Deck 13: Energetics and Catabolism

Question 1

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) biofilm formation

Answer 1

B

Question 2

Glycolytic reactions with a near-zero DG°' can participate in the overall pathway of gluconeogenesis because they

A) are irreversible.
B) are reversible.
C) contradict the laws of thermodynamics.
D) have low energy of activation values.
E) do not depend on concentrations of reactants and products.

Answer 2

B

Question 3

All of the following are reasons to oxidize glucose in a series of steps EXCEPT to

A) generate smaller amounts of energy in a controlled fashion and when needed.
B) control the usage of energy in a cell by using more steps.
C) minimize the release of heat with more small steps.
D) control the catabolism versus biosynthetic aspects of oxidizing glucose via concentrations of reactants and end products.
E) increase the DG of the reaction.

Answer 3

E

Question 4

The DG for a reaction can be calculated by using DG⁰ and adding in

A) entropy, enthalpy, and the log of the ratio of reactants to products.
B) entropy, enthalpy, pH, and the log of the ratio of the reactants to products.
C) the gas constant, absolute temperature, and the log of the ratio of the reactants to products.
D) the log of the ratio of the reactants to products.
E) the gas constant, absolute temperature, pH, and the log of the ratio of the reactants to products.

Question 5

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) Electrons can be obtained from inorganic chemicals such as H₂S.
E) Oxygen can serve as an electron donor.

Question 6

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) chlorophyll; NADPH
E) pyruvate; acetyl-S-CoA

Question 7

Hydrogen-generating reactions in Syntrophus and Syntrophomonas have DG°' > 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 (DG°' < 0) drives the process forward.
D) Yes, but only when oxygen is present.
E) Yes-this happens in sewage but never in a laboratory setting.

Question 8

The molecule shown below carries energy in the cell but it needs to be stabilized. It is a ________ molecule and is stabilized when it ________.

A) NADPH; forms a cyclic molecule
B) NADPH; complexes with Mg2+
C) ATP; donates its electrons to a cytochrome
D) ATP; complexes with Mg2+
E) ATP; forms a cyclic molecule

Question 9

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) molecular stability
E) activation energy

Question 10

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) sulfur bacterium; chemolithotroph

Question 11

Which of the following statements is FALSE 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) Some can generate methane as an end product.
E) They utilize glycolysis and other pathways to generate energy.

Question 12

When studying an enzymatic reaction, should one consider DG, DG⁰, or DG⁰' when considering the thermodynamics of the reaction, and why?

A) ΔDG0, because it considers standard conditions as well as biochemically relevant conditions such as the concentrations of substrates and products
B) ΔDG0, because it considers standard conditions
C) ΔDG, because it considers defined conditions such as pH
D) ΔDG, because it considers concentrations of reactants as products.
E) ΔDG0, because it considers entropy and enthalpy.

Question 13

A metabolic process allowing for anaerobic degradation of benzoate to acetate is diagrammed below. This metabolism can happen because

A) benzoate contains a great deal of energy and ATP can be made.
B) the catabolism of benzoate by the cell on the left produces hydrogen that is then used by the cell on the right to reduce sulfate.
C) the catabolism of benzoate by the cell on the left produces hydrogen that is then used by a methanogen.
D) the catabolism of benzoate to acetate releases so much energy that it overcomes the positive DG of H₂ production.
E) the cell on the left swims away from the H₂ that it produces in order to balance the thermodynamics.

Question 14

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) use carbon dioxide as the carbon source.
E) pull electrons off minerals to donate to electron transport systems.

Question 15

In their work with soil bacteria, McInerney and colleagues have found microorganisms that display metabolic pathways with net DG 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) growth that depends on the concentration of reactants but not products.
E) enthalpic growth.

Question 16

Using the table below, what is the best method for obtaining energy from catabolizing ethanol, and why?

A) the catabolism of ethanol without an oxidant, because the DG is almost positive
B) the oxidation of ethanol with as the oxidant is because of the large yield of energy released
C) the oxidation of ethanol with oxygen, because the DG is the largest negative number indicating the large yield of energy released.
D) The oxidation of ethanol yields too little biomass to be catabolized.
E) None-ethanol can only be catabolized syntrophically.

Question 17

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

A) DG = DG° + RT ln Keq.
B) DG = DH - TDS.
C) ADP + Pi D ATP + H₂O.
D) K = T°C + 273.
E) DG = -2.303 RT log [C] [D] / [A] [B].

Question 18

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) mass spectroscopy
E) measurement of light levels

Question 19

In amphibolic pathways, enzymes do NOT

A) function only in the biosynthetic direction.
B) function only in the catabolic direction.
C) function in both directions.
D) carry out reactions that are otherwise thermodynamically impossible.
E) have activity dependent on concentrations of reactants and products.

Question 20

In most environments, the nutrient concentrations outside the cell are lower than inside the cell. If the concentration gradient is NOT favorable, a microbial cell obtains nutrients through

A) active, energy-dependent transport.
B) facilitated diffusion.
C) swim and tumble.
D) forming biofilms.
E) simple diffusion.

Question 21

The figure shown below diagrams three pathways for the metabolism of glucose. Pathway ________ is most likely to be used for biosynthesis because it can be used to ________.

A) 1; generate glucose
B) 2; make carbon backbones of many lengths
C) 3; make carbon backbones of many lengths
D) 1; make carbon backbones of many lengths
E) 3; generate glucose

Question 22

Which of the following is FALSE 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) FADH₂ can be used as a substitute.
E) NADPH is more often used in biosynthesis.

Question 23

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 24

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

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

Question 25

The process of prioritized consumption of substrates is known as catabolite

A) induction.
B) poisoning.
C) competition.
D) repression.
E) attenutation.

Question 26

The activity of the enzyme below is controlled in various ways using several of the binding sites shown. The two sites are the ________ site and the ________ site.

A) active; inhibitor
B) catalytic; inhibitor
C) substrate; inhibitor
D) substrate; allosteric
E) catalytic; allosteric

Question 27

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) adenosine and PO4
E) ribose and RNA

Question 28

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

A) acetyl-phosphate
B) malonyl-S-CoA
C) acetyl-S-CoA
D) citrate
E) pyruvate

Question 29

Although ATP is the main energy carrier in living organisms, other molecules may also serve as energy carriers in metabolic reactions. Which of the following molecules does NOT carry energy?

A) nucleotides such as GTP
B) phosphoenolpyruvate
C) creatine phosphate
D) glucose
E) nucleotides such as CTP and UDP

Question 30

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) Glucose is not phosphorylated.

Question 31

Hydrolysis of ATP with the release of pyrophosphate is the driving force of which of the following reactions?

A) DNA and RNA synthesis
B) peptide bond formation
C) fatty acid synthesis
D) transport across a membrane
E) production of glucose-6-phosphate from glucose

Question 32

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 33

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) oxaloacetate

Question 34

Which of the following is NOT 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) NADH can accept electrons from an electron transport system.

Question 35

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) oxidative phosphorylation.

Question 36

The graph shown below diagrams the energy involved in the

A) difference in activation energy of a reaction with and without an inhibitor at an allosteric site.
B) difference in the activation energy of a reaction with and without an enzyme.
C) activation energy needed to initiate the Embden-Meyerhof pathway.
D) difference in synthrophic reactions with and without a hydrogen utilizing partner.
E) difference in activation energy with NADH versus NADPH.

Question 37

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 38

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

A) carbon dioxide
B) acetone
C) pyruvate
D) butanol
E) propionate

Question 39

Bacteria synthesize ribose for nucleotides using which pathway?

A) Embden-Meyerhof-Parnas
B) Entner-Doudoroff
C) pentose phosphate shunt
D) tricarboxylic acid cycle
E) electron transport system

Question 40

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 41

Pyruvate dehydrogenase complex connects glycolysis to respiration. Which is a correct mechanism for how the activity of this enzyme complex is regulated?

A) There is no need to regulate this enzyme complex.
B) The activity is inhibited by CoA and NAD+.
C) Gene expression is repressed by carbon starvation and low oxygen levels.
D) The activity is inhibited by citrate.
E) The activity is enhanced by the presence of acetyl-CoA and NADH.

Question 42

Define "organotroph" and "heterotroph." Are these terms equivalent?

Question 43

How can a technique such as calorimetry be used to measure DG?

Question 44

Which of the diagrammed molecules is a global signal of nutritional status?

A) pyruvate
B) 2-oxoglutarate
C) oxaloacetate
D) acetyl-CoA
E) acetyl-P

Question 45

Which of the following is evidence that the Entner-Doudoroff (ED) route might have evolved earlier than the Embden-Meyerhof-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) They are both used to catabolize glucose.
E) They both use ATP to phosphorylate glucose.

Question 46

What are the differences among DG, DG°, and DG°'?

Question 47

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) oxidation of glucose to carbon dioxide

Question 48

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 49

________ 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) Acetyl phosphate; citrate

Question 50

The energy yield from fermentation is lower than from respiration because

A) fermentation uses NAD+, not NADP+.
B) respiration completely oxidizes glucose to CO₂, resulting in greater generation of NADH and thus ATP.
C) respiration uses the TCA cycle, which has many steps that directly produce ATP or GTP.
D) fermentation shunts much of the carbon from glucose to biosynthesis.
E) fermentation relies on the glyoxylate bypass, which bypasses ATP production.

Question 51

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) catechol 2,3, monooxygenase.

Question 52

Pathways involving both anabolic and catabolic reactions are referred to as

A) amphibolic.
B) amphipathic.
C) ambivalent.
D) ambidextrous.
E) syntrophibolic.

Question 53

Each of the following was used to elucidate the TCA cycle EXCEPT

A) using radiolabeled acetate to determine which carbons were oxidized to CO₂ .
B) the use of crude enzyme preparations from a variety of sources such as cucumber seeds and beef liver.
C) adding a variety of short-chain fatty acids commonly found in cells to detect activity.
D) the use of C14-labeled carbon compounds as a source of carbon under anoxic conditions.
E) using C13 to determine which intermediates are enriched under various growth conditions.

Question 54

Ethanolic fermentation is used in making beverages such as beer, wine, and pulque. It is carried out by yeast and

A) lactobacillus.
B) leuconostoc.
C) propionibacterium.
D) zymomonas.
E) clostridium.

Question 55

Some bacteria in the human gut microbiota primarily feed on glucose derivatives from mucus secretions. Which of the following is NOT 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 pathway.
C) Sugar acids must be converted to 6-phosphogluconate in order to enter the Entner-Doudoroff pathway.
D) The glucose derivatives are converted to glucose and degraded via the Embden-Meyerhof-Parnas pathway.
E) This metabolism has been studied via genomics and genetic studies.

Question 56

Species of Pseudomonas and Rhodococcus can degrade benzoate and other aromatic molecules, either aerobically or anaerobically. Which of the following is NOT 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) It proceeds via production of catechols.
E) The high initial investment of energy comes from either anaerobic phototrophy or anaerobic respiration.

Question 57

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) MacConkey; white

Question 58

All oxidative catabolism of toluene and other benzene derivatives proceeds through

A) benzoyl-S-CoA.
B) aniline.
C) catechols.
D) cis, cis-muconate.
E) D-gluconate.

Question 59

Amino acids can be synthesized using which one of the molecules from the diagram below?

A) isocitrate
B) succinyl-CoA
C) oxaloacetate
D) 2-oxoglutarate
E) fumarate

Question 60

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) propanol and mixed acids

Question 61

Hans Krebs's 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 62

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

Question 63

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 64

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

Question 65

Define the human metagenome. Describe an example to demonstrate the importance of the metagenome.

Question 66

Soils and waters become contaminated with industrial aromatic compounds and efforts are made to use bacteria to clean up these areas. Describe the experiment and finding from phenanthrene metabolism in the Antarctic.

Question 67

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

Question 68

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 69

Treponema pallidum, the causative agent of syphilis, was shown to be lacking a TCA cycle. Explain the significance of this finding.

Question 70

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

Question 71

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

Question 72

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 73

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 74

The catabolism of glucose is central to the overall hydrolysis of polysaccharides in an environment. Compare and contrast the analogous catabolism of polyaromatic compounds found in nature.

Question 75

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

Question 76

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

Question 77

Why is magnesium an essential nutrient for all living cells?