PART I: MULTIPLE CHOICE (50 points)
Circle the letter next to the single best answer. Two points per question.
1. The main reason for producing fermentation products is to:
a) neutralize acid in the medium
b) protect against oxygen
c) generate ATP
d) recycle reduced NADH
e) none of the above
2. Yeast fermentation differs from E. coli as follows:
a) yeast produces formate instead of carbon dioxide
b) yeast produces lactic acid under acidic conditions
c) yeast converts pyruvate directly to acetaldehyde
d) yeast converts pyruvate directly to acetyl phosphate
e) yeast uses reduced NADPH instead of NADH
3. Glycolysis results in the net production, per original hexose of:
a) 2ATP + 2NADH
b) 4ATP + 2NADH
c) 2ATP + NADH
d) 4ATP + NADH
e) 2ATP + 2FADH2
4. Oxygen toxicity is largely due to:
a) peroxide ions destroying enzymes
b) superoxide ions attacking RNA
c) oxygen molecules oxidizing -SH groups
d) superoxide ions destroying the lipid bilayer
e) hydrogen peroxide degrading cytochromes
5. The hexose monophosphate (gluconate) pathway is used for the production of
a) ATP
b) NADPH
c) NADH
d) acetyl-CoA
e) none of the above
6. Phosphoenol pyruvate is a high energy compound because of:
a) being an acid anhydride not a phosphate ester
b) being held in an unfavorable conformation by the phosphate
c) competing resonance
d) repulsion due to negative charges
7. The glyoxylate cycle is used for generating:
a) precursors for synthesis of lipopolysaccharides
b) precursors for synthesis of aromatic amino acids
c) NADPH
d) 4-carbon intermediates when cells grow on acetate
e) 4-carbon intermediates during growth on hexoses
8. Flavin cofactors:
a) Carry two electrons
b) Carry two hydrogen atoms
c) Carry one electron
d) Carry one hydrogen atom
9. The most important factor in protection against oxygen toxicity is:
a) superoxide dismutase
b) peroxide dismutase
c) catalase
d) peroxide degradation by flavoproteins
e) carotenoids trapping hydroxyl radicals
10. Pyruvate dehydrogenase is regulated by:
a) repression by phosphoenolpyruvate
b) induction by pyruvate
c) activation by oxaloacetate
d) inhibition by high levels of succinyl-CoA
e) inhibition by high levels of glyoxylate
11. The correct equation for the reduction of nicotinamide adenine dinucleotide phosphate is:
a) NADP+ + 2H+ = NADPH+ + H+
b) NADP + H+ + [H] = NADPH2
c) NADP+ + 2[H] = NADPH + H+
d) NADP + 2[H+] + 2e- = NADPH2
e) None of the above is correct
12. TMAO reductase and nitrate reductase both require:
a) Fnr protein for induction
b) Cyclic AMP and Crp protein for induction
c) Manganese and FeS groups for activity
d) Presence of formate for induction
e) NarL protein for induction
13. Formate dehydrogenase:
a) converts formate to water and carbon dioxide
b) only works if nitrate reductase is present
c) contains selenium and nickel
d) contains molybdenum and copper
e) none of the above is true
14. The two enzymatic subunits of NADH-Dehydrogenase contain:
a) Heme and a manganese atom
b) Molybdenum and selenium
c) Iron-sulfur groups and a flavin cofactor
d) A copper atom and iron-sulfur groups
e) None of the above is true
15. During its photochemical cycle the light absorbing pigment of Halobacteria:
a) Transfers protons into the cytoplasm
b) Alternates between a free and a protein bound form
c) Alternates between cis and trans isomers
d) All of the above
16. Cytochrome oxidases generally differ from other cytochromes as follows:
a) Their heme ring contains cobalt instead of iron
b) They are only found in mitochondria
c) They contain iron plus copper
d) The iron atom alternates between 2+ and 4+
e) None of the above
17. Uncouplers
a) Carry sodium ions across membranes
b) Inhibit the electron transport chain
c) Hydrolyse high energy phosphates
d) Carry protons across membranes
e) Inhibit the ATP synthase reaction
18. The correct order of a typical respiratory chain is:
a) UQ >> cyt a >> cyt b >> cyt c >> oxygen
b) UQ >> cyt b >> cyt c >> cyt a >> oxygen
c) UQ >> cyt c >> cyt b >> cyt a >> oxygen
d) UQ >> cyt c >> cyt a >> cyt b >> oxygen
e) UQ >> cyt b >> cyt a >> cyt c >> oxygen
19. Release of oxygen during photosynthesis by cyanobacteria or chloroplasts is due to:
a) Ferredoxin and plastocyanin
b) Cytochrome oxidase working in reverse
c) NADPH dehydrogenase working in reverse
d) Molybdenum containing enzyme and protein D
e) None of the above
20. The photosynthetic antenna contains:
a) Pheophytin and retinaldehyde
b) Chlorophyll a and carotenoids
c) Chlorophyll b and pheophytin
d) Bacteriorhodopsin and plastoquinone
e) Retinaldehyde and chlorophyll a
21. The electron transport chain of purple bacteria contains:
a) Menaquinone and cytochrome f
b) Plastocyanin and cytochrome b
c) Plastoquinone and cytochrome f
d) Bacterio-pheophytin and cytochrome b
e) Ferredoxin and ubiquinone
22. During methane synthesis reducing equivalents are transferred from hydrogen gas by:
a) F420
b) HTP-SH (component B)
c) Coenzyme M
d) Ferredoxin
e) Tetrahydromethanopterin
23. Halobacteria use light energy to:
a) Pump protons into the cytoplasm
b) Pump chloride ions into the cytoplasm
c) Generate reduced NADPH
d) Generate reduced NADH
e) Generate reduced ferredoxin
24. In Archebacterial membranes, an ether linkage connects glycerol to:
a) The phosphate of phospholipids
b) Fatty acids which are longer than in other bacteria
c) Isoprenoid hydrocarbon chains
d) Negatively charged sugar derivatives
e) Lipoproteins in the cell wall
25. Iron sulfur proteins function by:
a) Acting as electron carriers
b) Acting as proton transporters
c) Protecting cells against oxygen toxicity
d) Helping to bind oxygen in cytochrome oxidase
e) They are involved in all of the above
PART II: SHORT ANSWER QUESTIONS (30 points)
26. (10 points) Choose any 3-carbon intermediate in the glycolytic pathway or any 4, 5, or 6-carbon intermediate of the Krebs cycle. So we have:
1) X is converted to your chosen intermediate by enzyme A
2) Your chosen intermediate is converted to Y by enzyme B
a) Name the enzyme which makes this compound (enzyme A)
b) Name the enzyme which consumes this compound (enzyme B)
c) Give the full name of your chosen compound (no abbreviations)
d) Draw the complete chemical structure of your chosen intermediate:
27. (10 points) For any FIVE of the following metals give one example of a cofactor or enzyme or other biological molecule which contains it and indicate which pathway this belongs to (e.g. glycolysis or respiratory chain or methane synthesis etc).
a) Magnesium:
b) Manganese:
c) Molybdenum:
d) Copper:
e) Iron:
f) Cobalt:
g) Nickel:
28. (10 points) Choose any FIVE of the following inhibitors or poisons and briefly describe how they work. (One example is enough for each inhibitor.)
a) Arsenite:
b) Oligomycin:
c) Tungstate:
d) Fluoroacetate:
e) Chlorate:
f) Valinomycin:
g) DCCD:
PART III ESSAY QUESTION Choose any ONE question (20 points)
29. Describe with diagrams how methane producing bacteria generate the proton motive force. Where do they get their supply of hydrogen from under natural conditions?
30. Describe Mitchells zig-zag scheme to show how the electron transport chain generates the proton motive force. Explain in outline one way to measure the charge gradient across the membrane.
31. Explain how E. coli adapts to use the following alternative electron acceptors for respiration. Include the regulatory systems which are involved as well as the respiratory pathways. a) high oxygen, b) low oxygen, c) nitrate, d) TMAO
32. Explain what is meant by E and by ÆE. Give the equation which relates ÆE and ÆG and explain what each of the symbols means. Calculate the standard ÆG for the oxidation of malate to oxaloacetate by NAD.
1) oxaloacetate + 2H+ + 2e- = malate Eo = -166mV
2) NAD+ + 2H+ + 2e- = NADH + H+ Eo = -320mV
F = 23 kcal/volt; R = 2.0 cal/ok/mole; lnX = 2.3 log X
33. Describe the Z-scheme for oxygen producing photosynthesis as carried out by blue-green bacteria or chloroplasts. Make sure you explain both how the proton motive force and how reducing power are generated.
PART I: MULTIPLE CHOICE (64 points)
Circle the letter next to the single best answer. Two points per question.
1. When carbon dioxide is converted to methane, the one carbon fragment is carried first on:
a) coenzyme M
b) ferredoxin
c) methanofuran
d) methanoquinone
e) HTP-SH (= component B)
2. When carbon dioxide is converted to methane, reducing equivalents are transferred by:
a) F420
b) F430
c) methanoquinone
d) ferredoxin
e) tetrahydromethanopterin
3. Consumption of hydrogen by methanogens allows:
a) obligate anaerobes such as Clostridium to convert ethanol to acetate
b) certain anaerobic sulfur bacteria to convert acetate to ethanol
c) obligate anaerobes such as Clostridium to excrete acetate instead of ethanol
d) facultative anaerobes such as E. coli to excrete acetate instead of ethanol
4. Halobacterium uses light energy to:
a) expel potassium ions from the cell
b) pump chloride ions into the cell
c) generate reducing power
d) fix carbon dioxide
e) none of the above
5. In Halobacterium light energy is absorbed by the pigment:
a) halochlorophyll
b) phycobilin
c) halopterin
d) carotenoids
e) bacteriorhodopsin
6. In Archebacterial membranes, an ether linkage connects glycerol to:
a) The phosphate of phospholipids
b) Fatty acids
c) Isoprenoid hydrocarbon chains
d) Negatively charged sugar derivatives
e) Proteins in the cell wall
7. Plastoquinone is used instead of ubiquinone for:
a) Photosynthesis (oxygen producing)
b) Anaerobic respiration with nitrate
c) Anaerobic respiration with fumarate
d) Methane production
e) Photosynthesis (anaerobic)
8. Photosynthetic oxygen release by cyanobacteria or chloroplasts is due to:
a) Ferredoxin and plastocyanin
b) Cytochrome oxidase working in reverse
c) Phaeophytin
d) Manganese containing enzyme
e) None of the above
9. The photosynthetic antenna contains:
a) Carotenes and quinones
b) Quinones and chlorophyll
c) Chlorophyll and carotenes
d) Pheophytin and quinones
e) None of the above
10. The electron transport chain of purple bacteria contains:
a) Menaquinone and cytochrome f
b) Plastocyanin and cytochrome b
c) Plastoquinone and cytochrome f
d) Bacteriopheophytin and cytochrome b
e) Ferredoxin and ubiquinone
11. The proton motive force, PMF, is given by:
a) PMF = Delta Psi - 60 Delta pH
b) PMF = Delta Psi - RT ln Delta pH
c) PMF = 60 Delta Psi - nF Delta pH
d) PMF = nF Delta Psi + 60 Delta pH
e) PMF = Delta Psi + 60 Delta pH
12. The NADH-Dehydrogenase has two enzymatic subunits which contain:
a) Heme group and Cu atom
b) Molybdenum and selenium
c) FeS group and flavin cofactor
d) Lipoic acid and thiamine pyrophosphate
e) Ubiquinone and heme
13. Cytochrome oxidase differs from other cytochromes as follows:
a) It contains cobalt instead of iron
b) Its iron atom alternates between 2+ and 4+
c) It is only found in mitochondria
d) It can bind molecular oxygen
e) None of the above
14. Iron sulfur proteins function by:
a) Acting as electron carriers
b) Acting as proton transporters
c) Protecting cells against oxygen toxicity
d) Helping to bind oxygen in cytochrome oxidase
e) They are involved in all of the above
15. The correct order of a typical respiratory chain is:
a) UQ >> cyt a >> cyt b >> cyt c >> oxygen
b) UQ >> cyt b >> cyt c >> cyt a >> oxygen
c) UQ >> cyt c >> cyt b >> cyt a >> oxygen
d) UQ >> cyt c >> cyt a >> cyt b >> oxygen
e) UQ >> cyt b >> cyt a >> cyt c >> oxygen
16. Which of the following are hydrogen carriers (as opposed to electron carriers):
a) NAD and FAD
b) FeS groups and menaquinone
c) Ubiquinone and FAD
d) Heme and Menaquinone
e) FeS groups and FAD
17. The charge gradient (Delta Psi) may be measured using a:
a) lipophilic cation
b) pH meter
c) weak acid
d) NMR machine
18. Formate dehydrogenase:
a) converts formate to water and carbon dioxide
b) only works if nitrate reductase is present
c) contains selenium and nickel
d) contains molybdenum and copper
e) none of the above is true
19. TMAO reductase and nitrate reductase both require:
a) Fnr protein for induction
b) Cyclic AMP and Crp protein for induction
c) Manganese and FeS groups for activity
d) Presence of formate for induction
e) NarL protein for induction
20. Free Energy and Equilibrium Constant are related by the equation:
a) DeltaG = - RT ln Keq
b) DeltaGo = - RT ln Keq
c) DeltaG = RT ln Keq
d) DeltaGo = RT ln Keq
21. Phosphoenol pyruvate is a high energy compound because of:
a) charge repulsion due to the phosphate
b) competing resonance
c) enol/keto isomerization
d) it is a phosphoric anhydride
e) None of the above is correct
22. Which of the following are "high energy compounds" (even if not found naturally)?
a) NAD+ and acetic anhydride
b) Adenosine monophosphate and acetyl-phosphate
c) Adenosine diphosphate and a dipeptide
d) Acetic anhydride and acetyl-CoA
23. The correct equation for the reduction of nicotinamide adenine dinucleotide phosphate is:
a) NADP+ + 2H+ = NADPH+ + H+
b) NADP + H+ + [H] = NADPH2
c) NADP+ + 2[H] = NADPH + H+
d) NADP + 2[H+] + 2e- = NADPH2
24. Which of the following enzyme reactions releases carbon dioxide:
a) Malate dehydrogenase
b) Isocitrate lyase
c) alpha-Ketoglutarate dehydrogenase
d) Citrate synthase
e) Aconitase
25. The glyoxylate cycle is used for generating:
a) precursors for synthesis of lipopolysaccharides
b) precursors for synthesis of aromatic amino acids
c) NADPH
d) 4-carbon intermediates when cells grow on acetate
e) 4-carbon intermediates during growth on hexoses
26. Pyruvate dehydrogenase is regulated by:
a) repression by phosphoenolpyruvate
b) induction by pyruvate
c) activation by oxaloacetate
d) inhibition by high levels of succinyl-CoA
e) inhibition by high levels of glyoxylate
27. In the Krebs cycle, citrate is made by condensing:
a) Acetyl-CoA with cis-aconitate
b) Malonyl-CoA with pyruvate
c) Acetyl-CoA with oxaloacetate
d) Malonyl-CoA with oxaloacetate
e) Acetyl-CoA with glyoxylate
28. The main reason for producing fermentation products is to:
a) neutralize acid in the medium
b) protect against oxygen
c) generate ATP
d) recycle reduced NADH
e) none of the above
29. Pyruvate formate lyase is regulated as follows:
a) the gene is induced under acidic conditions
b) the enzyme is activated under anaerobic conditions
c) the gene is repressed under acidic conditions
d) the enzyme is inactivated by phosphoenolpyruvate
e) the enzyme is activated allosterically by pyruvate
30. During fermentation in E. coli an ATP is made:
a) during conversion of pyruvate to formate
b) during conversion of acetyl-CoA to acetate
c) during conversion of acetyl-CoA to alcohol
d) during conversion of pyruvate to lactate
e) during conversion of pyruvate to acetaldehyde
31. Oxygen toxicity is largely due to:
a) peroxide ions destroying enzymes
b) superoxide ions attacking RNA
c) oxygen molecules oxidizing -SH groups
d) superoxide ions destroying the lipid bilayer
e) hydrogen peroxide degrading cytochromes
32. The most important factor in protection against oxygen toxicity is:
a) superoxide dismutase
b) peroxide dismutase
c) catalase
d) peroxide degradation by flavoproteins
e) carotenoids trapping hydroxyl radicals
PART II: SHORT ANSWER QUESTIONS (16 points)
33. (8 points) For any FOUR of the following metals give one
example of a cofactor or enzyme or other biological molecule which
contains it and indicate which pathway this belongs to (e.g.
glycolysis or respiratory chain or methane synthesis etc).
a) Magnesium:
b) Manganese:
c) Selenium:
d) Copper:
e) Cobalt:
f) Nickel:
34. (8 points) Choose any FOUR of the following inhibitors or
poisons and briefly describe how they work. (One example is enough
for each inhibitor.)
a) Arsenite:
b) Uncouplers:
c) Fluorocitrate:
d) Malonate:
e) Chlorate:
f) DCCD:
PART III ESSAY QUESTION (20 points) Choose any ONE question
35. Explain how E. coli adapts to grow anaerobically using nitrate as alternative electron acceptors. What differences are there between nitrate respiration and respiration using oxygen? Describe the role of either the ArcAB or the NarQXL regulatory systems in switching between respiration using oxygen and nitrate respiration.
36. Describe how bacteria like Rhodobacter use light to generate the proton motive force. How is reducing power generated when these bacteria are using light as their source of energy?
37. Describe how the proton motive force is used:
a) to generate ATP
b) to provide energy for flagellar motion
c) to transport nutrients
38. Explain why a) ATP and b) phosphoenolpyruvate are high energy compounds.
39. Describe with diagrams how Halobacterium generates the proton motive force using sunlight as a source of energy. And, briefly: Where does it get its reducing power from? What does it do with most of the energy it generates?
40. Outline the reaction scheme for the pyruvate dehydrogenase complex. How is pyruvate dehydrogenase regulated in bacteria like E. coli?
PART I: MULTIPLE CHOICE (60 points)
Circle the letter next to the single best answer. Two points per question.
1. The most important factor in protection against oxygen toxicity is:
a) superoxide dismutase
b) peroxide dismutase
c) catalase
d) peroxide degradation by flavoproteins
e) carotenoids trapping hydroxyl radicals
2. When retinaldehyde absorbs a photon:
a) it is released from the protein to which it was bound
b) it transfers an electron to a quinone
c) it changes from the trans to the cis isomer
d) it transfers an electron to cytochrome b
e) it changes from the disulfide form to the sulfhydryl form
3. Uncouplers
a) carry chloride ions across membranes
b) inhibit the electron transport chain
c) hydrolyse high energy phosphates
d) carry protons across membranes
e) block the proton channel in the F0 subunit of ATP synthase
4. The cell wall of Halobacteria is made of:
a) peptidoglycan plus lipopolysachharide
b) lipopolysachharide only
c) proteins with carbohydrate side chains
d) halorhodopsin
e) proteins with phosphate side chains
5. The step which releases most energy in the electron transport chain of mitochondria is:
a) from NAD to ubiquinone
b) from ubiquinone to cytochrome b
c) from cytochrome b to cytochrome c
d) from cytochrome c to cytochrome a
e) from cytochrome a to oxygen
6. Purple photosynthetic bacteria:
a) release oxygen if they are provided with light energy
b) cannot release oxygen under any circumstances
c) generate reduced NADPH by using light energy
d) have areas of purple membrane which contain bacteriorhodopsin
e) release oxygen only if they are provided with both light energy and an alternative electron acceptor
7. Halobacteria generate the PMF from light energy as follows:
a) they use components of their respiratory chains running in reverse
b) light is absorbed by carotenoids
c) bacteriorhodopsin pumps protons out
d) halopheophytin moves chloride ions using light energy
e) they cannot generate a complete PMF but only the DY
8. In archebacterial membranes, an ether linkage connects glycerol to:
a) Isoprenoid hydrocarbon chains
b) The phosphate of phospholipids
c) Fatty acids
d) sulfate groups
e) retinaldehyde
9. The primary lethal effects of oxygen toxicity results from:
a) peroxide ions destroying enzymes
b) superoxide ions attacking RNA
c) oxygen molecules oxidizing -SH groups
d) superoxide ions destroying the lipid bilayer
e) hydrogen peroxide degrading cytochromes
10. Cyanobacteria:
a) are not really bacteria but primitive photosynthetic eukaryotes
b) cannot release oxygen under any circumstances
c) have membrane lipids consisting of isoprenoid chains and sulfate groups
d) require H2S to generate reducing power
e) generate reduced NADPH by using light energy
11. The reaction centre complex of purple photosynthetic bacteria contains:
a) bacteriochlorophyll, phylloquinone and bacteriopheophytin
b) bacteriochlorophyll, cytochrome c and bacteriopheophytin
c) bacteriochlorophyll, ubiquinone and bacteriopheophytin
d) bacteriopheophytin, ubiquinone and cytochrome b
e) bacteriopheophytin, phylloquinone and cytochrome b
12. When the ATP synthase makes ATP by using the proton motive force:
a) protons go through a channel in the F0 subunit
b) ADP is bound by the F0 subunit
c) two phosphate groups are added to AMP by the a and b subunits
d) the F1 subunit transports the protons across the membrane
e) the F0 subunit releases the ATP on the inside of the cytoplasmic membrane
13. Cytochrome oxidase differs from other cytochromes as follows:
a) It contains nickel instead of iron
b) Its iron atom alternates between 2+ and 4+
c) It is only found in mitochondria
d) It can bind molecular oxygen
e) None of the above
14. When the PMF of E. coli is used to energize the flagella:
a) the proton channel of the ATP synthase supplies protons to the basal body of the flagellum instead of using them to make ATP
b) protons are bound by acceptor groups on a rotating ring of protein found at the base of the flagellum in the cytoplasmic membrane
c) protons are bound by acceptor groups on a ring of protein at the base of the flagellum which is embedded in the cell wall and does not move
d) sodium ions are used to operate the flagellum and later they are exchanged for protons by a separate transport protein
e) protons move from the basal body down the inside of the flagellum and exit into the culture medium
15. The correct order of a typical respiratory chain is:
a) quinone >> cyt a >> cyt b >> cyt c >> oxygen
b) quinone >> cyt c >> cyt b >> cyt a >> oxygen
c) quinone >> cyt c >> cyt a >> cyt b >> oxygen
d) quinone >> cyt b >> cyt a >> cyt c >> oxygen
e) quinone >> cyt b >> cyt c >> cyt a >> oxygen
16. A significant difference between the electron transport chains of mitochondria and E. coli is that in E. coli:
a) menaquinone is used instead of ubiquinone
b) cytochrome oxidase uses molybdenum instead of copper
c) there is no cytochrome b
d) cytochrome c is missing
e) NADP is used instead of NAD
17. When the Dpsi of E. coli is measured with electrodes and a voltmeter:
a) mecillinam is used to produce giant spherical cells
b) oligomycin must be used to inhibit the ATP synthase
c) TPMP is used because it is positively charged and lipophilic
d) DMO is used because its undissociated acid form can cross the membrane
e) the proton channels must be blocked first
18. Adenosine diphosphate is a high energy compound because of:
a) isomerization between enol and keto forms
b) the ester linkage between the phosphate groups
c) charge repulsion due to the phosphates
d) all of a), b) and c) are correct
e) none of the above is correct
19. Pyruvate kinase is the last step of glycolysis and it is regulated by:
a) allosteric inhibition of the enzyme by ATP
b) repression of the gene by fructose diphosphate
c) allosteric activation of the enzyme by phosphoenol pyruvate
d) induction of the gene by pyruvate
e) repression of the gene by phosphoenol pyruvate
20. When the electron transport chain to nitrate is in operation, electrons flow from the quinone to:
a) FeS groups >> cytochrome b >> molybdopterin >> nitrate
b) cytochrome b >> FeS groups >> molybdopterin >> nitrate
c) cytochrome b >> molybdopterin >> FeS groups >> nitrate
d) cytochrome b >> selenocysteine >> molybdopterin >> nitrate
e) FeS groups >> cytochrome b >> selenocysteine >> nitrate
21. The NarXLPQ regulatory system:
a) represses fumarate reductase in the presence of nitrate
b) induces nitrate reductase whenever oxygen is absent
c) consists of three sensor proteins, one each for nitrate, nitrite and TMAO, and a single regulator protein
d) represses cytochrome d in the presence of nitrate (but not TMAO or nitrite)
e) induces TMAO reductase if TMAO is available
22. Free Energy and Equilibrium Constant are related by the equation:
a) DeltaG = &endash; RT ln Keq
b) DeltaGo = &endash; RT ln Keq
c) DeltaG &endash; DeltaGo = RT ln Keq
d) DeltaGo = RT ln Keq
e) DeltaGo &endash; DeltaG = &endash; RT ln Keq
23. Which of the following steps of glycolysis incorporates inorganic phosphate:
a) triose phosphate isomerase
b) pyruvate kinase
c) phosphoglycerate kinase
d) glyceraldehyde phosphate dehydrogenase
e) enolase
24. Pyruvate dehydrogenase and a-ketoglutarate dehydrogenase both:
a) convert NADP+ to NADPH
b) are regulated by attaching a phosphate group to the enzyme
c) produce acetyl-CoA
d) share lipoamide dehydrogenase as their third subunit
e) are induced by their substrates
25. A significant difference between the Krebs cycle of mitochondria and of E. coli is that in E. coli:
a) NADP is used instead of NAD by isocitrate dehydrogenase
b) NADP is used instead of NAD by malate dehydrogenase
c) ATP is used instead of GTP by a-ketoglutarate dehydrogenase
d) ATP is used instead of GTP by citrate synthase
e) NAD is used instead of FAD by succinate dehydrogenase
26. Coenzyme A is able to carry:
a) acetyl groups attached to the phosphate group of CoA
b) succinyl groups attached to the phosphate group of CoA
c) succinyl groups attached to the sulfhydryl group of CoA
d) phosphate groups attached to the sulfhydryl group of CoA
e) acetyl groups attached to the ribose ring of CoA
27. The ArcAB regulatory system:
a) induces the genes for most Krebs cycle enzymes in the presence of air
b) represses the genes for most Krebs cycle enzymes in the absence of air
c) induces the genes for nitrate and fumarate reductase in the absence of air
d) represses nitrate and fumarate reductase in the presence of air
e) induces the genes for the cytochrome d complex in the presence of air
28. When bacteria grow anaerobically by fermentation, approximately what percentage of the carbon source is wasted as fermentation products:
a) 10
b) 25
c) 50
d) 75
e) 90
29. Alcohol dehydrogenase of E. coli is regulated as follows:
a) the gene is induced under anaerobic conditions
b) the enzyme is activated under acidic conditions
c) the gene is repressed under acidic conditions
d) the enzyme is inactivated by alcohol
e) the enzyme is activated allosterically by pyruvate
30. During fermentation in E. coli an ATP is made:
a) during conversion of formate to carbon dioxide
b) during conversion of acetyl-CoA to acetate
c) during conversion of acetyl-CoA to alcohol
d) during conversion of pyruvate to lactate
e) during conversion of pyruvate to acetaldehyde
PART II: SHORT ANSWER QUESTIONS (20 points)
31. (10 points) Choose any FIVE of the following inhibitors or
poisons and briefly describe how they work. (One example is enough
for each inhibitor.)
a) Arsenate:
b) Fluoride:
c) Fluoroacetate:
d) Malonate:
e) Chlorate:
f) Oligomycin:
g) Valinomycin:
h) Tungstate:
32. (10 points) Choose any FIVE of the following molecules and
briefly describe what their function is. (One example is enough for
each molecule.)
a) Bacteriopheophytin:
b) Cytochrome c:
c) Menaquinone:
d) Plastocyanin:
e) Chlorophyll:
f) Molybdopterin:
g) Lipoic acid:
h) Thiamine Pyrophosphate:
PART III ESSAY QUESTION (20 points) Choose any ONE question
Write only on one side of the paper provided. Include DIAGRAMS.
33. Describe how bacteria like E. coli generate the proton motive force when they are respiring in the presence of oxygen. (You are NOT required to make ATP.) What differences are found between high oxygen (=normal aeration) and low oxygen (=microaerophilic) conditions?
34. Explain what is meant by E and by DeltaE. Give the equation
which relates DeltaE and DeltaG and explain what each of the symbols
means. Calculate the standard DeltaG for the oxidation of malate to
oxaloacetate by NAD.
1) oxaloacetate + 2H+ + 2e- = malate Eo = -166 mV
2) NAD+ + 2H+ + 2e- = NADH + H+ Eo = -320 mV
F = 23 kcal/volt; R = 2.0 cal/ok/mole; lnX = 2.3 log X
35. Describe with diagrams how Halobacterium generates the proton motive force using sunlight as a source of energy. And, briefly: Where does it get its reducing power from? Also, briefly: What does it do with most of the energy it generates?
36. Describe the Z-scheme for oxygen producing photosynthesis as carried out by blue-green bacteria or chloroplasts. Make sure you explain both how the proton motive force and how reducing power are generated.
37. Describe how you would measure the the proton motive force. Explain one method for finding the pH difference (DeltapH) and one method for finding the charge difference (Delta Psi).
38. Describe the mixed acid fermentation scheme for E. coli growing anaerobically. How is pyruvate formate lyase regulated? Why is it more favorable to convert pyruvate to an acetate/ethanol mixture than to lactate?