1.What are the laws of thermodynamics.

The findings of Joule and others led Rudolf Clausius, a German physicist, to state in 1850 that "In any process, energy can be changed from one form to another (including heat and work), but it is never created or destroyed." This is the first law of thermodynamics. An adequate mathematical statement of this first law is delta E = q - w, where delta E is the change (delta) in internal energy (E ) of the system, q is the heat added to the system (a negative value if heat is taken away), and w is work done by the system. In thermodynamic terms, a system is defined as a part of the total universe that is isolated from the rest of the universe by definite boundaries, such as the coffee in a covered Styrofoam cup; a closed room; a cylinder in an engine; or the human body. The internal energy, E, of such a system is a state function; this means that E is dependent only on the state of the system at a given time, and not on how the state was achieved. If the system considered is a chemical system of fixed volume--for example, a substance in a sealed bulb--the system cannot do work (w) in the traditional sense, as could a piston expanding against an external pressure. If no other type of work (such as electrical) is done on or by the system, then an increase in internal energy is equal to the amount of heat absorbed at constant volume (the volume of the system remains constant throughout the process). If the heat is absorbed at constant pressure instead of constant volume (which can occur to any unenclosed system), the increase in the energy of the system is represented by the state function, H, which is closely related to the internal energy. Changes in H (heat content) are called changes in enthalpy,. In 1840, before Joule had made his determinations of the mechanical equivalent of heat, Germain Henri Hess reported the results of experiments that indicated that the heat evolved or absorbed in a given chemical reaction (delta H) is independent of the particular manner (or path) in which the reaction takes place. This generalization is now known as Hess’s law and is one of the basic postulates of thermochemistry.

The steam engine developed by James Watt in 1769 was a type of heat engine, a device that withdraws heat from a heat source, converts some of this heat into useful work, and transfers the remainder of the heat to a cooler reservoir. A major advance in the understanding of the heat engine was provided in 1824 by N. L. Sadi Carnot, a French engineer, in his discussion of the cyclic nature of the heat engine. This theoretical approach is known as the Carnot cycle. A result of the analysis of the heat engine in terms of the Carnot cycle is the second law of thermodynamics, which may be stated in a variety of ways. According to Rudolf Clausius, "It is impossible for a self- acting machine, unaided by external agency, to convey heat from a body at one temperature to another body at a higher temperature." William Thomson (Lord KELVIN), a British thermodynamicist, proposed that "it is impossible by a cyclic process to take heat from a reservoir and convert it into work without, in the same operation, transferring heat from a hot to a cold reservoir."

Entropy- The second law of thermodynamics leads to a new state function S, the entropy of a system. The increase in the entropy of a system when heat is added to it must be at least q/T, where q is the added heat and T is the absolute temperature. If the heat is added in an idealized (reversible) process, delta S = q/T, but for real (irreversible) processes, the entropy change is always greater than this value. Ludwig Boltzmann, an Austrian physicist, demonstrated the significance of entropy on the molecular level in 1877, relating entropy to disorder. J. Willard Gibbs, an American mathematical physicist, referred to entropy as a measure of the "mixed-upedness" of the system. The second law of thermodynamics may also be stated in terms of entropy: in a spontaneous irreversible process, the total entropy of the system and its surroundings always increases; for any process, the total entropy of a system and its surroundings never decreases.

2.Explain how energy moves through living systems.

All organisms need a constant supply of energy to fuel the activities of life. Directly or indirectly, almost all of the energy for living systems comes from the sun. Energy from the sun enters living systems when sunlight is absorbed by molecules found in plants, algae, and certain bacteria. In the process, electrons in these molecules are boosted to higher energy states. Like a boulder on top of a hill, an electron that has been boosted to a higher energy state has additional energy because it is farther away from the nucleus of an atom. This additional energy is released by dropping the electron back to a lower energy state. The energy is then used to do work, or it is captured and stored. Organisms that harvest energy by boosting electrons use it to produce energy-storing macromolecules. Most of these organisms boost electrons with energy from sunlight and convert light energy to chemical energy. The process that converts light energy to chemical energy is called photosynthesis. Instead of using sunlight, certain bacteria obtain energy for boosting electrons from inorganic molecules and convert it to organic chemical energy. The process that converts inorganic chemical energy to organic chemical energy is called chemosynthesis. Organisms that harvest energy from either sunlight or chemicals are called autotrophs. The word autotroph comes from the Greek words autos, meaning "self", and trophikos, meaning "to feed." Organisms that cannot harvest energy directly from sunlight or inorganic molecules but consume food instead are called heterotrophs. The word heterotroph comes from the Greek words heteros, meaning "other", and trophikos meaning "to feed." Heterotrophs obtain their energy from other organisms. Energy stored in food is released by a process that is similar to burning. This process which is called cellular respiration, is a series of chemical reactions that converts energy stored in food to a more useful form. While burning converts almost all of the energy in a fuel to heat, much of the energy released during cellular respiration is used to make ATP, which fuels the activities of living. The flow of energy through the living systems is energy flows through an ecosystem from sunlight or inorganic chemicals to autotrophs and then to heterotrophs. Because some heat escapes with every energy conversion, much of the energy captured by autotrophs eventually flows out of living systems.

3. Discuss oxidation-reduction reactions and how they play a role in photosynthesis and respiration.

Electrons possess differing amounts of potential energy depending on their distance from the atomic nucleus and the attraction of the nucleus for electrons. An input of energy will boost an electron to a higher energy level, but without added energy an electron will remain at the lowest energy level available to it. Chemical reactions are essentially energy transformations in which energy stored in chemical bonds is transferred to other, newly formed chemical bonds. In such transfers, electrons shift from one energy level to another. In many reactions, electrons pass from one atom or molecule to another. These reactions, which are of great importance in living systems, are known as oxidation-reduction reactions. The loss of an electron is known as oxidation, and the atom or molecule that looses the electron is said to be oxidized. The reason electron loss is called oxidation is that oxygen, which attracts electrons very strongly, is most often the electron acceptor. Reduction is, conversely, the gain of an electron. Oxidation and reduction always take place simultaneously because an electron that is lost by the oxidized atom is accepted by another atom, which is reduced in the process. Redox(reduction) reactions may involve only a solitary electron, as when sodium loses an electron and becomes oxidized to Na⁺, and chlorine gains an electron and is reduced to Cl^- . Often, however, the electron travels with a proton, that is, as a hydrogen atom. In such cases, oxidation involves the removal of hydrogen atoms, and reduction the gain of hydrogen atoms. Foe example, when glucose is oxidized, hydrogen atoms are lost by the glucose molecule and gained by oxygen:

C₆H₁₂O₆ + 6O₂ à 6CO₂ + 6H₂O + Energy

The electrons are moving to a lower energy level, and energy is released. Conversely, in the process photosynthesis, hydrogen atoms are transferred from water to CO₂, thereby reducing the CO_s to form glucose:

6CO₂ + 6H₂0 + Energy à C₆H₁₂O₆ + 6O₂

In this case, the electrons are moving to a higher energy level, and an energy input is required to make the reaction occur. In living systems, the energy-capturing reactions (photosynthesis) and energy releasing reactions (glycolysis and respiration) are oxidation-reduction reactions. As we have seen, the complete oxidation of a mole of glucose releases 686 kilocalories of free energy (conversely, the reduction of carbon dioxide to form a mole of glucose stored 686 kilocalories of free energy in the chemical bonds of glucose). If this energy were to released all at once, most of it would be dissipated as heat. Not only would it be of no use to the cell, but the resulting high temperature would be lethal. However, mechanism have evolved in living systems that regulate these chemical reactions – and a multitude of others – in such a way that energy is stored in particular chemical bonds from which it can be released in small amounts as the cell needs it. These mechanisms generally involve sequences of reactions, some of which are oxidation-reduction reaction. Although each reaction in the sequences represents only a small change in the free energy, the overall free energy change for the sequence can be considerable.

4. Relate the functions of a co-enzyme NAD to oxidation-reduction reactions and biochemical pathways.

In many metabolic pathways, energy released from one set of reactions is transferred to another set of reactions. Remember that in living systems, electrons carry energy from one atom or molecule to another in oxidation-reduction reactions. Often, high-energy electrons are passed from the active site of the enzyme that is catalyzing a reaction to an organic molecule called a coenzyme. The coenzyme that carries the electrons to another enzyme that is catalyzing a different reaction. NAD⁺ accepts high energy electrons (paired with protons as hydrogen atoms) and becomes NADH, which transfers the electrons from one set of enzyme-catalyzed reactions to another. When NADH reaches an enzyme in a second set of reactions, it releases the electrons (and their energy) to the reaction that this enzyme is catalyzing. NAD⁺ can then return to the enzyme in the first set of reactions and get more electrons.

Just as tanker trucks transport energy (in the form of gasoline) from storage tanks to gas stations, coenzymes shuttle energy (in the form of hydrogen atoms with high-energy electrons) from one place to another in a cell. One of the most important coenzymes in cell metabolism is nicotinamide adenine dinucleotide, usually referred to by the abbreviation NAD⁺. When NAD⁺ acquires a hydrogen atom from the active site of an enzyme, it becomes NADH (and has been reduce). In cells, hydrogen atoms with high-energy electrons are stripped from food molecules and donated to NAD⁺, forming NADH. The NADH molecules then carry high-energy electrons. Like carrying money in a wallet, cells carry hydrogen atoms with high-energy electrons (one form of their energy "money") in molecules like NADH. And just as you can exchange one type of money for another, cells can exchange one type of energy carrier for another. The energy in NADH, can be converted to the cell’s main energy currency – ATP.

5.Explain how metabolism is controlled in cells.

ATP supplies most of the energy that drives metabolism. In a sense, it is a cell’s "energy currency"—the "money" it used to "pay for" endergonic processes. Each ATP molecule is made of three parts: ribose, a sugar; adenine, a nitrogen-containing base; and a chain of three phosphate groups. Energy that was temporarily stored in an ATP molecule is made available for use by a cell when the end phosphate group is transferred to another molecule. In this exergonic reaction, a sizable packet of energy is transferred along with the phosphate group. This energy then activated a reaction involving the molecule that received the phosphate group. Almost all of the endergonic reactions in cells require less activation energy than that transferred with a phosphate group from ATP. The breakdown of ATP is thus able to power many of a cell’s endergonic activities. An enzyme that catalyzes an endergonic reaction in cells has two active sites.

The ATP site splits the end phosphate group from an ATP molecule, releasing energy. The phosphate group (P) and some of the energy released are received by the reactant molecule attached to the second active site. This transfer of a phosphate group and its energy drives the reaction at the second active site. Since both reactions occur on the surface of the same enzyme, they are physically linked, or coupled. An endergonic reaction that is driven by the splitting of ATP molecules is therefore called a coupled reaction. In a similar way, you can make water in a swimming pool leap straight up in the air, despite the fact that gravity prevents water from rising spontaneously – just jump in the pool! The energy you add going in mire than compensates for the force of gravity holding the water down.

A cell may contain thousands of different kinds of enzymes, each specific to a particular substrate and each promoting a different chemical reaction. The enzymes that are active in a cell at any one time determine what happens in that cell, much as traffic lights determine the flow of traffic in a city. An increase in a particular enzyme’s concentration slows the rate of the reaction it catalyzes. Conversely, a decrease in an enzyme’s concentration slows the rate of the reaction it catalyzes. Furthermore, not all cells contain the same enzymes. The chemical reactions occurring in a nerve cell are very different from those occurring in a red blood cell because the two kinds of cells have a different array of enzymes. By controlling the concentration of enzymes and when they are active, a cell is able to control its chemical reactions, just as a conductor controls the music an orchestra produces by dictating the tempo and volume at which the music is played. Because an enzyme must have a precise shape to work correctly, it is possible for a cell to control an enzyme’s activity by altering the enzyme’s shape. Many enzymes have shapes that can be altered by the binding of "signal" molecules to their surfaces. Such an enzyme is called an allosteric enzyme. Allosteric, which means "other shape", is derived from the Greek words allos, meaning "other". And stereos, meaning "solid". If an allosteric enzyme is unable to bind to a substrate because of the new shape produced by the binding of a signal molecule, the signal molecule is said to repress the enzyme’s activity. If an allosteric enzyme is unable to bind to a substrate unless a signal molecule is bound to it, the signal molecule is said to activate the enzyme. The site where the signal molecule binds to an allosteric enzyme’s surface is called the allosteric site. A signal molecule may affect an allosteric enzyme because an allosteric enzyme has an active site and an allosteric site. When a signal molecule binds to the allosteric site, the enzyme and its active site change shape. When a cell already has an adequate amount of the chemical produced by a biochemical pathway, the pathway will often shut down. Thus, wasteful overproduction is avoided. How does a pathway "know" to shut itself down? The first enzyme in the pathway is an allosteric enzyme with a site that has the shape of the pathway’s product. The binding of the product molecule to the allosteric enzyme inhibits the enzyme’s activity so that when the concentration of the product is high, the first step in the pathway is effectively turned off. The shutting down of a biochemical pathway caused by a key enzyme’s sensitivity to the level of the pathway’s product is called feedback inhibition. When the product concentration drops, the pathway is reactivated. Feedback inhibition is another way that cells simply and effectively regulate their biochemical activities.