BIOL275 Exam 3|Graded A+

BIOL275 Exam 3|Graded A+ Highly exothermic redox reactions lead to high levels of released energy. This wouldn't be compatible with life if too much energy is released at once, because this would be wasteful and potentially damaging to the cell. If the cartoon above represents a molecular reaction taking place between common biological molecules in a living cell, why would we expect that the change in energy level of electrons would NOT be highly exothermic? Living functions in the cell depend on the ability to assemble and disassemble biological molecules. Metastable means the molecule can stay intact indefinitely by itself, but can be broken down by reactions with other molecules. Life would not work if it depended on molecules that fell apart by themselves (unstable) or could not be broken down in chemical reactions (overly stable). Why is it significant that life evolved to use biological molecules that are metastable? What is the meaning of that word? Contrast this to what would happen if cells depended on molecules that are unstable or overly stable. (Hint: think of the ball on the hill). Each step between molecules in the picture represents a redox reaction where electrons have rearranged to form lower energy bonds compared to the previous arrangement. Therefore energy is being released at each step, and the resulting new molecule represents a lower energy molecule than the one before it. Why is there "Diminishing availability of energy" as you go from a more reduced state to a more oxidized state in the above figure? The 686 kcal / mol is how much energy is represented by a mol of glucose. On the left side the glucose is being broken down to release the energy, and thus it is a negative change in G, whereas on the right side the energy of the sun is used to assemble the CO2 and H20 into a glucose molecule, and therefore it is (+) delta G. Explain where the 686 kcal / mol of energy comes from on the left and right sides of the above figure, and what is meant by one side being ( - ) delta G and the other side ( + ) delta G. The generation of heat is a byproduct of energy released in chemical reactions, and is therefore not a direct purpose of breaking chemical bonds. Of the six different categories of energy functions in a living cell that we discussed in lecture, which one is not considered a direct use of energy, but rather a very important byproduct? Because biological molecules are metastable, that means their chemical bonds won't simply break on their own and must require the input of some energy to disrupt them. That amount of energy is represented by the transition state. A molecular catalyst would lower the height of the transition state (lower the energy of activation) thereby making the reaction proceed faster because less energy is required to initiate it. The above figure depicts the change in G going from ATP to ADP. Explain why in any biochemical reaction there is a "hump" or Transition State involved? How does the presence of a molecular catalyst impact the shape of this curve? (Hint: think again about biological molecules being metastable) Catalase enzyme binds to iron and to hydrogen peroxide, thereby bringing the two together. The association of iron with the peroxide greatly encourages the bonds of the peroxide to break, so the presence of the catalase speeds up the reaction dramatically. Our cells need to catalyze this reaction because peroxide is damaging to the cell, so the cell cannot afford to wait for the peroxide to fall apart on its own. Explain how the presence of a catalase enzyme speeds up the dissociation of hydrogen peroxide in our cells? Why do our cells need an enzyme like this rather than letting peroxide break down by itself? (Hint: for full credit mention the role of iron and what that has to do with the catalytic reaction) Although the red regions are far apart in the linear polypeptide chain, once the protein folds up into its normal tertiary structure these regions are brought together to form the 3D active site of the protein. The R group side chains of the specific amino acids labeled above are the ones that are most important for the proper shape of the active site where a substrate will fit. If the active site is not shaped correctly, the enzyme may not bind substrate. The polypeptide chain shown above is that of an enzyme (like the catalase discussed in Question 7). Explain how in the functional enzyme the five different red sites could be involved in binding one single substrate molecule if they are so far apart in the peptide chain? Why do you think the amino acids that are identified by name are the most critical ones that MUST be correct in the sequence in order for the enzyme to work? The big brown blob is actually a polypeptide chain that is folded up into a specific 3D shape determined by all of the amino acid side chains finding energetically favorable positions. If there is a disruption to one side of the protein, there is a ripple effect throughout the protein as the side chains shift around to find a new low energy position. Thus the ability of the substrate binding site to assume the correct shape will change depending on whether an allosteric activator or inhibitor binds the enzyme. The above image depicts allosteric activation and inhibition of an enzyme. Explain how the binding of the little square activator molecule or little triangular inhibitor molecule results in a change in the substrate binding site of the protein? (Hint: the cartoon shows the protein as a big brown blob, but what is it really, and how could something interacting on one side of the blob cause the other side to change?) In the equation E = enzyme, S = substrate, ES = the intermediate transition state, and P = product(s). The reason the arrows go in both directions is that in this case the enzyme can catalyze both the breaking OR assembly of the bonds between the molecular components (in other words, in reverse the products can be considered the substrates that get joined together). The above image depicts a biological chemical reaction that is catalyzed by an enzyme. Explain what "E", "S", "ES", and "P" stand for, and why the three steps of the equation are written this way. Why do the arrows point in both directions? Glucose is the raw fuel for cells but that energy must be converted into a form that the cell's many biochemical pathways are designed to use. That is why the energy of glucose must be converted into ATP molecules so that proteins and other biological molecules can use it. If glucose is the primary fuel source for cells, why do we need ATP? Why can't the cell's energy-requiring pathways simply "plug in" to glucose directly? NAD+ is an electron acceptor/ carrier. Enzymes make use of these to hold the (e-) that are being transferred. If the enzyme was itself reduced, then you'd need another enzyme to remove the electrons from the first one, and that would not be practical. What is the function of a co-enzyme such as NAD+? Why would it not be practical to expect an enzyme to handle the function NAD+ itself? Life on Earth evolved under anaerobic conditions (little atmospheric oxygen) so ancient microbes evolved glycolysis as a way to get ATP from glucose without the need for oxygen. Only later once Earth's atmosphere began to fill with oxygen as a waste product did it become feasible to depend on oxygen for aerobic respiration. So aerobic respiration was added on to the glycolysis. If the complete biological oxidation of glucose requires O2 as the key reagent (aerobic), why do cells from all living things use glycolysis (anaerobic) as the first process of glucose catabolism? NAD+ is the electron receptor/carrier in glycolysis, where it is reduced to NADH. The NADH is oxidized during fermentation to restore NAD+ so that glycolysis can continue. Glycolysis represents only very limited oxidation of glucose into pyruvate, and may be followed up by fermentation involving reduction of pyruvate, not further oxidation. Explain how one molecule of NAD+ plays important roles in both parts of the these reactions, specifically mentioning how it is involved in both oxidation and reduction. These enzymes catalyze reactions in either direction. Therefore the original naming as dehydrogenases is correct, since they can oxidize lactate or ethanol back to fermentation intermediates. The enzymes involved in the reduction of pyruvate to lactate or ethanol using electrons from NADH have names such as lactate dehydrogenase and alcohol dehydrogenase. Those names suggest removal of hydrogen from a substrate…which would be oxidation, wouldn’t it? Are these enzymes named incorrectly? Why are they named this way? The pyruvate our cells generate from glycolysis is fed into the aerobic respiration pathways, namely conversion to acetyl-co A for entry into the citric acid cycle. When anaerobic fermentation is used, this results in the lactate pathway, not alcohol pathway. Humans most certainly have the alcohol dehydrogenase gene that codes for the enzyme ADH. Our cells make pyruvate from glycolysis, so why don’t we end up making ethanol in our body’s tissues? In phase I of glycolysis, inorganic phosphate is added to the glucose monomer (glycogen or starch) by a phosphorylase enzyme, making glucose-1-phosphate, so although it may seem like it can bypass the need for an ATP, an ATP is still being used to break the glucose monomer from the glycogen. Therefore, 3 ATP is still used in glycolysis if you start with either glycogen or starch.