Biology 111B

Study Questions 5

METABOLISM

RESPIRATION AND FERMENTATION

1. What do the following terms mean?

oxidation - the loss of electrons from a compound

reduction - the gain of electrons by a compound

oxidizing agent - a compound that pulls electrons away from another compound (oxidizing that other compound and becoming reduced itself).

reducing agent - a compound that gives electrons away to another compound (reducing that other compound and becoming oxidized itself).

2. What is the summary reaction for cellular respiration?

C₆H₁₂O₆ + 6O₂ ---> 6CO₂ + 6H₂O

3. What is the "goal" or purpose of cellular respiration?

To convert the chemical energy in glucose into ATP, the energy currency of the cell

4. What are the main reactions of cellular respiration? Where in the cell does each take place?

1. Glycolysis takes place in the cytosol
2. Pyruvate oxidation takes place at the inner mitochondrial membrane
3. The Krebs cycle takes place in the mitochondrial matrix (inside the inner membrane)
4. The electron transport chain takes place along the mitochondrial inner membrane and uses the inter-membrane space

5. What are the functions of NAD⁺ and FAD?

These two compounds are electron carriers. In the forms shown, they can pick up electrons during glycolysis, pyruvate oxidation, and the Krebs cycle to become NADH and FADH₂.

6. At what stage is oxygen used? What happens if oxygen is not available? What are the relative yields of ATP in the presence and absence of oxygen?

Oxygen is not used until the electron transport chain. If oxygen is not available, then only glycolysis (of the four aerobic respiration components) functions. To regenerate the NAD⁺ necessary to continue glycolysis, pyruvate gets reduced to form lactic acid or ethanol.

7. What is chemiosmosis? Why is it important? What membrane acts in this process, and how does it function?

Chemiosmosis is the name given to the coupling of ATP synthesis with the flow of electrons down the electron transport chain to oxygen, through the intermediate step of building a H⁺ ion concentration in the intermembrane space and using that potential energy to drive the ATP synthesis. This oxidative phosphorylation mechanism is what produces most of the ATP generated in aerobic respiration (32 of 36 ATPs per glucose). The important membrane is the mitochondrial inner membrane.

8. What are the possible products of fermentation? Why does a cell make these products? How much ATP does a cell make by fermentation?

Fermentation results in pyruvate being reduced to either ethanol or lactic acid. This reduction is necessary to regenerate the NAD⁺ used in glycolysis. If the NAD⁺ were not regenerated, even the measly 2 ATPs per glucose that glycolysis produces would not be available to the cell and the cell would die.

9. Which of the following is in its reduced state? CIRCLE ALL CORRECT ANSWERS

a. NAD⁺

b. FAD

c. molecular oxygen (0₂)

d. oxygen in water

e. carbons in carbon dioxide

 

10. When molecules are broken apart in respiration. CIRCLE ALL CORRECT ANSWERS

a. the heat produced is used to drive biological reactions.

b. the oxygen in the compounds broken apart is used an as energy source.

c. the energy released in respiration is channeled into molecules of ATP.

d. NADH is reduced to form NAD⁺.

e. CO₂ is released as a waste product.

11. Which molecules do each of the following parts of cellular respiration PRODUCE?

glycolysis __B, C____	A. O2
fermentation ______D________	B. NADH
Krebs cycle ______B, C_______	C. ATP
respiratory electron transport ____C, D________	D. NAD+

12. Pyruvate is the last product of glycolysis. Which statement(s) below are true?

a. There is more energy in 6 molecules of CO₂ than in 2 molecules of pyruvate.

b. There is more energy in pyruvate than in lactic acid.

c. There is more energy in 1 molecule of glucose than in 2 molecules of pyruvate

d. There is more energy in 1 NADH than in 1 ATP

13. What is the correct sequence of the following compounds, in order, from the one that contains the most energy to the one that contains the least energy?

a. NADH -> ATP -> glucose -> pyruvate -> lactic acid

b. ATP -> NADH -> pyruvate -> lactic acid -> glucose

c. glucose -> pyruvate -> lactic acid -> NADH -> ATP

d. glucose -> lactic acid -> pyruvate -> NADH -> ATP

e. pyruvate -> glucose -> lactic acid -> ATP -> NADH

14. The transformation of pyruvate to ethanol doesn't provide a yeast cell with any energy. One reason that cells do the reaction is to get rid of pyruvate that would be toxic in high concentrations. But yeast cells would have to carry out the formation of ethanol even if pyruvate were harmless. Why?

a. because the cell needs ethanol to survive

b. because the cell needs NAD⁺ to continue to do glycolysis

c. because the cell needs NADH to continue to do glycolysis

d. because the cell needs O₂ to survive

e. because people need ethanol to make beer and wine

 

15. Why can prokaryotes extract about 38 ATPs from a molecule of glucose, whereas most eukaryotic cells can extract only about 36 ATPs?

Prokaryotes can extract 38 ATPs per molecule of glucose because the NADH formed in glycolysis can directly enter the electron transport chain instead of having to pass its electrons to another carrier (FADH₂), losing energy in the process, to get them across the mitochondrial membrane.

 16. DNP (dinitrophenol) is a metabolic poison that makes membranes leaky to hydrogen ions. Symptoms of DNP poisoning include lack of energy, weight loss, and excessive sweating. Why does DNP cause these symptoms?

Because DNP makes the inner mitochondrial membrane leaky to H+ ions, the H+ concentration built up in the intermembrane space that normally makes ATP by flowing back through ATP synthase is free to move back to the mitochondrial matrix anywhere. This means that the potential energy formerly held by the H+ gradient is released without making ATP. This inability to make ATP resulted in the lack of energy. As the body tried unsuccessfully to make more ATP, glycolysis and the Krebs cycle sped up, using more and more stored fuel (fat) which results in weight loss. Finally, the energy not captured by ATP is released as heat, making the poisoned individual very hot and causing sweating to cool the body.

17. Yeast can carry out metabolism of glucose either in the presence of O₂ or in the absence of O₂. However, in the absence of O₂, yeast use glucose at a much faster rate than in the presence of O₂. Explain this observation.

The yeast cells require a given number of ATPs per time unit to carry out their activities; let's imagine that number is 100 per minute. If those ATPs are supplied through aerobic respiration, then each glucose supplies 36 ATPs. To supply 100 ATPs per minute, then roughly 3 glucose molecules need to be sent through aerobic respiration per minute. But if those ATPs are supplied through anaerobic respiration, then each glucose supplies only 2 ATPs, and roughly 50 glucose molecules need to be sent through anaerobic respiration per minute...a much higher rate of glucose use.

18. White snakeroot is a toxic plant sometimes consumed by dairy cattle. The cattle concentrate the toxin in their milk and can pass it along to humans, sometimes with fatal consequences. The symptoms of poisoning are intensified by vigorous exercise. Knowing that the toxin interferes with the conversion of lactic acid to pyruvate in the liver, how can you explain the effect of exercise?

Since white snakeroot toxin interferes with the conversion of lactic acid to pyruvate in the liver, anything that increases the amount of lactic acid the liver has to process is going to make the symptoms worse. Vigorous exercise is likely to be anaerobic--using oxygen faster than the bloodstream can deliver it, resulting in temporary anaerobic conditions in the muscle cells and a build-up of lactic acid that gets transported to the liver to be converted back to pyruvate. This increase in lactic acid intensifies the problem.

19. Normally, a solution of isolated mitochondria only make ATP when supplied with pyruvate. However, isolated mitochondria will also make ATP if they are placed in an acid solution. Why? What does this phenomenon tell you about the mitochondrial outer membrane?

An acid solution has a high concentration of H⁺ ions. These start out outside the mitochondria, but since they cause ATP to be produced, they must be moving through the ATP synthase and supplying energy to phosphorylate ADP to ATP. The H⁺ concentration gradient is being supplied artificially rather than being generated by the electron transport chain. This phenomenon could only take place if the outer mitochondrial membrane allowed those H⁺ ions to pass through so that they could reach the ATP synthase located in the inner mitochondrial membrane.

 

PHOTOSYNTHESIS

20. What is the summary reaction for photosynthesis?

6 CO₂ +12 H₂O (+18 ATP + 12 NADPH) -----> Glucose (C₆H₁₂O₆) + 6 O₂ + 6 H₂O

21. What is the "goal" or purpose of photosynthesis?

To capture light energy as chemical energy (trapped in the non-polar bonds) in glucose.

22. What are the main reactions of photosynthesis? Where in the cell does each take place? What is the "goal" or purpose of each?

Photosynthesis consists of the light (-dependent) reactions, which capture light energy and convert it to chemical energy in the forms of ATP and NADPH, and the Calvin cycle (or light-independent reactions), which use the unstable ATP and NADPH to make the much more stable glucose molecule. The light reactions take place in the thylakoid membranes; the Calvin cycle takes place in the chloroplast stroma.

23. What is the green photosynthetic pigment? Why is it green in color? How does it "capture" light?

Chlorophyll is the green photosynthetic pigment. It is green because it reflects/transmits (= does not absorb) green wavelengths (it absorbs red and blue wavelengths). Chlorophyll captures light energy when light excites an electron to a higher orbital. That electron can now be taken by an electron acceptor and used to either form ATP via an electron transport chain (chemiosmosis) or be used as one of a pair of electrons to reduce NADP⁺ to NADPH.

24. What is rubisco and what function does it carry out?

Rubisco (ribulose bisphosphate carboxylase/oxidase) is the enzyme that grabs CO₂ out of the internal leaf atmosphere and attaches it to RuBP (ribulose bisphosphate) to start the Calvin cycle.

25. What is the problem rubisco has when oxygen concentrations get too high? Why do dry conditions cause oxygen concentrations to build up? Why do hot conditions cause oxygen concentrations to build up? Why (evolutionarily) does rubisco have this problem?

Under high oxygen concentrations, rubisco will pick up O₂ rather than CO₂, attach the O₂ to RuBP, causing the resulting 5C compound to split into a 3C and 2C. The 2C compound gets exported out of the chloroplast and broken down to CO₂ without harvesting any of the energy available. This waste of energy is known as photorespiration and can reduce photosynthetic efficiency by as much as 50%.

Dry conditions cause O₂ to build up because the plant has to close its stomates to conserve water. With the stomates closed and photosynthesis continuing, CO₂ concentrations go down and O₂ concentrations go up.

Hot conditions are a little more subtle in how they create high O₂ conditions. As temperature increases, metabolic processes speed up, but photosynthesis speeds up more than does respiration (at least up to a point). This means that the production of O₂ via photosynthesis goes a lot faster (instead of just somewhat faster) then the production of CO₂ via respiration. This increases the concentration of O₂ in the internal leaf atmosphere, creating conditions that increase photorespiration.

The fact that rubisco has this sensitivity to O₂ concentration suggests that it is a very old enzyme, probably pre-dating the build-up of O₂ in our atmosphere due to photosynthesis.

26. What solution have tropical plants evolved to deal with rubisco's problem under hot conditions? What solution have desert plants evolved to deal with ribisco's problem under dry conditions?

Tropical plants use C4 photosynthesis to reduce photorespiration. This pathway is used in conjunction with the Calvin cycle and functions to isolate rubisco from the high O₂ concentrations to which it is sensitive. C4 plants separate their photosynthetic cells into two cell types: typical mesophyll cells and cells that surround the vascular bundles--"bundle sheath" cells. The bundle sheath cells are also isolated from the internal leaf spaces that have high O₂ buildup. With this separation from the internal leaf spaces, however, the Calvin cycle is also isolated from its CO₂ supply, which is the raw material of the Calvin cycle. Therefore, the typical mesophyll cells pick up CO₂ from the internal leaf atmosphere using a more recently evolved enzyme, PEP carboxylase, that will not pick up O₂ regardless of O₂ concentrations. The CO₂ is first attached to PEP, a 3C compound, to form a 4C compound (hence the name of the pathway), then this 4C compound is shuttled over to the bundle sheath cells where the CO₂ is released and picked up by Rubisco to use in the Calvin cycle. In releasing the CO₂ from the 4C compound, the PEP is regenerated and cycles back to the mesophyll cells to be carboxylated again. This shuttle system keeps the CO₂ concentration high around rubisco and drastically reduces photorespiration.

Desert plants use CAM photosynthesis to simultaneously reduce water loss and photorespiration, although the major problem is probably water loss. In CAM plants, the stomates are closed during the day when high temperatures would cause excessive water loss, and open at night when temperatures are cooler. This reduces water loss, but presents the problem that light energy that produces ATP and NADPH is available at one time (and these compounds aren't very stable) and CO₂ is available at a different time. The solution for CAM plants is to store CO₂ during the night, and run the Calvin cycle during the day when the light energy is available. However, because diffusion of CO₂ into the stomates depends on maintaining a higher concentration of CO₂ outside than inside, the internal CO₂ is picked up and attached to an organic molecule to keep its concentration low in the internal leaf atmosphere. Then in the day, when the stomates are closed, the organic molecules release the stored CO₂ for use in the Calvin cycle. Therefore, whereas C4 plants separate the fixation of CO2 from the Calvin cycle in space, CAM plants separate the fixation of CO₂ from the Calvin cycle in time.

28. A solution of isolated chlorophyll molecules fluoresces (glows red) when illuminated. A solution of isolated chloroplasts fluoresces when illuminated only if all CO₂ is removed from the atmosphere in the flask. Explain why the chloroplast solution fluoresces only in the absence of CO₂.

The fluorescence is caused by the excited electrons falling back to their ground state because they were not captured by an electron acceptor. Isolated chlorophyll molecules have no electron acceptors around (they're isolated!). Isolated chloroplasts, on the other hand, have all their membranes intact and all the electron acceptors in place. So when illuminated, these chlorophyll molecules have their acceptors ready to take electrons...unless they're already full of electrons. The electron acceptors normally give their electrons to NADP⁺ (reducing it to NADPH), which uses the electrons to reduce CO₂ to glucose. So CO₂ is really the final acceptor of chlororphyll electrons excited by light and captured by electron acceptors. If CO₂ is removed, all the electron acceptors end up full of electrons and can't take any more. So the chlorophyll electrons now excited by light have nowhere to go but fall back down to the ground state, emitting red light (= fluorescence) as they fall.

29. The rate of the light-dependent reactions can be determined by measuring the rate of O₂ formation by a solution of isolated chloroplasts. Adding bicarbonate, a source for dissolved CO₂, increases the rate at which the light-dependent reactions proceed. If CO₂ is used in the Calvin cycle and O₂ is produced in the light-dependent reactions, why should adding CO₂ increase the rate of O₂ production?

As we saw in the last question, the two sets of reactions are linked by the energy shuttles ATP and NADPH. Anything that speeds up the reduction of CO₂ will make more NADPH available to pick up electrons from the light reactions. So increasing the CO₂ supply allows the electron carrier NADP⁺ to be recycled more quickly and, therefore, speeds up the light reactions. Speeding the light reactions means O₂ will be generated at a faster rate.

30. If the stroma of a chloroplast could experimentally be made more acidic than it naturally is, would more or less ATP be formed? Why?

ATP is formed by H⁺ flowing through ATP synthase from the thylakoid interior into the stroma. The flow of H⁺ ions is generated by diffusion--there is a higher concentration of H⁺ inside the thylakoid than in the stroma. If the stroma of a chloroplast were made more acidic than it normally is, that would reduce the difference in H⁺ concentration between the thylakoid interior and the stroma and reduce the rate of ATP formation.

 

Now that you've reviewed photosynthesis, go on to the metabolism questions that integrate/compare/constrast respiration, fermentation, and photosynthesis.

 

METABOLISM (Respiration, photosynthesis, fermentation ...)

31. In the blank next to each process, write an R if it occurs in respiration and/or a P if it occurs in photosynthesis. Write an N if the process occurs in neither respiration nor photosynthesis.

_R/P_ Chemiosmotic synthesis of ATP	_R/P_ Reduction of electron carriers
_R_ Reduction of oxygen	_P_ Oxidation of water
_P_ Reduction of CO2	_R_ Oxidation of glucose

32. Which of the following descriptions on the left match with the terms on the right? Be as specific as possible.

_M_ 3C compound product of glycolysis	A. ATP
_D_ site of glycolysis in eukaryotes	B. ADP
_I_ site of NADH oxidation	C. H2O
_F_ compound that initially oxidizes glucose	D. cytosol
_I_ site of O2 use	E. thylakoid membrane
_E_ site of O2 formation	F. NAD+
_C_ compound oxidized by chlorophyll	G. NADH
_H_ site of [H+] build-up in photosynthesis	H. interior of thylakoid
_L_ sites of glucose synthesis	I. mitochondrial electron transport chain
	J. Krebs cycle
	K. intermembrane space
	L. stroma
	M. pyruvate
	N. NADP+

33. Why does a photosynthetic plant first make glucose and then break it down in cellular respiration? Why not just use ATP directly?

The separation of glucose synthesis and breakdown allow the plant to store its energy in a much more stable and compact form than ATP. ATP is relatively unstable...it would stay around for only a few hours (at most) before breaking down, whereas glucose is very stable. In addition, to store sufficient energy as ATP to get the plant through the night (when ATP can't be generated), the plant would have to have about 10-20% of its body weight equivalent of ATP stored (assuming no spontaneous losses). The problem would be even worse for a mammal...to supply all of our energy needs for a day using only ATP, we'd have to have about the equivalent of our body weight in ATP available (again assuming no losses).

34. If a plant is growing, which reaction is going faster, photosynthesis or respiration?

If a plant is growing, it must mean that photosynthesis is making glucose faster than respiration is breaking it down. To have the energy to build new cells and supply more and more cells, photosynthesis has to go on faster than respiration. In addition, recall that plant cell walls are made of cellulose (a polymer of glucose), so glucose is used as a building material as well as an energy source.