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Energy in Chemical Reactions
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Energy is a tough thing to define - it's recognizable, but difficult to pin down with words. The classic definition has it as "ability to do work," but that's not terribly useful. But however you define it, there are some rules that energy follows.
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Energy behaves according to some of the Laws of Physics, in this case the Laws of Thermodynamics. The First Law of Thermodynamics is often called the Conservation Law: energy can't be created from nothing or disappear to nothing. It can, however, change its form. This means that, as energy works through living systems, it gets transferred, changes, and lost as random molecular motion, but it doesn't disappear. It also came from somewhere.
One of Einstein's Laws, the famous E = mc2, established that energy and matter are forms of the same stuff. Matter can be accelerated to the form of energy (this happens in nuclear weapons and power plants), and energy could be slowed down and become matter. The First Law applies to matter, too: in biological systems, matter neither appears from nowhere nor disappears to nothing.
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More on the conservation of energy.
Different energy forms.
Background on Einstein's theory, including his own recorded explanation.
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The Second Law of Thermodynamics often is called the Law of Entropy; it helps explain where energy goes in living systems when it seems to disappear. The Law applies to systems with internal order, and says that, without energy input and usage, such as system will eventually lose its order (entropy means disorder). Life is a very ordered system, and without constant energy input would stop working. We have a huge energy source that virtually every living thing depends upon to keep the system going: the Sun. Sunlight gets converted, through photosynthesis, into the chemical energy that holds sugar molecules together; that energy is shifted into an energetic but very usable molecule, adenosine triphosphate (ATP), from which most chemical reactions in cells get a boost. Every single reaction loses some energy in its process, which "bleeds" out through the random motion of the atoms and molecules involved. This random motion is heat; temperature is a measurement of how fast the local particles are moving.
In a food chain, materials get moved through and eventually recycled by decomposers, but almost every bit of the energy gets lost as heat. This is why the chain absolutely requires the organisms on the first link to be able to capture more energy in a usable form.
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More on the Second Law.
Shakespeare and the 2nd Law (really!).
Energy Flow in Ecosystems (video).
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Chemical reactions need an energy "push" to get started. This activation energy varies from reaction to reaction: some need vary little, some need so much that they will likely never happen.
Chemical reactions fall into two broad classes based on their activation energy. Exergonic reactions (sometimes called exothermic) release enough energy during the reaction to give activation to more reacting: get them started, and they keep themselves going (lighting a piece of paper is exergonic). Endergonic reactions (or endothermic) always require energy fed into them to happen and continue to happen. Most synthesis reactions are endergonic, since the energy is being stored in bonds and not released. It is common for reactions in cells to link an exergonic reaction to an endergonic one to "feed" it energy; these are called coupled reactions. These reactions, moving energy around in a living thing, are called metabolic reactions, and all of them in a defined system (it could be an organelle, a cell, an organ, a population, an ecosystem...) are called metabolism.
Reactions often occur in long sequences. The product of the first step is the reactant for the second, and its product is the reactant for the third, and so on. These reaction sequences are called metabolic pathways. In prokaryotes, the enzymes for the pathways often have genes in sequence on the chromosome, since the reactions can take place right near where the codes are. In eukaryotes, the enzymes are made far from the codes in the nucleus, and this sequencing of genes is rare.
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A video on activation energy.
Demonstration video of the two classes of reactions.
Coupled reactions.
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Enzyme Roles in Chemical Reactions
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Enzymes, as catalysts, lower the activation energy needed to get a reaction started. That's how they get stuff to happen that would easily happen by itself.
Enzymes have spots on their molecules where they attach to the reactants (called substrates when they do this); these attachment spots are called active sites. Enzymes are not the only proteins with spots that attach to other molecules: proteins like receptors, carriers, and antibodies attach to ligands to do their jobs. Specificity is a term applied to measure how particular these attachment sites are: will they attach to just one molecule, or several similar ones?
One or more substrate molecules attach to the active site, and something happens to them there that vastly increases the likelihood that they will react: maybe a bond is stressed to the breaking point, or an electron is fed in to ionize a substrate, or two molecules are put physically where they are likely to bond together. The substrates react and change, and the products aren't built to stay in the active sites; they come loose, and the enzyme is free to grab more substrates. At the end, the reactants change but the enzymes don't. There is also a minimum time it takes for a reaction to happen on the enzyme, which means that how fast a cell can do something is limited by that time and the number of enzyme molecules it has working.
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Animation video showing activation energy and enzyme function.
Enzyme in action (video).
Simple graphic image of enzyme action.
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Many reactions that are moved along by enzymes are not processes that need to be running all of the time. For a very occasional reaction, a cell may build the enzyme, use it, then break it down and reuse the amino acids in something else. But if an enzyme is used regularly, it's better to have some way to deactivate it and then reactivate it later. This is typically done with control molecules called inhibitors.
Inhibitors can work several ways. Direct inhibitors (also called competitive inhibitors) actually attach right in the active site so that a substrate won't fit in. They don't have to be particularly like the substrate, or even fill the active site up, so long as they get in the way. Getting in the way is used by one type of indirect (noncompetitive) inhibitor: these molecules attach to the enzyme in such a way as to keep the substrate from being able to get at the active site. Another type of indirect inhibitor attaches to a regulatory site on the enzyme molecule, changing the shape of the molecule, and changing the active site shape so the substrate won't attach there. To turn the enzyme back "on," the inhibitors are taken back off. This is reversible inhibition. Irreversible inhibition sometimes happens to turn a system off permanently; this may be done when the enzyme is going to be recycled. It also is a common effect of toxins: a poison may have its effect by attaching to and changing the shape of a critical protein.
In end-product inhibition, the first enzyme in a production pathway has a regulatory site that will loosely attach to the eventual pathway product. As product builds up, it shuts down the beginning of production; as it gets used, the pathway builds more.
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More on inhibition.
Reversible direct inhibition.
Inhibition
with some variant terminology.
Shape-changiug (allosteric) inhibition.
End-product inhibition.
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Factors in Enzyme Activity
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Enzymes depend upon a particular shape to be able to do what they do. Factors that affect their shape affect their activity as well. If a protein shape unwinds to the point that the protein loses its function, it has denatured. Denaturation may be reversible or not.
Temperature is a measurement of the random motion of particles; small particles move faster as they get warmer, and big molecules shake and twist as well as moving faster. Any protein, including enzymes, will have a range of temperatures where they have a good working shape: this is called their optimal (or optimum) temperature. For enzymes, cooler-than-optimum temperature affects their shape slightly, and also changes the particle speeds, making it harder to get reactants and release products, lowering their activity. Warmer-than-optimum temperatures lead to the denaturation of the enzyme, also lowering their activity. A curve showing the relationship between temperature and enzyme activity follows a bell-like shape, peaking at the optimum. The shape of the bell has a lot to do with the evolution of the system and the conditions the system works under: you can probably tell what the optimum temperature is for most human cell reactions. Plants have curves that tend to be broad and low: activity doesn't get too high, but the enzymes stay active across a wide range of temperatures.
In the same way that there is an optimum temperature, enzymes each have an optimal pH. pH, remember, is a measure of how common H+ ions or OH- ions are in a solution; a shift will have a strong effect on the hydrogen bonds that hold a protein in its working shape. Below the optimum pH, too many H+ ions disrupt the shape; above, too many OH- ions do it.
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Denaturation.
Denaturation explained (video).
Temperature effects.
Temperature curve
for a human enzyme.
pH optimums.
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Enzymes often work with other molecules. Sometimes ions or metal atoms are used to help electrons move, or small helper molecules do a variety of helpful things. Single-atom helpers are called cofactors; small molecule helpers are called coenzymes.
Coenzymes that we can't build ourselves, that we need to get from our food in their working form, are called vitamins. Vitamins are important because they are critical contributors to our many metabolic pathways.
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How cofactors may work.
Coenzymes.
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Adenosine Triphosphate, ATP, has a core structure with a string of 3 phosphates attached. The bonds that hold the phosphates on hold a lot of energy.
Breaking off a phosphate can release energy that can be fed into cellular reactions. Also, transferring a phosphate to a reactant (phosphorylation) can destabilize the reactant and get it to react. When ATP loses a phosphate, it becomes ADP (Adenosine Diphosphate). ADP picks a phosphate back up in systems such as respiration and photosynthesis, covered in the next 2 chapters. Sometimes the end phosphate of ADP can be pulled off to fuel a reaction, leaving AMP (Adenosine Monophosphate). AMP has some form variations that are used for other purposes than energy.
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More on ATP
(video).
ADP and ATP.
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