to be healthier.


Watch the video: FE Review - Thermodynamics (August 2022).