The Lone Ranger
01-07-2007, 05:04 AM
An Introduction to Human Anatomy and Physiology
Chapter Three: Energy Flow in the Life of a Cell
Introduction:Chemical reactions (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) either release or absorb energy as they proceed. Whether a reaction releases or absorbs energy as it progresses is determined by whether there is more energy stored in the chemical bonds of the reactants (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) or the products (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start).
Among the fundamental characteristics of living organisms is their ability to regulate and control the various chemical reactions within their cells. These chemical reactions allow organisms to generate and utilize the energy they need in order to maintain themselves.
The ultimate source of energy for living organisms is almost always sunlight. Plants, algae and some bacteria are known as autotrophs (“self-feeders”) because they can use molecules such as chlorophyll and rhodopsin to absorb solar energy. The captured solar energy is then used to build organic molecules (especially the monosaccharide carbohydrate (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=36#content_start) glucose) from carbon dioxide and water. Thus, autotrophs are organisms that can make their own food.
This process, in which plants and similar organisms capture solar energy and use the captured energy to make food, is known as photosynthesis. (“Photosynthesis” means “to make with light.”) In a typical photosynthesis reaction, solar energy is used to combine six carbon dioxide molecules and six water molecules, forming a single molecule of glucose. Six molecules of diatomic oxygen are left over after the reaction is complete, and so photosynthesis releases oxygen as a byproduct.
Photosynthesis: 6CO2 + 6H2O + sunlight energy → C6H12O6 + 6O2
Where does the energy go that was used to assemble the glucose molecule? Well, since photosynthesis is an endothermic reaction (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start), it absorbs energy (in this case, solar energy) from its surroundings as it occurs. The absorbed energy is used to assemble glucose molecules, and so it is stored in the chemical bonds of the glucose.
When a plant needs to use energy (for repairing damaged tissues, for example, or for building molecules more complex than glucose), it can decompose (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start) the glucose that was produced during photosynthesis back into CO2 and water. Decomposition of glucose is an exothermic reaction (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start), of course, because there is more energy stored in the bonds of the original glucose than is present in the bonds of the CO2 and water that result from its decomposition. So, the captured solar energy that had been stored in the chemical bonds of the glucose is released when the glucose is decomposed, and the plant can use the released energy to do work.
http://www.freethought-forum.com/forum/gallery/files/5/0/photosynthesis.jpg
Plants use glucose to store energy for later use, often by converting it to the polysaccharide (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=37#content_start) starch. Animals and other heterotrophs (“other-feeders”) acquire glucose either by eating autotrophs or by eating other heterotrophs. That is to say, a “heterotroph” is an organism that cannot manufacture its own food. So ultimately, all heterotrophs are dependent on autotrophs for their food, either directly or indirectly.
Organisms typically decompose glucose in the process called cellular (aerobic) respiration. This releases the stored solar energy that was originally used to manufacture the glucose during photosynthesis. The released energy can then be used to drive the various chemical reactions that living organisms depend upon for growth, maintenance and repair of their bodies.
Chemically speaking, aerobic respiration is precisely the opposite of photosynthesis. Aerobic respiration is accomplished by adding six oxygen molecules to a single glucose molecule. This oxidation (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=33#content_start) of glucose causes it to decompose into six carbon dioxide molecules and six water molecules. Because there is less energy stored in the chemical bonds of the carbon dioxide and water than was stored in the bonds of the glucose, the “excess” energy is released and can be used to do work. In other words, the breaking of a glucose molecule’s chemical bonds releases the energy that was originally used to manufacture it.
Aerobic Respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + energy
Organisms use the nucleotide (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=46#content_start) adenosine triphosphate (ATP) to transfer energy from one part of a cell to another, so ATP is known as an energy carrier molecule. The energy released during cellular respiration is used to add a phosphate group to a molecule of adenosine diphosphate, making ATP. (ADP, of course, has two phosphate groups, and ATP has three.) The ATP can then be transported to wherever it is needed by the cell, and when the third phosphate group is split off, the energy released is used to power chemical reactions.
[B]ATP Synthesis: ADP + Phosphate Group (Pi) + energy → ATP
http://www.freethought-forum.com/forum/gallery/files/5/0/atp_289063_original.jpg
A molecule of adenosine triphosphate consists of a molecule of the sugar ribose bound
to three phosphate groups on one side, and the nitrogenous base adenine on the other side.
http://www.freethought-forum.com/forum/gallery/files/5/0/adp_atp_original.jpg
In the cells of a living organism, energy is used to add a third phosphate group to a molecule of
adenosine diphosphate (ADP), forming a molecule of adenosine triphosphate (ATP). The ATP can
then be transported to wherever the cell needs energy. When the third phosphate group is
split off the ATP to regenerate ADP, energy is released that can be used to do work.
The Nature of Energy:Energy, as noted earlier, is the capacity to do mechanical work – that is, to move matter (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=3#content_start). Organisms need an energy supply because they need energy to build and maintain body structures. On a more basic level, organisms need energy to power the chemical reactions in which these body structures are built and maintained.
[b]Kinds of Energy:
Kinetic energy is the energy of movement. In other words, anything that is moving has kinetic energy. For instance, light (electromagnetic energy) is moving photons. Heat (thermal energy) is the random movement of atoms, ions, and molecules. Electricity is moving electrons.
Potential energy is energy that is stored in some way. Chemical bonds are a form of potential energy, because when they’re broken, the energy that was used to make them is released. The electrical energy stored in batteries is potential energy, because it can be converted to electricity when a circuit is completed. When work is done to lift an object against the pull of gravity, the energy that was used to move it is stored as positional energy in the object itself. If the object is then released, it falls as its potential energy is re-converted to kinetic energy.
http://www.freethought-forum.com/forum/gallery/files/5/0/potential_and_kinetic_energy_original.jpg
[b]The Laws of Thermodynamics and You: Thermodynamics is the study of energy; specifically, it is the study of how energy moves and how it causes movement in matter. We use the laws of thermodynamics to describe the behavior of energy.
The First Law of Thermodynamics tells us that energy can be neither created nor destroyed. Energy can be converted from one form to another, such as conversion of electricity to light, but energy cannot be created, nor can it be destroyed. This means that there’s a finite amount of energy in the Universe. Fortunately, there’s no concern about running out anytime soon.
A closed system is one in which energy can neither enter nor leave. Therefore, according to the first law of thermodynamics, the total energy within a closed system is constant. (The Universe is the ultimate closed system.) You can move energy around within a closed system, and you can transform energy from one kind into another within the system, but nothing you can do will change the amount of energy in the system.
This fact must be kept in mind when you consider why it is that every living organism requires an outside source of energy in order to survive. During its daily activities it will inevitably lose energy to its surroundings, and it cannot make more. Therefore, to replenish its energy stores, it must somehow acquire energy from an outside source.
http://www.freethought-forum.com/forum/gallery/files/5/0/firstlaw.jpg
The [b]First Law of Thermodynamics tells us that the total amount of energy in a closed system
is constant. Energy can be moved from one part of the system to another, or transformed from one kind
to another, but nothing you can do will change the amount of energy that’s present in the system.
The Second Law of Thermodynamics tells us that whenever energy is converted from one form to another, some of the usable energy in the system is converted into random, unusable energy – usually heat.
Between them, the first and second laws tell us that while the total amount of energy in a closed system is constant, the amount of usable energy in a closed system necessarily decreases over time. Sadly, then, there can never be any such thing as 100% efficiency in energy conversion. Some of the usable energy in a system is always lost when energy is converted from one form to another. That’s one of the reasons why a “perpetual motion machine” is physically impossible – no one has every built one, and no one ever will.
Consider your car. It burns gasoline to produce energy. Gasoline consists of various types of hydrocarbon molecules blended together. (Hydrocarbons are molecules that contain only hydrogen and carbon atoms.) When gasoline is burned in your car’s engine, it is combined with oxygen, and the resulting chemical reactions convert the hydrocarbons into water (H2O) and carbon dioxide (CO2). Since the chemical bonds of the products (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) (H2O and CO2) contain less stored energy than did the bonds of the reactants (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) (various hydrocarbons), this chemical reaction is exothermic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) and releases energy.
Not all of the energy released when gasoline is burned goes into moving your car, however. Much of it is wasted as sound, and much of the remainder is released as heat. Only a fraction of the energy released actually goes to moving your car.
The same is true of human beings. When you decompose (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start) food molecules for energy, most of the energy released is not used to build body tissues or to provide power for movement. Instead, most of the energy that is released is lost, mostly in the form of heat.
I should point out, however, that this is not an entirely bad thing. Remember that heat is energy, and the more heat (thermal energy) there is in the system, the faster will the various molecules of the system be moving. Since all chemical reactions involve moving around atoms and molecules, adding heat to the system causes most chemical reactions to occur at a faster rate.
The reason that most chemical reactions occur at a faster rate as more heat is added to the system is because faster-moving atoms and molecules are more likely to bump into each other and so react to form products. However, if too much heat is added to the system, proteins (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start) and other large organic molecules begin to denature (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=45#content_start). Since proteins make up many of the structures inside cells, and because enzymes (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start) regulate the chemical activities of cells, the cell dies very quickly if its proteins begin to denature.
http://www.freethought-forum.com/forum/gallery/files/5/0/secondlaw.jpg
The First Law of Thermodynamics tells us that the total amount of energy in a closed system is
constant. The [b]Second Law of Thermodynamics tells us that whenever energy is converted
from one form to another, some of the usable energy is converted to unusable forms such as
random thermal energy (heat). This means that, over time, the amount of usable energy in any
closed system will decline. Eventually, it will no longer be possible to do any kind of work within
this system, because there will be no usable energy left. The only remedy is to supply additional
energy from the outside. This is why all living things must take in energy in order to survive.
One consequence of the Second Law is that the amount of disorder or entropy in a closed system tends to increase over time. This is because every energy-transformation process releases randomized energy, usually in the form of heat. Naturally, this randomized energy will tend to break apart any organized, orderly structures that might be present in the system.
Strictly, the entropy of a system is the amount of energy in the system that cannot be used to perform work. For practical purposes, it can be seen as the amount of disorder or randomness in the system.
We’re all familiar with this phenomenon. Highly-ordered systems spontaneously become more disordered over time unless we import energy into them and use it to maintain them. For instance, your house gets messy over time and you must therefore expend energy to dust, vacuum and tidy it. Similarly, your car breaks down over time, and you must expend energy to maintain and repair it.
The upshot of this is that living organisms, being highly complex and highly organized, need to use energy in order to maintain themselves. Otherwise, their complex and highly-organized molecular arrangements will begin to spontaneously break down, and homeostasis (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=6#content_start) will no longer be possible. We call an organism that is no longer using energy to maintain itself “dead.”
Since energy cannot be produced, organisms must acquire it from outside of themselves. And since usuable energy is lost as it is used, organisms must constantly replenish their energy stores if they are to survive.
http://www.freethought-forum.com/forum/gallery/files/5/0/entropy_original.jpg
Robert Heinlein came up with the acronym TANSTAAFL, which stands for “There Ain’t No Such Thing As A Free Lunch.” That’s actually a pretty good summary of the significance of the First and Second Laws of Thermodynamics to living organisms. Living creatures, in order to survive, must acquire and use energy, because they cannot manufacture it. But the body tissues you build and repair with that energy will not remain in their highly-ordered state. Indeed, the very process of using energy to build and maintain body structures releases randomized energy that causes breakdown of those same structures.
So you must continue to consume energy if you are to survive, in order to keep up with the breakdown that inevitably begins just as soon as you stop maintaining body structures. When this cycle is broken, life ceases.
Natural processes tend to proceed such that the entropy of the Universe increases. So “life,” someone once said, “is a continual battle against the Second Law of Thermodynamics.” In the end, though, entropy always wins.
The First and Second Laws of Thermodynamics are sometimes summed up thus:
[b]The First Law: You can’t win. [Nothing you can do will increase the amount of usable energy in a closed system.]
The Second Law: You can’t break even. [Every time you use some of that energy, the amount of usable energy in the system decreases.]
So eat, drink and be merry, for sooner or later, you will die!
http://www.freethought-forum.com/forum/gallery/files/5/0/entropy2.jpg
Orderly systems spontaneously become more disorderly over time – that is, the entropy of the system
increases. To combat this, it is necessary to expend energy to restore the system’s orderly state.
[B]Chemical Reactions and Energy:You may recall that chemical bonds are, in effect, stored energy. As chemical bonds are broken, the energy that was used to make them is released. Since chemical reactions involve the making and breaking of chemical bonds, the reactions either release or absorb energy as they progress, depending upon whether there’s more energy stored in the bonds of the reactants or in the bonds of the products.
Exergonic (exothermic) reactions (such as aerobic respiration), as you recall, are those in which the chemical bonds in the products of the reaction store less energy than do the bonds in the reactants. The “excess” energy is released as the chemical reactions take place, and so exergonic reactions release energy as they progress.
Endergonic (endothermic) reactions (such as photosynthesis), are those in which the chemical bonds in the products store more energy than do the bonds in the reactants. Such reactions can only progress by absorbing energy from their surroundings.
Your metabolism (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=9#content_start) functions because your body couples reactions. What this means is that energy-releasing exergonic reactions are used to power the energy-absorbing endergonic reactions that build body structures.
http://www.freethought-forum.com/forum/gallery/files/5/0/coupled.jpg
In a coupled reaction, an exergonic reaction provides the energy for an endergonic reaction.
[B]Factors that Affect the Rates of Chemical Reactions: In order for covalent bonds (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=17#content_start) to form, atoms (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=6#content_start) or molecules (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=6#content_start) must be brought sufficiently close together that their valence shells (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=14#content_start) effectively merge. Of course, since like charges repel, the negatively-charged electrons (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=7#content_start) in each atom’s orbitals (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=7#content_start) will cause the atoms to repel each other, and so resist forming bonds. This means that a certain amount of energy must be supplied to the atoms or molecules in order to overcome the repulsive forces generated by their electrons and bring them close-enough together that they can form chemical bonds.
Because heat causes molecules to move faster, most chemical reactions (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) therefore occur at faster rates when temperatures are warmer. This is because faster-moving molecules are more likely to “bump into” each other, and are more likely to do so with sufficient kinetic energy (http://www.freethought-forum.com/forum/showthread.php?t=11574&garpg=4#content_start) to overcome the repulsive forces generated by their electrons.
As you recall, the amount of energy that reactants must have before they will chemically react is known as the activation energy (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start) of a chemical reaction. A spontaneous reaction is one in which enough energy is available in the normal environment for the reaction to proceed. For example, oxygen in the atmosphere spontaneously combines with iron to form rust – you don’t have to heat the iron or add a catalyst in order for this to happen. This is why iron objects must be protected from atmospheric oxygen. Of course, other factors being equal, iron will rust faster in a warmer environment than in a cold environment.
An example of a chemical reaction that is not spontaneous is the oxidation of wood. That is, wood does not spontaneously burst into flames at room temperature; it must be heated to a considerably higher temperature before the molecules of the wood have enough energy that they’ll begin combining with oxygen molecules.
Certain substances can lower the activation energies of chemical reactions, and so greatly increase the rates at which those reactions occur. These substances, if they are not consumed themselves in the reactions, are known as catalysts (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start). You’ll notice that catalysts don’t actually cause chemical reactions to occur. A catalyst simply makes it easier for a reaction to occur, by reducing the amount of energy that must be supplied before the reaction will occur. So, while a catalyst speeds up the rate at which a chemical reaction occurs, it will not cause a reaction to occur if that reaction is energetically unfavorable.
http://www.freethought-forum.com/forum/gallery/files/5/0/catalyst.jpg
The [b]activation energy (Ea) is the amount of energy that must be supplied to
the reactants before they will react to form products. A catalyst lowers
the activation energy of the reaction, but is not itself consumed in the reaction.
Enzymes: Enzymes (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start), as you recall, are organic molecules (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=34#content_start) – proteins (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start), generally – that function as catalysts. Without enzymes, the chemical reactions that support life would occur at only a tiny fraction of the rate necessary to keep us alive.
Enzymes tend to be very specific as to which chemical reactions they facilitate. By changing the amounts and activities of specific enzymes, a cell can therefore regulate its metabolism (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=9#content_start) very precisely.
[b]Enzyme Structure: Generally speaking, enzymes are thought to work by bringing reactants sufficiently close together that they can easily react with each other. They do this by forming temporary bonds with the reactants. Since the shape of an enzyme determines which reactant molecule(s) can bond to, the function of an enzyme is very-much dependent on its shape.
Reactant molecules (known as the substrate molecules when we’re talking about enzymatic reactions) temporarily bond with the enzyme at what are known as the enzyme’s active site(s). Since the substrate molecules change shape when they react with each other, the product(s) will no longer fit into the enzyme’s active sites. So after the chemical reaction occurs, the products are released by the enzyme. The enzyme is then free to bond to more substrate, and the reaction can occur again.
Because the function of an enzyme is utterly dependent on its shape, anything that causes the enzyme molecule to change its shape will either alter or destroy its ability to function as a catalyst. As you may recall, even a slight change in temperature, pH (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=31#content_start) or salinity can cause a protein to change shape or denature (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=45). This is one of the most important reasons why it’s so crucial for living organisms to maintain blood pH, body temperature, electrolyte (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=30#content_start) balance, and other factors within very narrow ranges. Even small departures from the normal ranges of these values can impact enzyme function with fatal results.
[b]Enzyme Function: One hypothesis regarding how enzymes function is known as the “lock-and-key” model. According to this hypothesis, a particular enzyme is shaped in such a way that the substrate molecule(s) fit into the active site(s) exactly, much as a key fits exactly into a particular lock. Substrate molecules are attracted to the enzyme’s active sites, and are thus brought close together, so that they can react. After the substrate molecules have reacted with each other, the product molecules will have a different overall shape. This means that they can no longer fit into the enzyme’s active site, and so they are released. The enzyme is now free to bond to more substrate molecules.
http://www.freethought-forum.com/images/anatomy3/lockandkey.jpg
The “Lock-and-Key” Model of Enzyme Function
http://www.freethought-forum.com/forum/gallery/files/5/0/enzymes_original.jpg
This enzyme catalyzes the hydrolysis (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start) of sucrose into glucose and fructose.
http://www.freethought-forum.com/forum/gallery/files/5/0/denatured_original.jpg
The ability of an enzyme to function is crucially dependent on its shape. If an enzyme is
denatured, it can no longer bond to its substrate molecule(s), and so can no longer function.
[b]Enzyme Cofactors: Some enzymes consist simply of a protein molecule that functions as a catalyst, while others must be bound to other substances before they can function. The other substances to which some enzymes must be bound before they can function are known as cofactors.
A cofactor may be inorganic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=34#content_start) or organic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=34#content_start). Some metals, for instance, function as enzyme cofactors, and so are necessary parts of your diet.
Organic cofactors are known as coenzymes. Many vitamins, for example, function as coenzymes, and so are essential parts of the diet. A well-known example of a coenzyme is Coenzyme A, which plays a crucial role in regulating the chemical reactions of aerobic respiration.
http://www.freethought-forum.com/forum/gallery/files/5/0/coa.jpg
Coenzyme A, an important regulator of aerobic respiration.
[b]Regulation of Enzyme Activity: One way that living cells can regulate the activity of enzymes is by controlling how much of a given enzyme is synthesized (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=26#content_start). You may recall that enzymes are proteins, and that the “instructions” for making proteins are encoded in the DNA (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=47#content_start) of a cell’s nucleus (http://www.freethought-forum.com/forum/showthread.php?t=11575&garpg=7#content_start). So, by regulating how many copies of a given enzyme are made, the cell can regulate the rate at which the chemical reactions it mediates proceed.
A cell can also temporarily alter the functions of enzymes, and so alter the rates at which chemical reactions take place. Typically, this is done by production of substances known as activators and inhibitors.
An activator is a substance that binds to a non-functioning enzyme and changes the enzyme’s shape in such a way as to cause it to begin functioning. An inhibitor is a substance that does the opposite; when it binds to a functioning enzyme, it changes the enzyme’s shape so as to stop it from functioning.
Allosteric regulation occurs when an activator or inhibitor binds to some portion of the enzyme other than the active site, and in so doing, changes the shape of the enzyme. (“Allo” means “other.”) By changing the enzyme’s shape, the allosteric activator or inhibitor alters its function.
For an example of allosteric regulation, imagine that enzyme “A” catalyzes a reaction that produces product “B.” If, after it is produced, “B” binds to the enzyme and changes its shape, the enzyme will either start to catalyze a different reaction and so produce a different product (product “C”), or it will simply cease to function. So, the more of product “B” is present in the cell, the less of it will be produced. (Note that this is an example of negative feedback (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=8#content_start).)
http://www.freethought-forum.com/forum/gallery/files/5/0/allosteric1.jpg
Allosteric activation of an enzyme. The inactivated enzyme cannot bind to
the substrate molecule, because its active site is the wrong shape. When
the allosteric activator binds to the enzyme, the shape of the enzyme’s
active site is changed, and the substrate can now bind to the enzyme.
The enzyme is now activated, and can catalyze reactions.
http://www.freethought-forum.com/forum/gallery/files/5/0/allosteric2.jpg
Allosteric inactivation of an enzyme. When the allosteric inactivator binds
to the enzyme, the shape of the enzyme’s active site is changed and it can
no longer bind to the substrate molecule. The enzyme is therefore inactivated.
[break=Competitive Regulation]
Competitive regulation is similar to allosteric regulation, except that the inhibitor(s) bind to the enzyme’s active site, and so stop the enzyme from functioning. When the inhibitor is occupying the enzyme’s active site, substrate molecules can’t bind to it, and so the enzyme is inactivated. The more of the inhibitor is present, the more enzyme molecules will have it bound to their active sites and thus be inactivated, and so the less product is produced.
By controlling the amounts of enzymes, activators and inhibitors that are produced, cells can very precisely regulate the production of substances through enzyme-mediated chemical reactions. And since enzymes mediate virtually every metabolic reaction in the body, by controlling production of enzymes, activators and inhibitors, a cell can very precisely regulate its metabolism.
http://www.freethought-forum.com/forum/gallery/files/5/0/competitive.jpg
Competitive inhibition of an enzyme. Note that the inhibitor can fit into the
same active site that the substrate does, so it competes for active sites
with the substrate. By preventing the substrate from binding to the enzyme’s
active site, the competitive inhibitor prevents the enzyme from functioning.
[break=Naming Enzymes]
[b]Naming Enzymes: Generally speaking, enzymes are named according to what they do, and the last part of the enzyme’s name consists of the suffix -ase. For example, the enzyme that catalyzes the breakdown of ethanol (an alcohol (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=38#content_start)) is known as alcohol dehydrogenase.
Amylases are enzymes that catalyze the breakdown of complex carbohydrates (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=36#content_start). The next time you eat some crackers, you may notice that if you hold them in your mouth for some time before swallowing, they begin to taste sweet. That’s because the amylase in your saliva breaks the starch in the crackers down into the sugar maltose.
Proteases are enzymes that accelerate the breakdown of proteins (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start) into their component amino acids (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start).
Lipases catalyze the breakdown of fats (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=40#content_start) and other lipids (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=39#content_start).
Nucleases catalyze the breakdown of nucleic acids (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=46#content_start). And so forth.
[B]Coupled Reactions and Energy-Carrier Molecules: Many of the chemical reactions in organisms’ metabolisms (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=9#content_start) are endergonic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start). How then, do cells manage to get those reactions going, since these reactions absorb energy as they progress? Cells do so by employing coupled reactions, in which exergonic reactions (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) provide the energy necessary to power endergonic reactions.
As you might expect, therefore, metabolic pathways often involve many chemical reactions that are closely interlinked, and the products of one reaction become the reactants in the next reaction. The synthesis (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=26#content_start) of particularly large organic molecules, for example, might easily involve dozens, hundreds, or even thousands of closely-interlinked chemical reactions.
As you recall, the principle molecule used by living organisms as an energy carrier, is ATP (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=50#content_start). Ultimately, breakdown of glucose is used to provide the energy for powering the various endergonic reactions in a cell’s metabolism. ATP transports energy from where it is released (when glucose is decomposed (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start)) to where it is needed, allowing necessary chemical reactions to proceed.
http://www.freethought-forum.com/forum/gallery/files/5/0/atp_289063_original.jpg
ATP is the principle energy carrier molecule in living organisms. Note that the last two phosphate groups are
attached to the rest of the molecule by high-energy bonds that are easily broken (indicated by the wavy red lines).
The energy released by decomposition of glucose is used to add a phosphate group to adenosine diphosphate (ADP)
to form adenosine triphosphate (ATP). The ATP can then be transported to wherever the cell needs energy to
power chemical reactions. When the phosphate group is split off to regenerate ADP, the energy that was
originally used to make the bond is released. The released energy can then be used to do cellular work.
http://www.freethought-forum.com/forum/gallery/files/5/0/adp_atp_original.jpg
Another way in which energy is transported within cells is by electron carriers. Some metabolic reactions produce high-energy electrons, which could damage cellular components if left free. Electron acceptors are molecules that can bind to these electrons, and so prevent them from doing damage. However, it would be a shame to waste all that energy, wouldn’t it? Metabolic pathways have evolved in which high-energy electrons are passed from one molecule to another, and at each step in the progression, some of the electrons’ energy is removed and used to make ATP. Electron carrier molecules can thus be used to transport energy from one part of a cell to another, in much the same way that ATP does.
Removal of energy from high-energy electrons to generate ATP is a key component of aerobic respiration. Ultimately, the “spent” electrons are captured by hydrogen and oxygen atoms to make water, which is one of the reasons why oxygen is necessary for aerobic respiration.
http://www.freethought-forum.com/forum/gallery/files/5/0/nad_original.jpg
NAD+ (nicotinamide adenine dinudeotide) is a coenzyme that functions as an electron-carrier.
It can bind to and transport hydrogen ions and electrons. When NAD+ is reduced through gain
of electrons, it forms NADH. Oxidation of NADH produces NAD+ and releases free electrons.
Chapter Three: Energy Flow in the Life of a Cell
Introduction:Chemical reactions (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) either release or absorb energy as they proceed. Whether a reaction releases or absorbs energy as it progresses is determined by whether there is more energy stored in the chemical bonds of the reactants (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) or the products (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start).
Among the fundamental characteristics of living organisms is their ability to regulate and control the various chemical reactions within their cells. These chemical reactions allow organisms to generate and utilize the energy they need in order to maintain themselves.
The ultimate source of energy for living organisms is almost always sunlight. Plants, algae and some bacteria are known as autotrophs (“self-feeders”) because they can use molecules such as chlorophyll and rhodopsin to absorb solar energy. The captured solar energy is then used to build organic molecules (especially the monosaccharide carbohydrate (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=36#content_start) glucose) from carbon dioxide and water. Thus, autotrophs are organisms that can make their own food.
This process, in which plants and similar organisms capture solar energy and use the captured energy to make food, is known as photosynthesis. (“Photosynthesis” means “to make with light.”) In a typical photosynthesis reaction, solar energy is used to combine six carbon dioxide molecules and six water molecules, forming a single molecule of glucose. Six molecules of diatomic oxygen are left over after the reaction is complete, and so photosynthesis releases oxygen as a byproduct.
Photosynthesis: 6CO2 + 6H2O + sunlight energy → C6H12O6 + 6O2
Where does the energy go that was used to assemble the glucose molecule? Well, since photosynthesis is an endothermic reaction (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start), it absorbs energy (in this case, solar energy) from its surroundings as it occurs. The absorbed energy is used to assemble glucose molecules, and so it is stored in the chemical bonds of the glucose.
When a plant needs to use energy (for repairing damaged tissues, for example, or for building molecules more complex than glucose), it can decompose (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start) the glucose that was produced during photosynthesis back into CO2 and water. Decomposition of glucose is an exothermic reaction (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start), of course, because there is more energy stored in the bonds of the original glucose than is present in the bonds of the CO2 and water that result from its decomposition. So, the captured solar energy that had been stored in the chemical bonds of the glucose is released when the glucose is decomposed, and the plant can use the released energy to do work.
http://www.freethought-forum.com/forum/gallery/files/5/0/photosynthesis.jpg
Plants use glucose to store energy for later use, often by converting it to the polysaccharide (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=37#content_start) starch. Animals and other heterotrophs (“other-feeders”) acquire glucose either by eating autotrophs or by eating other heterotrophs. That is to say, a “heterotroph” is an organism that cannot manufacture its own food. So ultimately, all heterotrophs are dependent on autotrophs for their food, either directly or indirectly.
Organisms typically decompose glucose in the process called cellular (aerobic) respiration. This releases the stored solar energy that was originally used to manufacture the glucose during photosynthesis. The released energy can then be used to drive the various chemical reactions that living organisms depend upon for growth, maintenance and repair of their bodies.
Chemically speaking, aerobic respiration is precisely the opposite of photosynthesis. Aerobic respiration is accomplished by adding six oxygen molecules to a single glucose molecule. This oxidation (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=33#content_start) of glucose causes it to decompose into six carbon dioxide molecules and six water molecules. Because there is less energy stored in the chemical bonds of the carbon dioxide and water than was stored in the bonds of the glucose, the “excess” energy is released and can be used to do work. In other words, the breaking of a glucose molecule’s chemical bonds releases the energy that was originally used to manufacture it.
Aerobic Respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + energy
Organisms use the nucleotide (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=46#content_start) adenosine triphosphate (ATP) to transfer energy from one part of a cell to another, so ATP is known as an energy carrier molecule. The energy released during cellular respiration is used to add a phosphate group to a molecule of adenosine diphosphate, making ATP. (ADP, of course, has two phosphate groups, and ATP has three.) The ATP can then be transported to wherever it is needed by the cell, and when the third phosphate group is split off, the energy released is used to power chemical reactions.
[B]ATP Synthesis: ADP + Phosphate Group (Pi) + energy → ATP
http://www.freethought-forum.com/forum/gallery/files/5/0/atp_289063_original.jpg
A molecule of adenosine triphosphate consists of a molecule of the sugar ribose bound
to three phosphate groups on one side, and the nitrogenous base adenine on the other side.
http://www.freethought-forum.com/forum/gallery/files/5/0/adp_atp_original.jpg
In the cells of a living organism, energy is used to add a third phosphate group to a molecule of
adenosine diphosphate (ADP), forming a molecule of adenosine triphosphate (ATP). The ATP can
then be transported to wherever the cell needs energy. When the third phosphate group is
split off the ATP to regenerate ADP, energy is released that can be used to do work.
The Nature of Energy:Energy, as noted earlier, is the capacity to do mechanical work – that is, to move matter (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=3#content_start). Organisms need an energy supply because they need energy to build and maintain body structures. On a more basic level, organisms need energy to power the chemical reactions in which these body structures are built and maintained.
[b]Kinds of Energy:
Kinetic energy is the energy of movement. In other words, anything that is moving has kinetic energy. For instance, light (electromagnetic energy) is moving photons. Heat (thermal energy) is the random movement of atoms, ions, and molecules. Electricity is moving electrons.
Potential energy is energy that is stored in some way. Chemical bonds are a form of potential energy, because when they’re broken, the energy that was used to make them is released. The electrical energy stored in batteries is potential energy, because it can be converted to electricity when a circuit is completed. When work is done to lift an object against the pull of gravity, the energy that was used to move it is stored as positional energy in the object itself. If the object is then released, it falls as its potential energy is re-converted to kinetic energy.
http://www.freethought-forum.com/forum/gallery/files/5/0/potential_and_kinetic_energy_original.jpg
[b]The Laws of Thermodynamics and You: Thermodynamics is the study of energy; specifically, it is the study of how energy moves and how it causes movement in matter. We use the laws of thermodynamics to describe the behavior of energy.
The First Law of Thermodynamics tells us that energy can be neither created nor destroyed. Energy can be converted from one form to another, such as conversion of electricity to light, but energy cannot be created, nor can it be destroyed. This means that there’s a finite amount of energy in the Universe. Fortunately, there’s no concern about running out anytime soon.
A closed system is one in which energy can neither enter nor leave. Therefore, according to the first law of thermodynamics, the total energy within a closed system is constant. (The Universe is the ultimate closed system.) You can move energy around within a closed system, and you can transform energy from one kind into another within the system, but nothing you can do will change the amount of energy in the system.
This fact must be kept in mind when you consider why it is that every living organism requires an outside source of energy in order to survive. During its daily activities it will inevitably lose energy to its surroundings, and it cannot make more. Therefore, to replenish its energy stores, it must somehow acquire energy from an outside source.
http://www.freethought-forum.com/forum/gallery/files/5/0/firstlaw.jpg
The [b]First Law of Thermodynamics tells us that the total amount of energy in a closed system
is constant. Energy can be moved from one part of the system to another, or transformed from one kind
to another, but nothing you can do will change the amount of energy that’s present in the system.
The Second Law of Thermodynamics tells us that whenever energy is converted from one form to another, some of the usable energy in the system is converted into random, unusable energy – usually heat.
Between them, the first and second laws tell us that while the total amount of energy in a closed system is constant, the amount of usable energy in a closed system necessarily decreases over time. Sadly, then, there can never be any such thing as 100% efficiency in energy conversion. Some of the usable energy in a system is always lost when energy is converted from one form to another. That’s one of the reasons why a “perpetual motion machine” is physically impossible – no one has every built one, and no one ever will.
Consider your car. It burns gasoline to produce energy. Gasoline consists of various types of hydrocarbon molecules blended together. (Hydrocarbons are molecules that contain only hydrogen and carbon atoms.) When gasoline is burned in your car’s engine, it is combined with oxygen, and the resulting chemical reactions convert the hydrocarbons into water (H2O) and carbon dioxide (CO2). Since the chemical bonds of the products (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) (H2O and CO2) contain less stored energy than did the bonds of the reactants (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) (various hydrocarbons), this chemical reaction is exothermic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) and releases energy.
Not all of the energy released when gasoline is burned goes into moving your car, however. Much of it is wasted as sound, and much of the remainder is released as heat. Only a fraction of the energy released actually goes to moving your car.
The same is true of human beings. When you decompose (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start) food molecules for energy, most of the energy released is not used to build body tissues or to provide power for movement. Instead, most of the energy that is released is lost, mostly in the form of heat.
I should point out, however, that this is not an entirely bad thing. Remember that heat is energy, and the more heat (thermal energy) there is in the system, the faster will the various molecules of the system be moving. Since all chemical reactions involve moving around atoms and molecules, adding heat to the system causes most chemical reactions to occur at a faster rate.
The reason that most chemical reactions occur at a faster rate as more heat is added to the system is because faster-moving atoms and molecules are more likely to bump into each other and so react to form products. However, if too much heat is added to the system, proteins (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start) and other large organic molecules begin to denature (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=45#content_start). Since proteins make up many of the structures inside cells, and because enzymes (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start) regulate the chemical activities of cells, the cell dies very quickly if its proteins begin to denature.
http://www.freethought-forum.com/forum/gallery/files/5/0/secondlaw.jpg
The First Law of Thermodynamics tells us that the total amount of energy in a closed system is
constant. The [b]Second Law of Thermodynamics tells us that whenever energy is converted
from one form to another, some of the usable energy is converted to unusable forms such as
random thermal energy (heat). This means that, over time, the amount of usable energy in any
closed system will decline. Eventually, it will no longer be possible to do any kind of work within
this system, because there will be no usable energy left. The only remedy is to supply additional
energy from the outside. This is why all living things must take in energy in order to survive.
One consequence of the Second Law is that the amount of disorder or entropy in a closed system tends to increase over time. This is because every energy-transformation process releases randomized energy, usually in the form of heat. Naturally, this randomized energy will tend to break apart any organized, orderly structures that might be present in the system.
Strictly, the entropy of a system is the amount of energy in the system that cannot be used to perform work. For practical purposes, it can be seen as the amount of disorder or randomness in the system.
We’re all familiar with this phenomenon. Highly-ordered systems spontaneously become more disordered over time unless we import energy into them and use it to maintain them. For instance, your house gets messy over time and you must therefore expend energy to dust, vacuum and tidy it. Similarly, your car breaks down over time, and you must expend energy to maintain and repair it.
The upshot of this is that living organisms, being highly complex and highly organized, need to use energy in order to maintain themselves. Otherwise, their complex and highly-organized molecular arrangements will begin to spontaneously break down, and homeostasis (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=6#content_start) will no longer be possible. We call an organism that is no longer using energy to maintain itself “dead.”
Since energy cannot be produced, organisms must acquire it from outside of themselves. And since usuable energy is lost as it is used, organisms must constantly replenish their energy stores if they are to survive.
http://www.freethought-forum.com/forum/gallery/files/5/0/entropy_original.jpg
Robert Heinlein came up with the acronym TANSTAAFL, which stands for “There Ain’t No Such Thing As A Free Lunch.” That’s actually a pretty good summary of the significance of the First and Second Laws of Thermodynamics to living organisms. Living creatures, in order to survive, must acquire and use energy, because they cannot manufacture it. But the body tissues you build and repair with that energy will not remain in their highly-ordered state. Indeed, the very process of using energy to build and maintain body structures releases randomized energy that causes breakdown of those same structures.
So you must continue to consume energy if you are to survive, in order to keep up with the breakdown that inevitably begins just as soon as you stop maintaining body structures. When this cycle is broken, life ceases.
Natural processes tend to proceed such that the entropy of the Universe increases. So “life,” someone once said, “is a continual battle against the Second Law of Thermodynamics.” In the end, though, entropy always wins.
The First and Second Laws of Thermodynamics are sometimes summed up thus:
[b]The First Law: You can’t win. [Nothing you can do will increase the amount of usable energy in a closed system.]
The Second Law: You can’t break even. [Every time you use some of that energy, the amount of usable energy in the system decreases.]
So eat, drink and be merry, for sooner or later, you will die!
http://www.freethought-forum.com/forum/gallery/files/5/0/entropy2.jpg
Orderly systems spontaneously become more disorderly over time – that is, the entropy of the system
increases. To combat this, it is necessary to expend energy to restore the system’s orderly state.
[B]Chemical Reactions and Energy:You may recall that chemical bonds are, in effect, stored energy. As chemical bonds are broken, the energy that was used to make them is released. Since chemical reactions involve the making and breaking of chemical bonds, the reactions either release or absorb energy as they progress, depending upon whether there’s more energy stored in the bonds of the reactants or in the bonds of the products.
Exergonic (exothermic) reactions (such as aerobic respiration), as you recall, are those in which the chemical bonds in the products of the reaction store less energy than do the bonds in the reactants. The “excess” energy is released as the chemical reactions take place, and so exergonic reactions release energy as they progress.
Endergonic (endothermic) reactions (such as photosynthesis), are those in which the chemical bonds in the products store more energy than do the bonds in the reactants. Such reactions can only progress by absorbing energy from their surroundings.
Your metabolism (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=9#content_start) functions because your body couples reactions. What this means is that energy-releasing exergonic reactions are used to power the energy-absorbing endergonic reactions that build body structures.
http://www.freethought-forum.com/forum/gallery/files/5/0/coupled.jpg
In a coupled reaction, an exergonic reaction provides the energy for an endergonic reaction.
[B]Factors that Affect the Rates of Chemical Reactions: In order for covalent bonds (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=17#content_start) to form, atoms (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=6#content_start) or molecules (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=6#content_start) must be brought sufficiently close together that their valence shells (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=14#content_start) effectively merge. Of course, since like charges repel, the negatively-charged electrons (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=7#content_start) in each atom’s orbitals (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=7#content_start) will cause the atoms to repel each other, and so resist forming bonds. This means that a certain amount of energy must be supplied to the atoms or molecules in order to overcome the repulsive forces generated by their electrons and bring them close-enough together that they can form chemical bonds.
Because heat causes molecules to move faster, most chemical reactions (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) therefore occur at faster rates when temperatures are warmer. This is because faster-moving molecules are more likely to “bump into” each other, and are more likely to do so with sufficient kinetic energy (http://www.freethought-forum.com/forum/showthread.php?t=11574&garpg=4#content_start) to overcome the repulsive forces generated by their electrons.
As you recall, the amount of energy that reactants must have before they will chemically react is known as the activation energy (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start) of a chemical reaction. A spontaneous reaction is one in which enough energy is available in the normal environment for the reaction to proceed. For example, oxygen in the atmosphere spontaneously combines with iron to form rust – you don’t have to heat the iron or add a catalyst in order for this to happen. This is why iron objects must be protected from atmospheric oxygen. Of course, other factors being equal, iron will rust faster in a warmer environment than in a cold environment.
An example of a chemical reaction that is not spontaneous is the oxidation of wood. That is, wood does not spontaneously burst into flames at room temperature; it must be heated to a considerably higher temperature before the molecules of the wood have enough energy that they’ll begin combining with oxygen molecules.
Certain substances can lower the activation energies of chemical reactions, and so greatly increase the rates at which those reactions occur. These substances, if they are not consumed themselves in the reactions, are known as catalysts (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start). You’ll notice that catalysts don’t actually cause chemical reactions to occur. A catalyst simply makes it easier for a reaction to occur, by reducing the amount of energy that must be supplied before the reaction will occur. So, while a catalyst speeds up the rate at which a chemical reaction occurs, it will not cause a reaction to occur if that reaction is energetically unfavorable.
http://www.freethought-forum.com/forum/gallery/files/5/0/catalyst.jpg
The [b]activation energy (Ea) is the amount of energy that must be supplied to
the reactants before they will react to form products. A catalyst lowers
the activation energy of the reaction, but is not itself consumed in the reaction.
Enzymes: Enzymes (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=29#content_start), as you recall, are organic molecules (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=34#content_start) – proteins (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start), generally – that function as catalysts. Without enzymes, the chemical reactions that support life would occur at only a tiny fraction of the rate necessary to keep us alive.
Enzymes tend to be very specific as to which chemical reactions they facilitate. By changing the amounts and activities of specific enzymes, a cell can therefore regulate its metabolism (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=9#content_start) very precisely.
[b]Enzyme Structure: Generally speaking, enzymes are thought to work by bringing reactants sufficiently close together that they can easily react with each other. They do this by forming temporary bonds with the reactants. Since the shape of an enzyme determines which reactant molecule(s) can bond to, the function of an enzyme is very-much dependent on its shape.
Reactant molecules (known as the substrate molecules when we’re talking about enzymatic reactions) temporarily bond with the enzyme at what are known as the enzyme’s active site(s). Since the substrate molecules change shape when they react with each other, the product(s) will no longer fit into the enzyme’s active sites. So after the chemical reaction occurs, the products are released by the enzyme. The enzyme is then free to bond to more substrate, and the reaction can occur again.
Because the function of an enzyme is utterly dependent on its shape, anything that causes the enzyme molecule to change its shape will either alter or destroy its ability to function as a catalyst. As you may recall, even a slight change in temperature, pH (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=31#content_start) or salinity can cause a protein to change shape or denature (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=45). This is one of the most important reasons why it’s so crucial for living organisms to maintain blood pH, body temperature, electrolyte (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=30#content_start) balance, and other factors within very narrow ranges. Even small departures from the normal ranges of these values can impact enzyme function with fatal results.
[b]Enzyme Function: One hypothesis regarding how enzymes function is known as the “lock-and-key” model. According to this hypothesis, a particular enzyme is shaped in such a way that the substrate molecule(s) fit into the active site(s) exactly, much as a key fits exactly into a particular lock. Substrate molecules are attracted to the enzyme’s active sites, and are thus brought close together, so that they can react. After the substrate molecules have reacted with each other, the product molecules will have a different overall shape. This means that they can no longer fit into the enzyme’s active site, and so they are released. The enzyme is now free to bond to more substrate molecules.
http://www.freethought-forum.com/images/anatomy3/lockandkey.jpg
The “Lock-and-Key” Model of Enzyme Function
http://www.freethought-forum.com/forum/gallery/files/5/0/enzymes_original.jpg
This enzyme catalyzes the hydrolysis (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start) of sucrose into glucose and fructose.
http://www.freethought-forum.com/forum/gallery/files/5/0/denatured_original.jpg
The ability of an enzyme to function is crucially dependent on its shape. If an enzyme is
denatured, it can no longer bond to its substrate molecule(s), and so can no longer function.
[b]Enzyme Cofactors: Some enzymes consist simply of a protein molecule that functions as a catalyst, while others must be bound to other substances before they can function. The other substances to which some enzymes must be bound before they can function are known as cofactors.
A cofactor may be inorganic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=34#content_start) or organic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=34#content_start). Some metals, for instance, function as enzyme cofactors, and so are necessary parts of your diet.
Organic cofactors are known as coenzymes. Many vitamins, for example, function as coenzymes, and so are essential parts of the diet. A well-known example of a coenzyme is Coenzyme A, which plays a crucial role in regulating the chemical reactions of aerobic respiration.
http://www.freethought-forum.com/forum/gallery/files/5/0/coa.jpg
Coenzyme A, an important regulator of aerobic respiration.
[b]Regulation of Enzyme Activity: One way that living cells can regulate the activity of enzymes is by controlling how much of a given enzyme is synthesized (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=26#content_start). You may recall that enzymes are proteins, and that the “instructions” for making proteins are encoded in the DNA (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=47#content_start) of a cell’s nucleus (http://www.freethought-forum.com/forum/showthread.php?t=11575&garpg=7#content_start). So, by regulating how many copies of a given enzyme are made, the cell can regulate the rate at which the chemical reactions it mediates proceed.
A cell can also temporarily alter the functions of enzymes, and so alter the rates at which chemical reactions take place. Typically, this is done by production of substances known as activators and inhibitors.
An activator is a substance that binds to a non-functioning enzyme and changes the enzyme’s shape in such a way as to cause it to begin functioning. An inhibitor is a substance that does the opposite; when it binds to a functioning enzyme, it changes the enzyme’s shape so as to stop it from functioning.
Allosteric regulation occurs when an activator or inhibitor binds to some portion of the enzyme other than the active site, and in so doing, changes the shape of the enzyme. (“Allo” means “other.”) By changing the enzyme’s shape, the allosteric activator or inhibitor alters its function.
For an example of allosteric regulation, imagine that enzyme “A” catalyzes a reaction that produces product “B.” If, after it is produced, “B” binds to the enzyme and changes its shape, the enzyme will either start to catalyze a different reaction and so produce a different product (product “C”), or it will simply cease to function. So, the more of product “B” is present in the cell, the less of it will be produced. (Note that this is an example of negative feedback (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=8#content_start).)
http://www.freethought-forum.com/forum/gallery/files/5/0/allosteric1.jpg
Allosteric activation of an enzyme. The inactivated enzyme cannot bind to
the substrate molecule, because its active site is the wrong shape. When
the allosteric activator binds to the enzyme, the shape of the enzyme’s
active site is changed, and the substrate can now bind to the enzyme.
The enzyme is now activated, and can catalyze reactions.
http://www.freethought-forum.com/forum/gallery/files/5/0/allosteric2.jpg
Allosteric inactivation of an enzyme. When the allosteric inactivator binds
to the enzyme, the shape of the enzyme’s active site is changed and it can
no longer bind to the substrate molecule. The enzyme is therefore inactivated.
[break=Competitive Regulation]
Competitive regulation is similar to allosteric regulation, except that the inhibitor(s) bind to the enzyme’s active site, and so stop the enzyme from functioning. When the inhibitor is occupying the enzyme’s active site, substrate molecules can’t bind to it, and so the enzyme is inactivated. The more of the inhibitor is present, the more enzyme molecules will have it bound to their active sites and thus be inactivated, and so the less product is produced.
By controlling the amounts of enzymes, activators and inhibitors that are produced, cells can very precisely regulate the production of substances through enzyme-mediated chemical reactions. And since enzymes mediate virtually every metabolic reaction in the body, by controlling production of enzymes, activators and inhibitors, a cell can very precisely regulate its metabolism.
http://www.freethought-forum.com/forum/gallery/files/5/0/competitive.jpg
Competitive inhibition of an enzyme. Note that the inhibitor can fit into the
same active site that the substrate does, so it competes for active sites
with the substrate. By preventing the substrate from binding to the enzyme’s
active site, the competitive inhibitor prevents the enzyme from functioning.
[break=Naming Enzymes]
[b]Naming Enzymes: Generally speaking, enzymes are named according to what they do, and the last part of the enzyme’s name consists of the suffix -ase. For example, the enzyme that catalyzes the breakdown of ethanol (an alcohol (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=38#content_start)) is known as alcohol dehydrogenase.
Amylases are enzymes that catalyze the breakdown of complex carbohydrates (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=36#content_start). The next time you eat some crackers, you may notice that if you hold them in your mouth for some time before swallowing, they begin to taste sweet. That’s because the amylase in your saliva breaks the starch in the crackers down into the sugar maltose.
Proteases are enzymes that accelerate the breakdown of proteins (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start) into their component amino acids (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=43#content_start).
Lipases catalyze the breakdown of fats (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=40#content_start) and other lipids (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=39#content_start).
Nucleases catalyze the breakdown of nucleic acids (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=46#content_start). And so forth.
[B]Coupled Reactions and Energy-Carrier Molecules: Many of the chemical reactions in organisms’ metabolisms (http://www.freethought-forum.com/forum/showthread.php?t=11573&garpg=9#content_start) are endergonic (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start). How then, do cells manage to get those reactions going, since these reactions absorb energy as they progress? Cells do so by employing coupled reactions, in which exergonic reactions (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=25#content_start) provide the energy necessary to power endergonic reactions.
As you might expect, therefore, metabolic pathways often involve many chemical reactions that are closely interlinked, and the products of one reaction become the reactants in the next reaction. The synthesis (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=26#content_start) of particularly large organic molecules, for example, might easily involve dozens, hundreds, or even thousands of closely-interlinked chemical reactions.
As you recall, the principle molecule used by living organisms as an energy carrier, is ATP (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=50#content_start). Ultimately, breakdown of glucose is used to provide the energy for powering the various endergonic reactions in a cell’s metabolism. ATP transports energy from where it is released (when glucose is decomposed (http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=27#content_start)) to where it is needed, allowing necessary chemical reactions to proceed.
http://www.freethought-forum.com/forum/gallery/files/5/0/atp_289063_original.jpg
ATP is the principle energy carrier molecule in living organisms. Note that the last two phosphate groups are
attached to the rest of the molecule by high-energy bonds that are easily broken (indicated by the wavy red lines).
The energy released by decomposition of glucose is used to add a phosphate group to adenosine diphosphate (ADP)
to form adenosine triphosphate (ATP). The ATP can then be transported to wherever the cell needs energy to
power chemical reactions. When the phosphate group is split off to regenerate ADP, the energy that was
originally used to make the bond is released. The released energy can then be used to do cellular work.
http://www.freethought-forum.com/forum/gallery/files/5/0/adp_atp_original.jpg
Another way in which energy is transported within cells is by electron carriers. Some metabolic reactions produce high-energy electrons, which could damage cellular components if left free. Electron acceptors are molecules that can bind to these electrons, and so prevent them from doing damage. However, it would be a shame to waste all that energy, wouldn’t it? Metabolic pathways have evolved in which high-energy electrons are passed from one molecule to another, and at each step in the progression, some of the electrons’ energy is removed and used to make ATP. Electron carrier molecules can thus be used to transport energy from one part of a cell to another, in much the same way that ATP does.
Removal of energy from high-energy electrons to generate ATP is a key component of aerobic respiration. Ultimately, the “spent” electrons are captured by hydrogen and oxygen atoms to make water, which is one of the reasons why oxygen is necessary for aerobic respiration.
http://www.freethought-forum.com/forum/gallery/files/5/0/nad_original.jpg
NAD+ (nicotinamide adenine dinudeotide) is a coenzyme that functions as an electron-carrier.
It can bind to and transport hydrogen ions and electrons. When NAD+ is reduced through gain
of electrons, it forms NADH. Oxidation of NADH produces NAD+ and releases free electrons.