Deck 13: Energetics and Catabolism

Question 1

Organotrophy is a term that describes microorganisms:

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

Answer 1

A

Question 2

In their work with soil bacteria, McInerney and colleagues have found microorganisms that display metabolic pathways with $\Delta$ 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

Answer 2

growth near thermodynamic equilibrium

Question 3

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; lithotroph
B) respiration; heterotroph
C) fermentation; organotroph
D) carbon fixation; phototroph
E) none of the above

Answer 3

A

Question 4

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 5

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 6

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

A) X-rays and other ionizing radiation can damage molecules.
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.

Question 7

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

Question 8

Which of the following statements is NOT true regarding the electron donors in bacterial and archaeal metabolism?

A) The use of organic compounds as electron donors is known as organotrophy.
B) Lithotrophy refers to the use of inorganic molecules as electron sources.
C) Light absorption provides electrons to phototrophic organisms.
D) All of the above statements are incorrect.
E) None of the above statements is incorrect.

Question 9

The laws of thermodynamics indicate that systems tend to become less ordered and that the __________, 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 10

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 11

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
B) $\Delta$ G = $\Delta$ H - T $\Delta$ S
C) ADP + PiATP + H₂O
D) K = T°C + 273
E) none of the above

Question 12

Peter Mitchell's chemiosmotic model proposes:

A) that there is a relationship between free energy and product-to-substrate concentration ratio
B) that the hydrolysis of ATP is accompanied by a free energy change of -31 kJ/mol
C) a mechanism for interconversion of NAD(P)H + H⁺ energy and that of ATP
D) that ATP synthesis and electron transport are coupled by a H⁺ gradient across a membrane
E) the regulation of key steps in highly complex pathways via allosteric effects on enzymes

Question 13

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 14

What technique can be used to determine entropy and enthalpy of biochemical reactions?

A) NMR
B) calorimetry
C) electron microscopy
D) all of the above
E) none of the above

Question 15

Although ATP is the main energy carrier in living organisms, these molecules 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 16

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 17

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 18

Which if 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 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 20

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 21

Some intestinal bacterial groups 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 22

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 23

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 24

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 25

Lactococcus lactis is used in the production of Swiss cheese. L. lactis converts the amino acid methionine to __________, a molecule that confers this cheese its characteristic flavor.

A) propionate
B) 2-oxobutyrate
C) methional
D) all of the above
E) none of the above

Question 26

What proportion of caloric intake in humans actually derive from catabolism of plant fiber brought about by gut microbiota?

A) 1%
B) 5%
C) 15%
D) 25%
E) 50%

Question 27

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 28

What molecule serves as the way of entry for lipid-derived fatty acids in the TCA cycle?

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

Question 29

The concept of metagenome establishes that:

A) eukaryotic chromosomes are formed by highly condensed DNA strands, tightly associated to histones and scaffold proteins
B) the gut microbiota is a functional part of the human body, and therefore the genomes of organisms composing the human gut microbiota are part of the human metagenome
C) DNA fragments should be repeatedly sequenced to avoid sequencing errors
D) all of the above
E) none of the above

Question 30

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

A) The aromaticity of the nicotinamide ring confers NAD⁺ with a relatively stable 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 has higher energy than the aromatic ring of NAD⁺.
E) All of the above are correct.

Question 31

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

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

Question 32

Which of the following isotopes would NOT be useful for NMR?

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

Question 33

__________ 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 34

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 35

Disparate animal groups, such as ruminants and termites, can ferment cellulose from grasses or wood because they harbor cellulase-bearing bacteria, such as:

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

Question 36

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 37

Some bacteria in the human gut microbiota primarily feed on glucose from mucus secretions. This 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 38

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

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

Question 39

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.

Question 40

Fermentation can be defined as completion of metabolism:

A) without an electron transport system
B) without a terminal electron acceptor
C) without further production of ATP after a few substrate-level phosphorylation reactions
D) in the absence of oxygen
E) all of the above

Question 41

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

Question 42

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

Question 43

In NMR, how are different sugars distinguished and why is each carbon associated with two different peaks?

Question 44

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

A) There are at least ten variations of the TCA known in microorganisms.
B) The TCA cycle is found in all bacterial species.
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 45

The genes for aromatic catabolism in species of Pseudomonas and Rhodococcus are encoded in:

A) the bacterial genome
B) transposons
C) small, multicopy plasmids
D) a large plasmid (100-450 kb)
E) none of the above

Question 46

What is isothermal titration and how does it work?

Question 47

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

Question 48

Compare and contrast the hydrolysis of ATP releasing phosphate and pyrophosphate. ATP hydrolysis with release of pyrophosphate is generally reserved for what types of reactions?

Question 49

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 50

__________ enters the TCA 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 51

Define organotroph and heterotroph. Are these terms equivalent?

Question 52

All of the nucleotide triphosphates carry energy. What reactions are driven by the release of energy from GTP, CTP, and TTP?

Question 53

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 54

Clostridium acetobutylicum has been used to produce the solvents:

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

Question 55

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

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

Question 56

Bacteria synthesize ribose for nucleotides using which pathway?

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

Question 57

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 58

Why is magnesium an essential nutrient for all living cells?

Question 59

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

Question 60

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 61

Briefly describe the experiment performed by Ebenau-Jehle and her group in which they demonstrated that aromatic compounds can be catabolized by anaerobic microbes through reductive degradation.

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

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

Why do the TCA cycle and the ETS have a larger ATP yield in mitochondria than in bacteria?

Question 65

E. 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 66

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

Question 67

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 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

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

Question 70

How can clone libraries be used in the discovery of genes for aromatic catabolism? How are aromatic aerobic catabolism genes organized in Burkholderia species?