Life is based on capturing energy released by spontaneous chemical reactions (that "want" to occur) and using this captured energy to force other chemical reactions to occur (that don't "want" to occur). Some chemical reactions "want to occur"! Which ones? Those that form stronger bonds between atoms. for example, the two O-H bonds in water (110.6 kcal/mole) are much stronger than the O=O bonds in oxygen gas (33 kcal/mole) and also stronger than H-H bonds in hydrogen gas. (104.2 kcal/mole) The energy released by burning Hydrogen ("Remember the Hindenberg!") can be calculated by subtracting the bond energies of the O=O and H-H bonds from the bond energies of the O-H bonds of H2O! 440.8 (110.6 * 4 -- Because 2 H2 + O2 -> 2 H2O; therefore 4 O-H bonds) -208.4 (104.2 * 2) - 33 ___________ 199.4 You don't need to know these details; just the ideas. In contrast, the NN triple bond in nitrogen gas is VERY strong; much stronger than the NO bonds in nitrates, which is how most explosives work! (& why the atmosphere has so much N2) Nitrogen WANTS to be a gas; (NN triple bond 226 kcal/mole!) but Oxygen and Hydrogen would "rather" be water. Bond energies are not quite all there is to it, however. Randomness tends to increase; can exert big forces, and can be exactly quantitated as entropy (which has units of energy per mole per degree of temperature, strange to say) Osmosis is an entropy effect; and other entropy effects can govern the directions of chemical reactions. Chemical reactions usually go to some kind of equilibrium; in which most of the reactants have been converted into products. Reactants <----> Products Reactants <----> Products Reactants <----> Products Reactants <----> Products Reactants <----> Products The greater the change in energy, the larger the fraction of the reactants that get converted to products. If there is zero energy difference, then the ratio will be 1:1 If the energy change is 1.4 kCal/mole, the ratio will be 1:Ten If the energy change is 2.8 kCal/mole, the ratio will be 1:Hundred A energy change of 14 kCal/mole gives a ratio 1:10,000,000,000 Energy change is more often calculated from the ratio of concentrations, than the ratio from the energy change. A harder question for any more gung-ho students: (better than the crossword puzzle; if you can calculate the answer then please tell me after class) Imagine that the ratio of concentrations of a chemical equilibrium happened to be one single molecule of reactants per every whole mole of products (gram molecular weight per liter volume); what would the energy change need to be to cause that? Hint: the # of molecules per mole is 6 times ten to the twenty third = 6 with 23 zeros after it. As a first approximation, suppose this number were one followed by 24 zeros. Chemical reactions will go to the same equilibrium state from either direction! Whether one starts with reactants or products. Two different chemical reactions will be coupled, if some mechanism will allow both reactions to occur \ ONLY if the other reaction occurs at the same time. (One change without the other is not permitted!) If the reaction AMP + Phos + Phos <--> ATP is coupled with some reaction that releases a lot of energy, this can force synthesis of ATP. If the reaction ATP <--> AMP + Phos + Phos is coupled with some reaction that absorbs energy, then the ATP's energy can force this other reaction to occur. ATP <--> ADP + Phos also occurs, but releases less energy so does ADP <--> AMP + Phos Pressure can also shift the directions of chemical reactions, toward whichever side of the equation is smaller. For example, at a thousand times atmospheric pressure NN and HH will become NH3 ammonia Because 1 N2 + 3 H3 <-> 2 NH3 (So 4 volumes of gas convert to two volumes, which is smaller.) When two amino acids form bonds to connect the amino group of one of them to the carboxylic acid group of the other, an H is released from the amino group and an OH is released from the acid group, and these form a water. A water molecule is also produced: # When two sugars form bonds in making polysaccharides # When ribose bonds to phosphate in making DNA & RNA # When purines bond to ribose, etc. # When fatty acids bond to glycerol in making phospholipids & lots of other times, too! To break these bonds, you have to split a water and give one hydrogen to one chemical and an -O-H to the other chemical. For each of these chemical separations, can you figure out which side gets the H and which side gets the OH? These separations are all examples of "hydrolysis" hydro= water; lysis=splitting. Although the bonds between H and O in water are quite strong, in all these reactions, hydrolysis is energetically favorable ("wants to occur") So cells need to put energy in, to force sugars to bond to each other, and force amino acids bond to each other etc. Human technology borrows energy from water running down hill to make electricity; and borrows energy from steam expanding to force trains to go up hills, etc. Living things borrow energy from oxidation of food chemicals, and use this energy to drive synthesis of other chemicals. (But they don't use steam or electricity) Instead they use certain chemicals that switch between high energy and low energy states, which differ in chemical bonding. The key requirement is that some energy releasing reaction is allowed to occur, but only on condition that some specific energy aborbing reaction also occurs. (This amounts to a "quid pro quo") "You can go to the movie if you clean up your room" A simple example is in the formation of chains of sugars. Glucose-Phosphate + glucose-glucose-glucose- --> (free) Phosphate + Glucose-glucose-glucose-glucose- glucose-glucose-glucose-glucose An energy absorbing reaction forming the glucose-glucose bond An energy-releasing reaction releasing the phosphate A net decrease in energy, a net increase in bond strengths Another example: Formation of RNA ATP is adenosineTriPhosphate adenine-ribose-phosphate-phosphate-phosphate ATP guanine-ribose-phosphate-phosphate-phosphate GTP cytosine-ribose-phosphate-phosphate-phosphate CTP uridine-ribose-phosphate-phosphate-phosphate UTP adenine adenine guanine cytosine ribose-phosphate-ribose-phosphate-ribose-phosphate-ribose-etc. plus two phosphates released for each link added to the chain. ATP starts with three phosphates: one of the 3 remains as a link between riboses the other two phosphates get released, which releases energy If just one phosphate were released per link, that wouldn't quite be enough energy! (it just so happens) A third example of energy coupling: When linking those glucoses to form chains, how did those phosphates get attached to the glucoses? ATP + Glucose --> Glucose-phosphate + ADP ADP is adenine-ribose-phosphate-phosphate Adnosine DiPhosphate ATP is the most important energy carrying molecule in all living things (Humans, bacteria, plants, everybody uses ATP) Sometimes GTP is also used for the same kind of purposes) Adenine-Ribose-Phosphate-Phosphate-Phosphate IT IS NOT A COINCIDENCE THAT THIS SAME CHEMICAL IS ONE OF THE 4 INGREDIENTS FOR MAKING RNA! But ATP energy is also used to drive synthesis of proteins, and many, many other chemical reactions. The energy released per ATP -> AMP + 2 Phosphates is only about 14 kilocalories per mole. Nevertheless, nearly all textbooks talk about these bonds as "high energy bonds" Actually, this is a relatively small amount of energy per bond. Unfortunately, elementary textbooks are written by (and for) people who never quite understood chemistry too well. So get used to the misunderstanding; but I wanted to teach the subject to you more or less correctly, so you won't have to unlearn it again in the future, if you go on to advanced courses. The reason for using ATP is evolutionary! Because it's the subunit for making RNA! And because cells have to have ATP anyway, to make RNA; so they also use it somewhat like money, for energy coupling of all different sorts of chemical reactions. Several other energy carrying molecules are also used: Notice that these all have chemical structures that are surprisingly similar to ATP: NAD = Nicotinamide Adenine Dinucleotide Adenine-Ribose-Phosphate-Phosphate-Ribose-Nicotinamide But this carries its energy in binding a hydrogen to the nicotinamide, NOT in the phosphates NADP = Nicotinamide Adenine Dinucleotide Phosphate Adenine-Ribose-Phosphate-Phosphate-Ribose-Nicotinamide Phosphate FAD = Flavine Adenine Dinucleotide Adenine-Ribose-Phosphate-Phosphate-Ribose-Flavine But this carries its energy in binding hydrogens to the flavine NOT in the phosphates AcetylCoEnzymeA Adenine-Ribose-Phos-Phos-Serine-Some other stuff- Acetic acid Questions that you should now be able to answer: 1) In a chemical reaction, are bonds between atoms broken? Or are new bonds formed? Or neither? Or both? Explain? 2) In general, in chemical reactions, do bonds change strengths, or do stronger bonds get replaced by weaker bonds? Or what? 3) If you knew all the bond energies in a set of reacting chemicals, both before and after the reaction, how could you calculate the amount of energy released or absorbed? 4) In what sort of units (pounds per square inch? furlongs per fortnight?) are bond energies measured? What per what? 5) What four letter word starting with M refers to the standard number of molecules of a substance, equal to the number of atoms in a gram of hydrogen, or in 12 grams of carbon, which happens to be a tiny bit more than 6 with 23 zeros after it? 6) Entropy is a chemical measure of what sort of variation? 7) If the products of a chemical reaction have more entropy than the reactants did (before the reaction), then how does this increase in entropy influence the reaction? (if at all) 8) In chemical reactions, does absolutely every last one of the reactant molecules get converted into product, or only a certain fraction of them, or what? 9) How is amount of energy released by a reaction related to this fractional amount that remain as reactants (not changed to product)? 10) If the difference in energy between products and reactants happened to be 1.4 kilocalories per mole, then what could you predict about the ratios of concentrations of products to reactants at equilibrium? *11) Would this ratio (at equilibrium) depend on whether you started with all products, with half and half, or with all reactants? *12) Suppose that the ratio of concentrations at equilibrium were one to one (equal concentrations) what would that tell you about the zero difference in energy between the products and reactants? **13) Diluting a chemical ten fold represents how large of an increase in entropy? (guess!) **14) Lowering the activation energy barrier to a reaction by 1.4 kilocalories per mole would speed the reaction up by how much? (guess!) 15) Suppose that the products of a reaction have a smaller volume than the reactants did before the reaction (= there is a volume decrease in the reaction), then how will the equilibrium ratio of concentrations be changed by increasing the pressure (such as in the deep ocean)? 16) If a given chemical (like water) expands when it freezes, then does that tell you anything about whether the frozen form will float or sink in the liquid form? *17) Does it tell you anything about whether the freezing point will change at high pressures? 18) In the polymerization of glucose to form starch or cellulose, is there a net increase or decrease in bond energies? 19) What provides the energy to force this reaction to occur? 20) Are any phosphates attached, and then detached, from the glucose molecules? 21) Where do these phosphates come from? 22) What provides the energy that makes them form bonds to the glucose molecules? 23) When cells make RNA, what 4 substances do they make it out of? (3 letter intials are OK here) 24) Suppose that the base sequence of a particular RNA happened to be AAAAAAAetc., then what would this be made out of? 25) Using the words "phosphate", "adenine" and "ribose", and drawing lines to connect them, draw the structure of a short length of this AAA... RNA. 26) Compare the source of the energy in the synthesis of RNA as compared with the source of energy in the synthesis of cellulose. 27) For what two kinds of purposes do cells use ATP? 28) What are the two different kinds of ways in which cells supply the energy for making ATP from AMP and phosphate? 29) Why do mitochondria (and also chloroplasts; and also procaryotes, and archaea) need to be closed membrane sacks in order to make ATP from AMP and phosphate? **30) Healthy cells keep their cytoplasmic concentration of ATP about a hundred times larger than the concentrations of AMP and phosphate; figure out why this increases the energy provided by 2.8 kilocalories per mole (relative to the energy available if the ratios of concentrations were one to one)! 31) Why would you expect changes in the acidity of the cytoplasm around mitochondria when they are making lots of ATP? 32) Besides ATP, what other some other molecules that cells use to transfer energy? (their initials are sufficient) 33) Do these transfer this energy by forming and breaking bonds to phosphates? 34) Do these other chemicals even contain any phosphates? 35) The ratios of energy per molecule of these other chemicals are about what fraction or multiple of that of ATP? *36) Given that the amount of energy needed to make ATP from AMP and phosphate is about 12 to 14 kilocalories per mole, is it somewhat misguided to call the bonds "high energy bonds"? (Is what is special about them their amount of bond energy? Is this bond energy especially large, or rather small?) 37) Is ATP more like fuel, or more like money? In which ways is it like each? 38) In biochemical reactions where hydrogens are forced to become part of some chemical, what usually provides this energy? *38) It is now widely believed that the first life consisted entirely or mostly of RNA: discuss whether the structures of ATP and the other energy coupling molecules make sense in terms of that origin of life. 39) What is meant by hydrolysis? **40) "Heavy water" is D2O, in which deuterium, the heavy isotope of hydrogen, is bound to water instead of hydrogen. Heavy water is somewhat poisonous to living things. Can you figure out why?

 

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