Deck 13: Energetics and Catabolism

Question 1

Some freshwater and marine bacteria can use ultraviolet and near-infrared light to perform photosynthesis. Why are wavelengths below UV and beyond IR not used for photosynthesis?

A) Wavelengths shorter than UV can cause molecular damage.
B) The quantum energy of radio waves and microwaves is insufficient to drive photochemistry.
C) The range of wavelengths used by photosynthetic organisms is energetically suitable for the formation and breakdown of molecular bonds in organic compounds.
D) All of the above.
E) None of the above.

Answer 1

D

Question 2

Which of the following is correct with respect to enzymes that use the reducing equivalents NADH and NADPH?

A) Some enzymes only use NADH.
B) Some enzymes only use NADPH.
C) Some enzymes may use either NADPH or NADH.
D) All of the above.
E) None of the above.

Answer 2

D

Question 3

Hydrogen-generating reactions in Syntrophus and Syntrophomonas have $\Delta$ G°' > 0. Can these organisms obtain energy from hydrogen formation?

A) No, they cannot.
B) No. They produce energy by breaking down molecules such as benzoate or butyrate.
C) Yes. Hydrogen-producing microorganisms coexist in syntrophy with H₂-consuming bacteria. Utilization of H₂ ( $\Delta$ G°' < 0) drives the process forward.
D) All of the above.
E) None of the above.

Answer 3

Yes. Hydrogen-producing microorganisms coexist in syntrophy with H₂-consuming bacteria. Utilization of H₂ ( $\Delta$ G°' < 0) drives the process forward.

Question 4

In most environments, the nutrient concentrations outside the cell are lower than inside the cell. How can a microbial cell obtain nutrients if the concentration gradient is NOT favorable?

A) through active, energy-dependent transport
B) using facilitated diffusion
C) swim and tumble
D) by forming biofilms
E) none of the above

Question 5

A bacterium capable of producing methane and water from carbon dioxide and hydrogen performs a type of metabolism called __________ and, given its sources of electrons, it is a __________.

A) methanogenesis; chemolithotroph
B) respiration; heterotroph
C) fermentation; chemoorganotroph
D) carbon fixation; phototroph
E) none of the above

Question 6

Chemoorganotrophy is a term describing microorganisms that:

A) use preformed organic compounds as a source of electrons and obtain energy through fermentations or organic respiration
B) obtain electrons and H⁺ via photolysis of H₂O or H₂S, producing O₂ or S₂, respectively
C) perform photolysis of small organic molecules
D) all of the above
E) none of the above

Question 7

In many bacteria, the electron carrier __________ is used for biosynthesis, whereas __________ feeds the electron transport system.

A) NADPH; NADH
B) FADH₂; NADPH
C) NADH; acetyl-S-CoA
D) all of the above
E) none of the above

Question 8

What technique can be used to determine entropy and enthalpy changes associated with biochemical reactions?

A) nuclear magnetic resonance
B) calorimetry
C) electron microscopy
D) all of the above
E) none of the above

Question 9

The base adenine forms from __________ in experiments simulating the origin of life on Earth.

A) carbon dioxide and nitrate
B) ethanol and urea
C) methane and ammonia
D) all of the above
E) none of the above

Question 10

The laws of thermodynamics indicate that systems tend to become less ordered and that __________, a measure of disorder or randomness of the universe, always increases.

A) entropy
B) enthalpy
C) Gibbs free energy
D) all of the above
E) none of the above

Question 11

Hydrolysis of ATP with the release of pyrophosphate is the driving force of which of the following reaction(s)?

A) DNA and RNA synthesis
B) peptide bond formation
C) fatty acid synthesis
D) all of the above
E) none of the above

Question 12

The Gibbs-Helmholtz equation describes the relationship between the components of free energy change and can be generally expressed as:

A) $\Delta$ G = $\Delta$ G° + RT ln Keq
B) $\Delta$ G = $\Delta$ H - T $\Delta$ S
C) ADP + Pi $\leftrightarrows$ ATP + H₂O
D) K = T°C + 273
E) none of the above

Question 13

In their work with soil bacteria, McInerney and colleagues have found microorganisms that display metabolic pathways with net $\Delta$ G values as small as -20 kJ/mol. This is an example of:

A) the capacity of microorganisms to conquer a wide variety of environments
B) microorganisms contradicting the laws of thermodynamics
C) growth near thermodynamic equilibrium
D) all of the above
E) none of the above

Question 14

The multiple negative charges of ATP are stabilized when it forms a complex with:

A) Mn²⁺
B) Na⁺
C) Mg²⁺
D) K⁺
E) Ca²⁺

Question 15

The intensity of solar radiation reaching Earth peaks in the range of:

A) ultraviolet and near-ultraviolet light
B) infrared light and microwaves
C) visible light
D) X-rays
E) none of the above

Question 16

Which of the following statements is NOT true regarding the electron donors in prokaryotic metabolism?

A) The use of organic compounds as electron donors is known as organotrophy.
B) Chemolithotrophy refers to the use of inorganic molecules as electron sources.
C) Photolysis of water provides electrons to phototrophic organisms such as cyanobacteria.
D) All of the above.
E) None of the above.

Question 17

Which of the following phenomena is sufficient to transport nutrients to cells that lack chemotactic motility?

A) active, ATP-dependent transport
B) diffusion
C) turbulent flow
D) quorum sensing
E) none of the above

Question 18

Which of the following statements is correct with respect to heterotrophic organisms?

A) They use preformed organic compounds for biosynthesis.
B) Most organotrophs are also heterotrophs.
C) Along with decomposers, they are ecologically defined as consumers.
D) All of the above.
E) None of the above.

Question 19

In an amphibolic pathway, some enzymes:

A) work only in the biosynthetic direction
B) work only in the catabolic direction
C) work in both directions
D) all of the above
E) none of the above

Question 20

Glycolytic reactions with a near-zero $\Delta$ G°' can participate in the overall pathway of gluconeogenesis because:

A) they are irreversible
B) they are reversible
C) they contradict the laws of thermodynamics
D) they have low energy of activation values
E) none of the above

Question 21

Not all enzymes are proteins; in some enzymes, the catalytic properties depend on:

A) DNA
B) RNA
C) polysaccharides
D) lipids
E) terpenoids

Question 22

Which of the following molecules is responsible for the distinctive flavor of Swiss cheese?

A) lactate
B) glucose
C) galactose
D) propionate
E) acetate

Question 23

Which of the following is correct regarding fermentation?

A) It consists of partial breakdown of organic molecules without an electron transport system.
B) In fermentative reactions, electrons from organic substrates are put back onto organic products.
C) It occurs in the absence of oxygen.
D) All of the above.
E) None of the above.

Question 24

In glycolysis, dihydroxyacetone phosphate is isomerized to __________, which reenters the pathway.

A) glucose 6-phosphate
B) glyceraldehyde 3-phosphate
C) phosphoenolpyruvate
D) fructose 6-phosphate
E) pyruvate

Question 25

Which of the following pairs is mismatched?

A) Embden-Meyerhof-Parnas pathway-2 ATP, 2 NADH
B) Entner-Doudoroff pathway-1 ATP, 1 NADH, and 1 NADPH
C) Pentose phosphate pathway-1 ATP, 2 NADPH
D) Glyoxylate bypass-2 NADH, 1 FADH₂
E) Bacterial tricarboxylic acid cycle-3 NADH, 1 FADH₂, 1 ATP

Question 26

Disparate animal groups, such as ruminants and humans, can digest a variety of plant fibers because they harbor cellulase-producing bacteria, such as:

A) Staphylococcus aureus and Bacillus subtilis
B) Salmonella and Shigella
C) Escherichia coli and Enterococcus faecalis
D) Bacteroides and Ruminococcus
E) Escherichia chrysanthemi and Erwinia uredovora

Question 27

Glucose is activated by __________ phosphorylation(s) by ATP during the first stage of the Embden-Meyerhof-Parnas pathway.

A) one
B) two
C) three
D) four
E) none of the above

Question 28

Which of the following is correct with respect to the redox pair NAD⁺/NADH?

A) The nicotinamide ring is a relatively stable aromatic structure.
B) The nicotinamide ring is a heteroaromatic because it has a noncarbon atom in position 4.
C) The nicotinamide ring may accept two electrons at carbon 1, becoming a nonaromatic ring.
D) The reduced, nonaromatic ring of NADH is at a higher energy than the aromatic ring of NAD⁺.
E) All of the above are correct.

Question 29

In the pentose phosphate shunt, glucose 6-phosphate is oxidized to 6-phosphogluconate, which is then decarboxylated to ribulose 5-phosphate. What is the main metabolic role of this pathway?

A) production of ATP and NADH + H⁺
B) regeneration of NADP⁺
C) production of carbohydrates with three to seven carbon atoms, which can be utilized in biosynthesis
D) production of pyruvate to feed the Krebs cycle
E) none of the above

Question 30

The enzyme pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to pyruvate; the phosphate group is transferred to ADP to form ATP. This reaction is an example of:

A) ATP synthesis by substrate-level phosphorylation
B) the use of a proton concentration gradient by [H⁺]-ATPases to synthesize ATP
C) ATP coupled to FADH₂ oxidation
D) a P-Type ATPase activity
E) none of the above

Question 31

Fatty acids enter the TCA cycle after being degraded to what molecule?

A) acetyl-phosphate
B) malonyl-S-CoA
C) acetyl-S-CoA
D) all of the above
E) none of the above

Question 32

The process of prioritized consumption of substrates is known as catabolite:

A) induction
B) poisoning
C) competition
D) repression
E) none of the above

Question 33

Humans who have consumed the seaweed Porphyra (the alga used to wrap sushi) were found to have strains of Bacteroides plebeius, whose genome, surprisingly, encodes enzymes to digest Porphyra's cell wall carbohydrates. What mechanism explains the presence of these genes in Bacteroides?

A) Mutations accumulated over time in B. plebeius have led to Sus-like genes.
B) Bacteroides was an endosymbiont of Porphyra in the distant past.
C) Sus-like genes were laterally transferred from the Porphyra-associated marine bacteria Zobellia and Microscilla.
D) All of the above.
E) None of the above.

Question 34

Although ATP is the main energy carrier in living organisms, __________ may also serve as energy carriers in metabolic reactions.

A) nucleotides such as GTP, CTP, and UDP
B) phosphoenolpyruvate
C) creatine phosphate
D) all of the above
E) none of the above

Question 35

The dye __________ turns __________ in the presence of acid products and is included in fermentation broth for some diagnostic tests.

A) phenol red; yellow
B) aniline blue; green
C) ethidium bromide; pink
D) malachite green; blue
E) none of the above

Question 36

Which of the following isotopes would NOT be useful for nuclear magnetic resonance?

A) ¹H
B) ¹³C
C) ³¹P
D) ³²P
E) all of the above are useful

Question 37

Bacteria synthesize ribose for nucleotides using which pathway?

A) Embden-Meyerhoff-Parnas
B) Entner-Doudoroff
C) pentose phosphate shunt
D) tricarboxylic acid cycle
E) all of the above

Question 38

Which of the following is NOT an end product of fermentation?

A) carbon dioxide
B) acetone
C) pyruvate
D) butanol
E) none of the above

Question 39

Some intestinal bacteria, such as Escherichia coli, feed on __________ from mucus secretions using the Entner-Doudoroff pathway.

A) gluconate
B) glucose
C) pyruvate
D) 2-oxoglutarate
E) none of the above

Question 40

__________ is a nondestructive technique that allows the measurement of cytoplasmic concentrations of ATP and NADH through the interactions of electron clouds with __________.

A) Thin-layer chromatography; ³²P
B) HPLC; ³¹P
C) NMR; ³¹P
D) Calorimetry; ³²P
E) none of the above

Question 41

All of the nucleotide triphosphates carry energy. Provide examples of reactions that are driven by the release of energy from GTP, CTP, and TTP.

Question 42

Species of Pseudomonas and Rhodococcus can degrade benzoate and other aromatic molecules, either aerobically or anaerobically. Which of the following is correct regarding anaerobic degradation of aromatic molecules?

A) It takes longer than aerobic degradation.
B) It is critical because bacterial anaerobic habitats are more abundant than aerobic ones.
C) Benzoate is activated to benzoyl-CoA prior to its degradation.
D) All of the above.
E) None of the above.

Question 43

Why is magnesium an essential nutrient for all living cells?

Question 44

What is the phosphotransferase system (PTS) and why is the advantage for a microbial cell to have a PTS?

Question 45

Some bacteria in the human gut microbiota primarily feed on glucose derivatives from mucus secretions. Which of the following is correct with respect to "mucus farming" by bacteria?

A) Bacteroides thetaiotaomicron and other bacteria induce the colon to produce mucus.
B) Mucus-derived sugar acids are metabolized via the Entner-Doudoroff (ED) pathway.
C) Sugar acids must be converted to 6-phosphogluconate in order to enter the Entner-Doudoroff (ED) pathway.
D) All of the above.
E) None of the above.

Question 46

Which of the following is evidence that the Entner-Doudoroff (ED) route might have evolved earlier than the Embden-Meyerhoff-Parnas pathway (EMP)?

A) ED involves a larger number of reactions and produces more energy and reducing equivalents with respect to EMP.
B) 6-phosphogluconate is dehydrated to form pyruvate and glyceraldehyde 3-phosphate, which may then reenter the EMP pathway.
C) ED involves fewer substrate-level phosphorylations and yields less energy and fewer reductants than EMP.
D) All of the above.
E) None of the above.

Question 47

Define organotroph and heterotroph. Are these terms equivalent?

Question 48

Oxidative catabolism of benzoate and other aromatic compounds is catalyzed by:

A) 2-oxoglutarate:NADPH oxidoreductase
B) benzoyl-S-CoA reductase
C) specific dioxygenases
D) NADPH:ferredoxin oxidoreductase
E) none of the above

Question 49

How can a technique such as calorimetry be used to measure $\Delta$ G?

Question 50

Oxidative catabolism of toluene and other benzene derivatives proceeds through:

A) benzoyl-S-CoA
B) aniline
C) catechols
D) all of the above
E) none of the above

Question 51

Describe the Entner-Doudoroff (ED) pathway. What are the advantages to microorganisms that display the ED pathway?

Question 52

The greatest amount of reduced coenzyme NADH + H⁺ is produced during which stage of aerobic respiration?

A) glycolysis
B) pyruvate conversion to acetyl-S-CoA
C) tricarboxylic acid cycle
D) glyoxylate bypass
E) oxidative phosphorylation

Question 53

__________ enters the tricarboxylic acid cycle by condensing with oxaloacetate to form __________.

A) Succinoyl-S-CoA; fumarate
B) Acetyl-S-CoA; citrate
C) Pyruvate; citrate
D) Citrate; isocitrate
E) none of the above

Question 54

What technique can be utilized to identify the degradation products of the polyaromatic hydrocarbons contained in creosote from railroad ties?

Question 55

Define the human metagenome. Why is it important to study it?

Question 56

Clostridium acetobutylicum has been used to produce which solvents?

A) acetate and butyrate
B) acetone and butanol
C) methanol and ethanol
D) formate and ethanol
E) none of the above

Question 57

Pathways involving both anabolic and catabolic reactions are referred to as:

A) amphibolic
B) amphipathic
C) ambivalent
D) ambidextrous
E) none of the above

Question 58

What is substrate-level phosphorylation? Provide two examples from bacterial metabolism.

Question 59

What are the differences among $\Delta$ G, $\Delta$ G°, and $\Delta$ G°'?

Question 60

Which of the following statements is NOT true with respect to the tricarboxylic cycle in microorganisms?

A) There are at least ten variations of the TCA cycle known in microorganisms.
B) Pathogens that depend on their host's metabolism keep the TCA cycle genes and enzymes.
C) The glyoxylate cycle bypass cuts out all loss of CO₂, but only one NADH is formed.
D) All of the above.
E) None of the above.

Question 61

Escherichia coli degrades human waste in the colon using mixed-acid fermentation. Why is this a factor of concern in some medical procedures, such as colonoscopy?

Question 62

The flavor and other properties of cheeses derive from the type of fermenting microorganisms used. How do the "eyes" and the characteristic flavor of Swiss cheese originate?

Question 63

Hans Krebs' strategy to determine the biochemical intermediates involved in aerobic respiration was to use substrate molecules of varying lengths. What led Krebs to take this approach?

Question 64

In the pentose phosphate shunt (PPS), sugars exchange short carbohydrate moieties to form carbohydrates with varying chain lengths. What metabolic mechanisms allow these exchanges to occur? What are the metabolic advantages of the PPS pathway?

Question 65

Catabolism of nicotine by Pseudomonas putida is accomplished by enzymes encoded by a genomic island, which has a sequence homologous to genes in other species, indicating horizontal transfer. How can this discovery be applied in bioremediation?

Question 66

What is mixed-acid fermentation? Provide examples of industrial uses of its products.

Question 67

What metabolic pathway does Mycobacterium tuberculosis use that allows it to grow slowly inside macrophages? What led to this discovery, and what practical application can further analysis of this pathway have?

Question 68

The genome of Treponema pallidum, the causative agent of syphilis, was surveyed and annotated. What did this survey reveal about its obligate association with the host cells?

Question 69

How does the efficiency of energy capture by ATP formation in bacterial tricarboxylic acid cycle compare with that of mitochondria?

Question 70

Describe the diagnostic use of sorbitol MacConkey agar to test for the presence of E. coli O157:H7.