Exam 3

27. Look at figure 1 at the end of the exam which shows the typical tricarboxylic acid (TCA) cycle. (4 pts) a. What steps are skipped if the glycoxylate bypass is done?

- 4 and 5 - Isocitrate to 2-oxoglutarate (alpha-ketoglutarate) - 2-oxoglutarate to succinyl CoA - succinyl CoA to succinate

24. What are two similarities between respiration and photosynthesis? (3 pts)

- Both use electron transport chains to capture energy - Both create proton gradients - Both synthesis ATP - Both use similar electron carriers (cytochrome and chlorophyll are similar, quinones)

26. List three factors that would affect the energetics of a reaction? (3 pts)

- Concentration of substrates vs products - Change in Gibbs free energy from substrate to products - Temperature - Reduction potential value - Entrophy of reaction (disorder)

27. Look at figure 1 at the end of the exam which shows the typical tricarboxylic acid (TCA) cycle. (4 pts) b. Which steps would be run backwards if the organisms was doing incomplete TCA cycle?

9-6, Oxalacetate to Succinyl-CoA

32. You are monitoring the growth of a culture. At time 0, the culture had 1.4 x 107 cells/ml and at 90 minutes later the culture was at 5.5 x 107 cells/ml. > Calculate the number of generations that occurred during that time and the growth rate in generations per hour. > Show your work to have the possibility for partial credit. g = t / n n = 3.3 * (log X - log X0) k = n / t

n = 3.3 x (log 5.5 x 107 - log 1.4 x 107) = 3.3 x (7.74 - 7.15) = 1.95 gen k = 1.95 / 1.5 hr = 1.3 gen/hr

32. You are monitoring the growth of a culture. At time 0, the culture had 1.2 x 107 cells/ml and at 3 hrs later the culture was at 4.8 x 107 cells/ml. Calculate the number of generations that occurred during that time and the growth rate in generations per hour. Show your work to have the possibility for partial credit. (4 pts) g = t / n k = n / t n = log (Nt / N0) / 0.301

n = log (4.8 x 107 / 1.2 x 107) / 0.301 = log (7.68-7.07) / 0.301 = 2 gen k = 2.0 / 3 hr = 0.66 gen/hr

24. Describe three differences between the phototrophy done by cyanobacteria and purple sulfur bacteria. (3 pts)

- Cyanobacteria are oxygenic (water donates electrons and produces O2), has two photosystems, have different members of the electron transport chain, give electrons to NADP+, pigments are chlorophyll and phycobilins and structures in thykaloid membranes - Purple sulfur bacteria do anoxygenic photosynthesis (get electrons from H2S, and produce S), has one photosystem (I), run electron chain backwards to generate NADPH, pigment used is bacteriochlorophyll, and occurs in membrane invaginations

29. Explain the role of electron transport system in metabolism in bacterial cells. (4 pts)

- Electron transport systems in respiration and oxidative phosphorylation accept electrons from an electron donor chemical such as NADH. - The electrons are transfer to different electron carries in the electron transport system and each transfer lowers the potential energy and then ultimately given to an electron acceptor such as O2 or NO3 which are then reduced. - Often during the process, hydrogen protons are pumped outside the cell to help create a proton gradient. - The proton gradient can be used to synthesize ATP. - An electron transport system is also used in photosynthesis where the electron excited by photons is passed to an electron transport system which can give the electron to generate NADPH and a protons are also transported so that ATP can be synthesized.

27. Describe two ways bacterial cells capture energy in forms that can be used later by the cell. (3 pts)

- Formation of ATP from ADP by Substrate level phorphorylation - Formation of ATP by using proton motive force - Using an electron transport chain to pump protons across the cell membrane to create proton motive force using electrons excited by light or from reduced electron carriers - Reduction of NAD+, NADP, or FAD to their reduced form NADH, NADPH or FADH2

25. Describe two ways bacterial cells capture energy in forms that can be used later by the cell. (3 pts)

- Formation of ATP from ADP by Substrate level phosphorylation - Formation of ATP by using proton motive force - Using an electron transport chain to pump protons across the cell membrane to create proton motive force using electrons excited by light or from reduced electron carriers - Reduction of NAD+, NADP, or FAD to their reduced form NADH, NADPH or FADH2

27. Some bacteria can grow using citrate as its sole carbon and energy source. Citrate is a metabolite in the Tricarboxylic acid cycle (TCA) and the citrate would enter the central metabolic pathways there. Explain how a bacterium could run the central metabolic pathways to obtain energy and to produce all the precursor metabolites it needs? (4 pts)

- It could run the TCA cycle forward to capture energy in the form of NADH or FADH or part forward and part in reverse. - The NADH and FADH could be used to generate a proton gradient and ATP via using respiration. - The TCA cycle would generate oxaloacetate which it could be converted to PEP so that it could then run glycolysis and pentose phosphate backwards to generate precursor metabolites.

26. Describe how an electron transport chain creates a proton gradient (3 pts)

- Protons and electrons enter the system and some of the electron carriers (Flaviprotein and Quinones) can accept two electrons and two protons but will pass only the electrons on to the next electron carrier and protons will be released on the other side of the membrane.

26. How is anaerobic respiration similar and different from aerobic respiration? (4 pts) a. Describe two similarities b. Describe two differences

- Similarities: Both can use the same central metabolic pathways (glycolysis, pentose phosphate cycle and citric acid) and an electron transport chain. Both fully oxidize carbon in sugars to CO2. Both generate a large amount of ATP (36-38 ATPs per glucose) - Differences: Anaerobic respiration uses an alternative final electron acceptor such as nitrate, nitrite, or sulfate instead of O2, the electron carriers will be different, and it generates slightly less maximum ATP.

29. Look at the Figure of a Metacyc Metabolism pathway printed on the separate page. For the reaction, indicated by the number 6, write down the following information? (4 pts) > Substrate(s) for the reaction: > Product(s) of the reaction: > Enzyme name: > Name of gene predicted to encode the enzyme:

- Substrate(s) for the reaction: Phosphoenolpyruvate, CO2 and H2O - Product(s) of the reaction: oxaloacetate and phosphate - Enzyme name: phosphoenolpyruvate carboxylase - Name of gene predicted to encode the enzyme: SC03127

28. Explain what the glycoxylate bypass is and why cells would do it? (4 pts)

- The glycoxylate bypass or cycle is a modified version of the TCA cycle in which cells add two new reactions which allow the cells to skip the two steps that cause the loss of CO2. - Cells do this when growing on acetate or fatty acids needs some intermediates in the TCA cycle are precursor metabolite as that are also used for biosynthesis. - To prevent the loss of carbon in TCA intermediates, the cells to the cycle so that the two carbons are not lost and the levels of the TCA intermediates does not fall too low.

29. List four features or properties of phototrophy that vary or differ in different types of phototrophic bacteria? (4 pts)

- Types or kinds of pigments used and the wavelengths of light absorbed by them - Organization of pigments in light harvesting complex - Structure of Photosynthetic membrane structures - - Electron donors (H2O, H2S, H2) and whether O2 produce - Photosystem used: number and whether cyclic or non-cyclic photosystems - Whether auto or heterotroph - How fix CO2

31. List three differences between phototrophy done by cyanobacteria and phototrophy done by green sulfur bacteria? (3 pts)

- Use different electron donors (H2O) for cyanobacterium vs H2S, S or H2 for green sulfur - Cyanobacterium produce oxygen while green sulfur do not. - Photosynthetic pigmens (cyanobacterium have phycobilins) - Cyanobacterium do both photosystem I and II while green sulfur bacterium do PS I - Carbon fixation: Cyanobacterium do Calvin cycle and Green sulfur do reductive TCA - Light harvesting apparatus different:

25. You are growing E. coli cells in the presence of oxygen and with its only source of carbon and energy being 2 carbon acetate. Acetate would enter the central pathways as acetyl-CoA. Describe how the central pathways would run in these cells in order to both capture energy and to generate precursor metabolites? (4 pts)

- Would do TCA cycle in the forward direction to capture energy from oxidation of acetate as NADH but would sometimes do the glyoxylate shunt or incomplete TCA to avoid losing all the carbon - Would do respiration with electron tranport chain which will generate proton gradient and ATP - Would do gluconeogenesis (run glycolysis backward) to generate precursor metabolites - Would do pentose phosphate reactions backwards to generate the C4, C5 and C7 precursor metabolites

31. You have characterizing a bacterial species isolated from hot spring whose water was at 60°C. In lab, you measure the growth rate of the bacterium when it is growing at 40, 45, 50, 55, 60, 65, 70, 75 and 80°C. Describe what you expect to observe. > You may draw a graph but include a description. (3 pts)

- You would expect the bacterium to grow fastest at one or two temperatures between 60-70 C. - You would also expect to observe a lower growth rate at temperature above and below the optimal growth temperature with perhaps no growth at the temperatures farthest from the optimal growth temperature.

30. Fill in the table showing three differences between glycolysis and the Entner-Doudoroff (ED) pathway?

1. Glycolysis generates 2 ATPs while the ED pathway generates 1 ATP 2. Glycolysis generates 2 NADHs while the ED pathway generates 1 NADH and 1 NADPH 3. Glycolysis breaks down 6 carbon sugars while the ED pathway can be used to breakdown sugar acids in addition to 6 carbon sugars 4. Glycolysis generates Fructose 6-phosphate as an intermediate while the ED pathway generates 6-phophogluconate

32. List four factors that affect the ability of bacteria to grow and the growth rate of bacteria. (4 pts)

1. Temperature 2. oxygen availability 3. osmotic pressure (salt) 4. pH 5. nutrient levels 6. type of nutrients or energy source, light for phototrophs

31. Give one reason for why the list of pathways predicted by Metacyc to occur in a specific bacterium could be inaccurate.

1. The Metacyc Database could predict a pathway to occur that does not actually occur because it found some but not all of the enzymes for a pathway and the enzymes found are used in another pathway which the organism does but the pathway is not done because it lacks the unique enzymes 2. The Metacyc Database could also fail to predict a pathway that does occur in the microbe because gene annotation/function prediction failed to find some of the enzymes needed for a pathway so Metacyc did not find enough enzymes for the pathway to predict it. However those needed enzymes could actually be there and the pathway occurs.

18. Which of the following is a list of pathways that utilize electron transport systems? A. Aerobic respiration, anaerobic respiration and phototrophy B. Aerobic respiration and fermentation C. Aerobic respiration, lithotrophy and fermentation D. Anaerobic respiration, glycolysis and butandiol fermentation E. Aerobic respiration, gluconeogenesis and fermentation

A. Aerobic respiration, anaerobic respiration and phototrophy

16. In the figure (below), what is shown? A. An electron transport chain involved in aerobic respiration B. An oxygenic photosystem found in aerobic bacteria C. A fermentation pathway D. A predicted metabolic pathway from the Metacyc web site E. An electron transport chain involved in anaerobic respiration

A. An electron transport chain involved in aerobic respiration

17. In the figure below, what is shown? A. An electron transport chain involved in aerobic respiration B. An oxygenic photosystem found in aerobic bacteria C. A fermentation pathway D. A predicted metabolic pathway from the Metacyc web site E. An electron transport chain involved in anaerobic respiration

A. An electron transport chain involved in aerobic respiration

20. Which of the following is the type of pigment can absorb light in the near infrared range (800-900 nm) that penetrates to deeper depths of water than red/blue light? A. Bacteriochlorophyll of Purple sulfur bacteria B. Chlorophyll of Cyanobacteria C. Carotenoids D. Phycobilins or phycobiliproteins E. Quinol

A. Bacteriochlorophyll of Purple sulfur bacteria

12. Which of the following is NOT a type of electron carrier found in the electron transport chains involved in respiration? A. Carotenoid B. Cytochrome C. Flavoprotein with riboflavin D. Iron-sulfur protein E. Quinone

A. Carotenoid

11. The bacterium Nitromonas obtains it energy and electrons from oxidizing ammonia to nitrite (NO2), this bacterium would be described as a ___________? A. Chemolithotroph B. Chemoheterotroph C. Chemoorganotroph D. Photoautotroph E. Photoheterotroph

A. Chemolithotroph

13. Which of the following would be a value or factor that makes a reaction energetically more favorable? A. Combining a reaction with a half reaction having a negative ΔG (Gibbs free energy) B. Reducing the concentration of all substrates C. Increasing the concentration of all products D. Combining with a reaction with a half reaction having a negative reduction potential (E°) E. Performing the reaction at a lower temperature

A. Combining a reaction with a half reaction having a negative ΔG (Gibbs free energy)

3. Which of the following would be a value or factor that would make a half reaction energetically more favorable? A. Combining the reaction with a half reaction having a negative ΔG (Gibbs free energy) B. Reducing the concentration of all the substrates C. Increasing the concentration of all the products D. Combining with a reaction with a negative reduction potential (E) E. Performing the reaction at a lower temperature

A. Combining the reaction with a half reaction having a negative ΔG (Gibbs free energy)

2. Which of the following is a pathway that can convert glucose or sugar acids to 2 pyruvates with 6-P-gluconate as an intermediate in the process and yields 1 ATP, 1 NADH and 1 NADPH? A. Entner-Doudoroff pathway B. Glycolysis or Embden-Meyerhof-Parnas (EMP) pathway C. Pentose phosphate pathway D. Calvin cycle E. Tricarboxylic acid (TCA) cycle

A. Entner-Doudoroff pathway

20. The oxidation of hydrogen sulfide (H2S) to sulfuric acid (H2SO4) could occur in bacteria doing _____. A. Lithotrophy B. Aerobic respiration C. Mixed acid fermentation D. Anaerobic respiration E. Oxygenic photosynthesis

A. Lithotrophy

4. Which of the following is NOT true about reactions in the central metabolic pathways? A. Most of the reactions can only be run in one direction and are not reversible B. Many reactions are oxidation and reduction reactions. C. Most reactions are catalyzed by a specific enzyme. D. Some reactions couple an energetically unfavorable half reaction with an energetically favorable half reaction. E. Some reactions are used in more than one metabolic pathway.

A. Most of the reactions can only be run in one direction and are not reversible

10. Which of the following is NOT a feature of bacterial growth? A. Observe large increases in the size of the cells B. Population doubles every round of division C. Most grow by binary fission D. Can reach very high densities E. Observe large increases in cell number

A. Observe large increases in the size of the cells

22. In which metabolic pathway is H2O split to generate O2. A. Oxygenic phototrophy B. Anoxygenic phototrophy C. Chemolithotrophy D. Anaerobic photosynthesis E. All of the above

A. Oxygenic phototrophy

5. All organisms need to do the central metabolic pathways (glycolysis, pentose phosphate and TCA cycle) in order to _________ A. generate precursor metabolites needed for biosynthesis B. capture energy in the form of NADH C. capture energy in the form of ATP D. oxidize the carbon in glucose to CO2 E. All of the above

A. generate precursor metabolites needed for biosynthesis

5. Which of the following is the pathway that converts glucose to 2 pyruvates via a fructose-1,6-bisphosphate intermediate and yields 2 NADHs and a net of 2 ATPs? A. Entner-Doudoroff pathway B. Glycolysis or Embden-Meyerhof-Parnas (EMP) pathway C. Pentose phosphate pathway D. Calvin cycle E. Tricarboxylic acid (TCA) cycle

B. Glycolysis or Embden-Meyerhof-Parnas (EMP) pathway

21. Which of the following contain a single type of photosystem and that photosystem gives up the excited electrons to NAD(P)+ to generate reduced NADPH? A. Cyanobacteria B. Green sulfur bacteria C. Purple nonsulfur bacteria D. Purple sulfur bacteria

B. Green sulfur bacteria

1. Which of the following is NOT true about fermentation? A. Several different ways of doing fermentation have been observed B. A species of bacteria will only do one fermentative pathway C. Produces and consumes NADH D. Results in only one or 2 ATPs being generated per glucose molecule E. Results in the production of an organic acid or an alcohol or both

B. A species of bacteria will only do one fermentative pathway

6. Which of the following is a common feature of all fermentations? A. All generate lactic acid as an end product. B. All regenerate NAD+ by reducing an organic intermediate C. All start from glucose. D. All generate an acid as an end product. E. All generate ATP via electron transport.

B. All regenerate NAD+ by reducing an organic intermediate

18. In which of the following processes could hydrogen sulfide (H2S) be oxidized to at least sulfur (S)? A. Aerobic respiration and anoxygenic photosynthesis B. Anoxygenic photosynthesis and lithotrophy C. Mixed fermentation and anaerobic respiration D. Anaerobic respiration and fermentation E. Lithotrophy and anaerobic respiration

B. Anoxygenic photosynthesis and lithotrophy

18. In which of the following processes could hydrogen sulfide (H2S) be oxidized to sulfur (S) or sulfuric acid (H2SO4)? A. Aerobic respiration and anoxygenic photosynthesis B. Anoxygenic photosynthesis and lithotrophy C. Mixed fermentation and anaerobic respiration D. Anaerobic respiration and fermentation E. Lithotrophy and anaerobic respiration

B. Anoxygenic photosynthesis and lithotrophy

23. Which of the following is true about bacterial cells? A. Bacterial cells growing at a faster rate are smaller B. Bacterial cells growing at a faster rate contain more stable RNA per cell C. Bacterial cells growing at a faster rate contain less protein per cell D. Bacterial cells growing at a faster rate contain less ribosomes per cell E. All of the above

B. Bacterial cells growing at a faster rate contain more stable RNA per cell

15. Which of the following is NOT a way that CO2 is fixed or incorporated into organic molecules by autotrophic bacteria? A. CO2 is incorporated by running the TCA cycle backwards so that CO2 is added molecule instead of being released B. By running glycolysis backwards C. By reducing CO2 and then fusing with another CO2 to make acetyl-CoA D. By linking to a 2 carbon sugar to create hydroxypropionate E. By linking CO2 to a 5-carbon sugar (ribulose-1,6-P)

B. By running glycolysis backwards

16. Which of the following is NOT a way that CO2 is fixed or incorporated into organic molecules by autotrophic bacteria? A. CO2 is incorporated by running the TCA cycle backwards so that CO2 is added to molecules instead of being released B. By running glycolysis backwards C. By reducing CO2 and then fusing with another CO2 to make acetyl-CoA D. By linking CO2 to a 2 carbon sugar to create hydroxypropionate E. By linking CO2 to a 5-carbon sugar (ribulose-1,6-P)

B. By running glycolysis backwards

1. Chemoautotrophs obtain their carbon from _______ and their energy from ______ A. CO2, light B. CO2, inorganic compounds C. organic compounds, organic compounds D. organic compounds, light E. organic compounds, inorganic compounds

B. CO2, inorganic compounds

5. Which of the following is NOT true about the Tricarboxylic acid (TCA) cycle? A. The TCA cycle can be run backwards (oxaloacetate to citrate). B. If an organism does the TCA cycle, it has to do all the steps. They cannot do only some of the reactions. C. Some of the metabolites produced in the pathway are precursor metabolites D. Can be used as a way to fix carbon E. Some bacteria can skip some of the steps to avoid the release of carbon as CO2

B. If an organism does the TCA cycle, it has to do all the steps. They cannot do only some of the reactions.

8. Which of the following is NOT a feature of bacterial growth? A. Observe relative small changes (<2 fold) in the size of the cells B. Most grow by producing 4 daughter cells C. Population doubles every round of division D. Can reach very high densities E. Observe increases in both cell number and cell mass

B. Most grow by producing 4 daughter cells

8. Which of the following is NOT a feature of bacterial growth? A. Observe relatively small changes (<2 fold) in the size of the cells B. Most grow by producing 4 daughter cells C. Population doubles every round of division D. Can reach very high densities E. Observe increases in both cell number and cell mass

B. Most grow by producing 4 daughter cells

14. The difference in charge and the difference in pH are two important factors in determining ______, A. ΔG or change in Gibbs Free energy B. Proton motive force C. Photon potential D. Chemolithotrophic potential E. Reduction potential

B. Proton motive force

15. The difference in charge and the difference in pH are two important factors in determining ______, A. ΔG or change in Gibbs Free energy B. Proton motive force C. Photon potential D. Chemolithotrophic potential E. Reduction potential

B. Proton motive force

16. The energy used to power the synthesis of methane from CO2 by methanogens comes from ________ A. Photons of light B. The oxidation or splitting of H2 C. The reduction of nitrate to ammonia D. Proton motive force E. The oxidation of sugars to CO2

B. The oxidation or splitting of H2

6. Which metabolic pathway would oxidize glucose to 6 CO2 and would then be able to reduce NO2 to N2 and generate up to 36 ATPs per glucose? The overall reaction is shown below. Glucose + NO2- → 6 CO2 + N2 + H2O + up to 36 ATPs A. Mixed acid fermentation B. Aerobic respiration C. Anaerobic respiration D. Anoxygenic photosynthesis

C. Anaerobic respiration

10. Which of the following has a porphyrin ring structure similar to the one found in cytochromes? A. Quinones B. Carotenoids C. Bacteriochlorophylls D. Flaviproteins E. Phycobilins

C. Bacteriochlorophylls

3. Which of the following is NOT a way cells capture energy in an useable form? A. Generation of ATP from ADP by substrate level phosphorylation B. Generation of reduced NADH from NAD+ by oxidizing chemicals C. Generation of oxidized NADP+ from NADPH by reducing chemicals D. Creation of a transmembrane ion gradient by pumping protons across a membrane E. Generation of ATP from ADP by using the flow of protons with the concentration gradient into the cell

C. Generation of oxidized NADP+ from NADPH by reducing chemicals

7. Which of the following lists the pathways that need to be run in some manner by all types of bacteria in order to generate precursor metabolites? A. Glycolysis and the Tricarboxylic acid cycle B. Glycolysis and Calvin cycle C. Glycolysis, Pentose phosphate and Tricarboxylic acid cycle D. Calvin cycle, Entner-Doudoroff, and Tricarboxylic acid cycle E. Entner-Dourdoroff, Pentose phosphate and Calvin cycle

C. Glycolysis, Pentose phosphate and Tricarboxylic acid cycle

1. Which of the following lists all the pathways that are considered part of the central metabolic pathways used by all bacteria? A. Glycolysis and Pentose phosphate cycle B. Glycolysis and TCA cycle C. Glycolysis, Pentose phosphate cycle and TCA cycle D. Glycolysis, Fermentation and TCA cycle E. Glycolysis, Entner-Doudoroff pathway and TCA cycle

C. Glycolysis, Pentose phosphate cycle and TCA cycle

3. Which of the following is the pathway that is noted to generate 4-, 5-, and 7-carbon intermediates that can also be biosynthetic precurrors or metabolites and yields NADPH? A. Glycolysis or the Embden-Meyerhof-Parnas (EMP) pathway B. Entner-Doudoroff pathway C. Pentose phosphate pathway D. Mixed acid fermentation E. Tricarboxylic acid (TCA) cycle or citric acid cycle

C. Pentose phosphate pathway

6. If an anaerobic respiratory pathway is described as dissimilarity, that means ____. A. The pathway is unique to that bacteria B. The pathway is not similar to aerobic respiration C. The end product of the pathway is not incorporated into organic molecules D. The electron chain does not create a proton gradient E. The electron chain does not oxidize oxygen

C. The end product of the pathway is not incorporated into organic molecules

17. The spectrum of light absorbed by phototrophic bacteria is principally determined by ________. A. Which photosystem they use B. Whether they are in the presence or absence of oxygen C. The types of pigments in their light harvesting antenna complexes D. Which electron carriers are in their photosystem E. The electron donor used

C. The types of pigments in their light harvesting antenna complexes

7. Why do almost all bacterium including photoautotrophs need to do the central metabolic pathways? A. To obtain energy by oxidizing glucose to CO2 B. In order to do oxidative phosphorylation C. To generate precursor metabolites for biosynthesis D. To generate a proton gradient across the membrane E. A and B

C. To generate precursor metabolites for biosynthesis

12. You have discovered a bacterium that only does fermentation. It lacks the enzyme to do respiration of any type. You also discovered that it has most of the enzymes for reactions of the tricarboxylic acid (TCA) cycle. Why would the organism do some of the reactions of the TCA cycle? A. To generate more NADPHs B. To consume NADHs C. To generate precursor metabolites need for biosynthesis D. To generate 5 carbon sugars needed for nucleotides E. A and D

C. To generate precursor metabolites need for biosynthesis

2. You have discovered a bacterium that only does fermentation. It lacks the enzyme to do respiration of any type. You also discovered that it has most of the enzymes for reactions of the tricarboxylic acid (TCA) cycle. Why would the organism do some of the reactions of the TCA cycle? A. To generate more NADPHs B. To consume NADHs C. To generate precursor metabolites need for biosynthesis D. To generate 5 carbon sugars needed for nucleotides E. A and D

C. To generate precursor metabolites need for biosynthesis

7. A bacterium that can grow in the presence and absence of oxygen and will use oxygen if it is available is _______. A. an obligate aerobe B. an obligate anaerobe C. a facultative anaerobe D. a microaerophile E. a facultative alkaliphile

C. a facultative anaerobe

19. After CO2 is fixed as part of the Calvin cycle, the products generated will undergo a series of reaction similar to _______? A. Glycolysis B. the TCA cycle C. the Pentose phosphate pathway D. Gluconeogenesis E. A and B

C. the Pentose phosphate pathway

12. Which is NOT true about glycolysis? A. Generates Fructose-6 phosphate as in intermediate B. Generates 2 pyruvates from each glucose C. Generates several precursor metabolites D. All bacteria do glycolysis E. Generates 2 net ATP and 2 NADH

D. All bacteria do glycolysis

9. Which of the following is true about the effect of temperature on the growth of bacteria? A. All bacterial species grow at 37°C. B. No bacterial species grow at 4°C. C. Bacteria grow faster as the temperature increases D. All bacteria have an optimum temperature at which they grow the fastest and they grow slower at temperatures above and below that temperature E. All of the above

D. All bacteria have an optimum temperature at which they grow the fastest and they grow slower at temperatures above and below that temperature

4. Which of the following is NOT true about fermentation? A. Several different ways of fermentation have been observed B. Produces an organic acid, alcohol and/or CO2 C. Regenerates NAD+ D. Always starts from a six carbon hexose sugar such as glucose E. Results in only one or 3 ATPs being generated via glycolysis from a glucose molecule

D. Always starts from a six carbon hexose sugar such as glucose

2. Which of the following is a difference between anaerobic respiration and aerobic respiration? A. Anaerobic respiration does not use glycolysis B. Anaerobic respiration does not utilize the TCA cycle C. Anaerobic respiration does not fully oxidize carbon atoms in sugars to CO2 D. Anaerobic respiration uses an alternative final electron acceptor besides O2 E. Anaerobic respiration does not use an electron transport chain to pump protons across the cell membrane in order to generate proton motive force

D. Anaerobic respiration uses an alternative final electron acceptor besides O2

21. The reduction of nitrate (NO3 -) or nitrate (NO2 -) to ammonia (NH3) occurs in bacteria as part of A. Anoxygenic phototrophy B. Oxygenic phototrophy C. Chemolitotrophy D. Assimilatory anaerobic respiration E. Dissimilatory anaerobic respiration

D. Assimilatory anaerobic respiration

23. The conversion of nitrate (NO3-) to ammonia (NH3) is observed in cells doing ____. A. Aerobic respiration B. Anoxygenic phototrophy C. Dissimilatory anaerobic respiration D. Assimilatory anaerobic respiration E. Lithotrophy

D. Assimilatory anaerobic respiration

17. Which of the following is a primitive protein complex that contains a pigment that can absorb photons and then use the energy to directly pump protons across the cell membrane? A. Quinone B. Carotenoids C. Cytochromes D. Bacteriorhodopsin E. Bacteriochlorophyll

D. Bacteriorhodopsin

10. A similarity between the Calvin cycle and the pentose phosphate cycle is ______? A. Both generate NADPH B. Both generate ATP C. Both generate NADH D. Both go through a series of sugar rearrangements to form sugars of different lengths E. Both generate CO2

D. Both go through a series of sugar rearrangements to form sugars of different lengths

21. Which of the following is a way that bacterial cells growing at a faster rate differ from cells growing at a slower rate? A. Cells growing at a faster rate are smaller B. Cells growing at a faster rate contain less DNA per cell C. Cells growing at a faster rate contain less protein per cell D. Cells growing at a faster rate contain more stable RNA per cell E. All of the above

D. Cells growing at a faster rate contain more stable RNA per cell

24. Which of the following is a way that bacterial cells growing at a faster rate differ from cells growing at a slower rate? A. Cells growing at a faster rate are smaller B. Cells growing at a faster rate contain less DNA per cell C. Cells growing at a faster rate contain less protein per cell D. Cells growing at a faster rate contain more stable RNA per cell E. All of the above

D. Cells growing at a faster rate contain more stable RNA per cell

15. The oxidation of H2, H2S, NH3, HNO3, or Fe3+ would be observed in _____ A. Fermentation B. Anaerobic photosynthesis C. Photoheterotrophy D. Chemolithotrophy E. Anaerobic respiration

D. Chemolithotrophy

19. A similar porphyrin ring structure is found in which of the following? A. Flavoproteins and Carotenoids B. Phycobilin proteins and iron-sulfur proteins C. Quinones and iron-sulfur proteins D. Cytochromes and chlorophylls E. Bacteriorhodopsins and Iron-sulfur proteins

D. Cytochromes and chlorophylls

14. Which of the following is the form of nitrogen that can be directly incorporated or assimilated into organic materials? A. N2 B. NO2 - C. NO3 - D. NH4+ E. NOH2+

D. NH4+

4. A bacterium that obtains its energy from light and its carbon from organic molecules would be described as a _______ A. Chemoheterotroph B. Chemoautotroph C. Photoautotroph D. Photoheterotroph E. Chemolithotroph

D. Photoheterotroph

9. A bacterium that grows at a temperature above 50°C is a ________ A. Mesophile B. Barophile C. Anaerobe D. Thermophile E. Thermostat

D. Thermophile

20. Nitrate (NO3-) can be converted to ammonia (NH3) or N2 by bacteria doing _______? A. Aerobic respiration B. Anoxygenic phototrophy C. Mixed acid fermentation D. Lithotrophy E. Anaerobic respiration

E. Anaerobic respiration

19. Metabolites of the TCA cycle are generated for more than one reason in cells. Cells may only do a 1 or few steps of the TCA and may do some steps backwards from the pathway is normal run. Which of the following is NOT a reason generate metabolites of the TCA cycle by doing reactions of the TCA cycle? A. For the fixing of CO2 into organic molecules B. As one branch or part of fermentation C. To generate precursor metabolites for biosynthesis D. For the capture of energy by the oxidation of carbon into CO2 E. As part of chemolithotrophy

E. As part of chemolithotrophy

13. 6-phosphogluconate is an intermediate in which of the following pathways? A. Glycolysis B. Pentose phosphate/hexose monophosphate pathway C. Entner-Doudoroff (ED) pathway D. Tricarboxylic acid (TCA) cycle E. B and C

E. B and C ----- B. Pentose phosphate/hexose monophosphate pathway C. Entner-Doudoroff (ED) pathway

25. In which of the following, would the cell numbers in a culture of bacterial cells be constant or not change? A. Bacterial cells in lag phase of a batch culture B. Bacterial cells in log or exponential phase of a batch culture C. Bacterial cells in stationary phase of a batch culture D. Bacterial cells in a continuous culture E. C and D

E. C and D --- C. Bacterial cells in stationary phase of a batch culture D. Bacterial cells in a continuous culture

14. A series of sugar arrangements in which two- or three-carbon units of sugars are transferred to other sugar metabolites to generate a series of different metabolites is a feature observed in which of the following pathways? A. Glycolysis B. TCA cycle C. Pentose phosphate/hexose monophosphate pathway D. Calvin cycle E. C and D

E. C and D --- C. Pentose phosphate/hexose monophosphate pathway D. Calvin cycle

22. Which of the following is a difference between growing bacterial cells in a continuous culture verse a batch culture? A. Cells grown in a continuous culture grow to a higher density B. Cells grown in continuous culture are smaller C. Cells grown in a continuous culture are in stationary phase D. Cells grown in a continuous culture grow at a faster rate E. Cells growing in a continuous culture can be maintained in a log phase growth state

E. Cells growing in a continuous culture can be maintained in a log phase growth state

9. Which of the following is NOT true about the product of the pentose phosphate pathway if one was starting from glucose? A. Generates a 4 carbon intermediate that is a precursor metabolite B. Generates a 5 carbon intermediate that is a precursor metabolite C. Generates a 7 carbon intermediate that is a precursor metabolite D. Generates some CO2 E. Generates NAD+

E. Generates NAD+

8. Which of the following is NOT true about the Entner-Doudoroff (ED) pathway? A. Alternative way to break down glucose to pyruvate done by some bacteria B. Generates 6-P-gluconate as an intermediate C. Generates NADPH in addition to NADH D. Enables the utilization of sugar acids E. Generates more ATP per glucose than glycolysis

E. Generates more ATP per glucose than glycolysis

13. You have grown a bacterium in media with glucose as the sole carbon source and then find in the culture media lactic acid, ethanol, and CO2. What type of metabolism was the bacterium doing? A. Anaerobic respiration B. Mixed acid fermentation C. Propionic acid fermentation D. Homofermentative lactic acid fermentation E. Heterofermentative lactic acid fermentation

E. Heterofermentative lactic acid fermentation

11. Which of the following produces succinate, lactic acid, acetic acid, ethanol, and formate or CO2 and H2 as endproducts of its fermentation? A. Homofermentaive lactic acid fermentation B. Alcohol fermentation C. Heterofermentative lactic acid fermentation D. Propionic acid fermentation E. Mixed acid fermentation

E. Mixed acid fermentation

11. You are going a bacterium in media with glucose as the carbon source and after incubation you observe the presence of succinate, lactic acid, acetic acid, ethanol, formate, CO2 and H2. What type of metabolism is the bacterium doing? A. Homofermentative lactic acid fermentation B. Alcohol fermentation C. Heterofermentative lactic acid fermentation D. Propionic acid fermentation E. Mixed acid fermentation

E. Mixed acid fermentation

22. Which is NOT true about carbon fixation? A. Is the incorporation of CO2 into organic molecules B. Multiple ways of fixing CO2 are observed in bacteria C. One mechanism involves using two CO2 molecules to create acetyl-CoA D. One mechanism involves adding CO2 to a 5 carbon sugar E. One mechanism involves running glycolysis backwards

E. One mechanism involves running glycolysis backwards

-- Fall 2017 ---

Fall 2017

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Fall 2018

28. Describe how an electron transport chain creates a proton gradient (3 pts)

Protons and electrons enter the system and some of the electron carriers (Flaviprotein and Quinones) can accept two electrons and two protons but will pass only the electrons on to the next electron carrier and protons will be released on the other side of the membrane.

23. How is anaerobic respiration similar and different from aerobic respiration? (4 pts) a) Describe two similarities b) Describe two differences

Similarities: -Both can use the same central metabolic pathways (glycolysis, pentose phosphate cycle and citric acid) and an electron transport chain. -Both fully oxidize carbon in sugars to CO2. Both generate a large amount of ATP (36-38 ATPs per glucose) Differences: - Anaerobic respiration uses an alterative final electron acceptor such as nitrate, nitrite, or sulfate instead of O2, the electron carriers will be different, and it generates slightly less maximum ATP.

30. Look at the Figure of a Metacyc Metabolism pathway printed on a separate page. (4 pts) a. Which of the numbered reactions (1-11) is predicted to be found in this organism? b. Which of the numbered reactions (1-11) was NOT found in this organism? c. Which of the reactions (1-11) is unique to this pathway? d. Would you predict that this pathway would occur is this organism? Explain your answer

a. Found: 3, 4, 5, 6,7 and 11 b. Not found: 1, 2, 8, 9. 10 c. Unique: 1, 2, 9, 10 d. Most likely not present due to, missing multiple enzymes needed for pathway especially the unique enzymes

28. Look at Figure 1 on a separate page which shows a pathway diagram from Metacyc. (4 pts) a. Which of the numbered reactions (1-9) are predicted to be found in this organism? b. Which of the reactions (1-9) are unique to this pathway?

a. Found: 4-9 b. Unique: 5,6

33. Look at Figure below of a metabolic pathway and of a pathway glyph from the Metacyc database. a. Which of the reactions with a number (1-5) beside them catalyzes a reaction that is unique to this pathway (only found in this pathway and not in any other metabolic pathway)? (1.5 pts) b. For which of the reactions with a number (1-5) beside them has no gene been predicted to encode the enzyme that catalyzes that reaction? (1.5 pts)

a. Which of the reactions with a number (1-5) beside them catalyzes a reaction that is unique to this pathway (only found in this pathway and not in any other metabolic pathway)? (1.5 pts) b. For which of the reactions with a number (1-5) beside them has no gene been predicted to encode the enzyme that catalyzes that reaction? (1.5 pts) a. 3 b. 1

30. You are monitoring the growth of a culture. At time 0, the culture had 3 x 107 cells/ml and at 2.5 hrs later the culture was at 7 x 107 cells/ml. (4 pts) Calculate the number of generations that occurred during that time and the growth rate in generations per hour. Show your work to have the possibility for partial credit. g = t / n k = n / t n = log (Nt / N0) / 0.301

n = log (7 x 107 / 3 x 107) / 0.301 = log (2.3) / 0.301 = 0.36 / 0.301 = 1.22 gen k = 1.22 / 2.5 hrs = 0.488 gen/ hr