Deck 15: Biosynthesis

Question 1

The most ancient CO₂ fixation pathway in methanogens is:

A) the reverse TCA cycle
B) the 3-hydroxypropionate cycle
C) the Calvin cycle
D) the reductive acetyl-CoA pathway
E) none of the above

Answer 1

D

Question 2

What is the most sensitive method to determine the presence of an isotope such as ¹⁴C in a sample?

A) nuclear magnetic resonance (NMR) spectroscopy
B) radioactive decay
C) mass spectroscopy
D) all of the above
E) none of the above

Answer 2

B

Question 3

The term "genome degeneration" refers to:

A) the loss of a particular biosynthetic pathway when an organism becomes dependent on other species in the environment
B) catabolic
C) the genetic regulatory mechanisms triggered after bacteria are exposed to UV
D) irreversible
E) none of the above

Answer 3

A

Question 4

Which of the following pathways is NOT a route for CO₂ assimilation?

A) reductive acetyl-CoA pathway
B) gluconeogenesis pathway
C) hydroxypropionate cycle
D) reductive pentose phosphate cycle
E) reverse TCA cycle

Question 5

__________ and __________ are unique in that they fix CO₂ as their sole carbon source.

A) Organotrophs; iron oxidizers
B) Photoheterotrophs; chemiolithotrophs
C) Photoautotrophs; lithotrophs
D) all of the above
E) none of the above

Question 6

How many turns of the Calvin cycle does it take to provide one molecule of glyceraldehyde-3-phosphate into the biosynthesis of glucose?

A) 1
B) 2
C) 3
D) 6
E) none of the above

Question 7

Which of the following molecules links glycolysis with the TCA cycle, and also serves as a precursor for many biosynthetic products?

A) malate
B) citrate
C) oxaloacetate
D) acetyl-CoA
E) succinate

Question 8

Which of the following is NOT correct regarding secondary metabolites produced by free-living microbes?

A) Many of them are used as antibiotics.
B) Some secondary metabolites can inhibit the growth of competitor microbes.
C) They are sources of carbon, nitrogen, and other elements in anabolic pathways.
D) All of the above.
E) None of the above.

Question 9

Which pathway is utilized for carbon fixation in chloroplasts and cyanobacteria?

A) the acetyl-CoA pathway
B) the reverse tricarboxylic acid cycle
C) the 3-hydroxypropionate cycle
D) the reductive pentose phosphate cycle
E) none of the above

Question 10

Where is the catalytic site of Rubisco located?

A) large subunit
B) small subunit
C) a cavity that forms between an LSU and an SSU
D) all of the above
E) none of the above

Question 11

Cyanobacteria are believed to generate the majority of oxygen gas in Earth's atmosphere. What allows them to produce oxygen?

A) photosynthesis in which H₂S is the electron source
B) photosynthesis in which water photolysis produces H⁺, e^-, and O₂
C) bacteriorhodopsin-based photosynthesis
D) all of the above
E) none of the above

Question 12

Which technique did Melvin Calvin use to elucidate the intermediates of phototrophic carbon fixation in the chloroplasts of Chlorella?

A) HPLC
B) gel electrophoresis
C) paper chromatography
D) column chromatography
E) none of the above

Question 13

How does the reductive (reverse) TCA cycle participate in carbon fixation?

A) Some of the TCA reactions occur in reverse, assimilating small amounts of CO₂.
B) CO₂ assimilation replenishes TCA intermediates for anabolic pathways.
C) Reverse TCA regenerates acetyl-CoA, which may enter gluconeogenesis via pyruvate.
D) All of the above.
E) None of the above.

Question 14

Which of the following statements is NOT true about Rubisco?

A) It catalyzes the addition of CO₂ to ribulose 1,5-bisphosphate.
B) It is present in all organisms that use the Calvin cycle to fix CO₂.
C) It is found in the carboxysomes of autotrophic bacteria.
D) All species contain the same number of large and small subunits.
E) Its structure is highly conserved across bacterial groups and chloroplasts.

Question 15

What kind of reaction is the formation of oxaloacetate from phosphoenolpyruvate?

A) anabolic
B) anaplerotic
C) carboxylation
D) all of the above
E) none of the above

Question 16

Rubisco catalyzes the reaction:

A) CO₂ + ribulose 1,5-bisphosphate $\rarr$ 2,3-phosphoglycerate
B) HCO₃^- + acetyl-CoA $\rarr$ malonyl-CoA + NADPH $\rarr$ 3-hydroxypropionate
C) H₂S + light $\rarr$ S⁰ + 2 H⁺ + 2 e^-
D) all of the above
E) none of the above

Question 17

The most ancient CO₂ fixation pathway in anaerobic phototrophic bacteria and archaea is:

A) the reverse TCA cycle
B) the 3-hydroxypropionate cycle
C) the Calvin cycle
D) the reductive acetyl-CoA pathway
E) none of the above

Question 18

What types of bacteria perform the reductive pentose phosphate cycle to fix CO₂?

A) cyanobacteria
B) purple phototrophs
C) lithotrophs
D) all of the above
E) none of the above

Question 19

Microbial biosynthetic processes require:

A) essential elements
B) reduction
C) energy
D) all of the above
E) none of the above

Question 20

The Calvin cycle is essentially:

A) started by the oxygen capture by Rubisco
B) a reductive pentose phosphate cycle
C) the reductive, or reverse, tricarboxylic acid cycle
D) all of the above
E) none of the above

Question 21

In anaplerotic reactions:

A) intermediates in a pathway are regenerated
B) nutrients are imported from the environment
C) molecules targeted for breakdown are salvaged for anabolism
D) all of the above
E) none of the above

Question 22

The incorporation of NH₄⁺ into 2-oxoglutarate is the first step in nitrogen assimilation in bacterial cells. This reaction is catalyzed by the enzyme ________ and produces __________.

A) glutamate dehydrogenase (GDH); glutamate
B) glutamine synthase (GS); glutamine
C) glutamate synthase (GOGAT); glutamate
D) all of the above
E) none of the above

Question 23

Which of the following is NOT correct regarding unsaturation in certain fatty acids?

A) Temperature regulates fatty acid composition.
B) The plasma membrane must maintain a certain degree of flexibility.
C) Low temperature induces expression of fabA, which encodes a dehydratase enzyme.
D) Low temperatures favor fewer unsaturated fatty acids.
E) All of the above.

Question 24

Why do most fatty acids contain an even number of carbon atoms?

A) The priming reaction involves condensation of the acetyl-CoA with ACP.
B) A C3-intermediate (malonyl-CoA) is decarboxylated during chain elongation.
C) Fatty acid biosynthesis incorporates succinyl-CoA.
D) Both A and B are correct.
E) None of the above.

Question 25

Which pair is NOT matched correctly?

A) NtrC-regulates nitrogenase gene expression in response to NH₄⁺ concentration
B) NtrB-phosphorylates NtrC when NH₄⁺ concentration is low
C) NifL-forms a two-component signal transduction system with NtrC
D) NifA-acts in concert with factor $\sigma$ -54
E) none of the above

Question 26

What is denitrification?

A) conversion of nitrate or nitrite to N₂ by anaerobic respirers
B) oxidation of NH₄⁺ to nitrate or nitrite by lithotrophs
C) conversion of N₂ to NH₄⁺
D) all of the above
E) none of the above

Question 27

The enzyme nitrogenase is inhibited by oxygen. Nitrogenase activity is protected by the following mechanism:

A) special thick-walled cells (heterocysts) in filamentous cyanobacteria, such as Anabaena
B) special nitrogenase-protecting proteins in Azotobacter species
C) temporal separation of nitrogen fixation (at night) and photosynthesis (during the day) in some species of cyanobacteria
D) all of the above
E) none of the above

Question 28

Based on the number of enzymes involved in its biosynthesis, which of the following is the most complex amino acid specified by the genetic code?

A) tryptophan
B) tyrosine
C) phenylalanine
D) leucine
E) isoleucine

Question 29

Gene expression of nitrogenase through NtrC is down-regulated in high concentrations of:

A) carbon dioxide
B) nitrogen
C) nitrate
D) ammonium
E) FeMo protein

Question 30

Many of the antibiotics and antitumor agents isolated from Streptomyces species are:

A) amides
B) polyketides
C) thioesters
D) fatty acids
E) lipids

Question 31

Which of the following is NOT correct regarding the broad-spectrum antibiotic erythromycin?

A) It is a polyketide where all R = -CH₃.
B) It was originally isolated from Streptomyces erythraeus.
C) It is a polyketide where R = -CH₃ or -CO-NH₂.
D) All of the above.
E) None of the above.

Question 32

Biological nitrogen fixation is energetically expensive. Assuming that NADPH is used as the reducing equivalent, how many ATPs are used in the enzymatic conversion of N₂ to NH₃?

A) 16
B) 32
C) 48
D) 64
E) none of the above

Question 33

This molecule CANNOT freely cross biological membranes:

A) O₂
B) CO₂
C) NH₄⁺
D) all of the above
E) none of the above

Question 34

Which of the following is the reducing agent in the saturation step of polyketide biosynthesis?

A) NADH
B) NADPH
C) ferredoxin
D) H₂
E) none of the above

Question 35

Which of the following is NOT correct about fatty acid biosynthesis?

A) It involves successive condensations of malonyl-ACP.
B) A dehydratase is used to generate an unsaturated bond.
C) It is regulated by the stringent response of carbon starvation.
D) NADPH is generally involved in hydrogenation.
E) Many single-component enzymes are involved.

Question 36

In the mechanism of nitrogen reduction, __________ directly takes the place of the H₂ in the FeMo subunit of the enzyme nitrogenase.

A) NH₃
B) N₂
C) HN=NH
D) H₂N-NH₂
E) any of the above

Question 37

The amino acid biosynthetic pathways are designated as families. Which family generates only one amino acid?

A) aspartate family
B) serine family
C) pyruvate family
D) aromatic family
E) histidine family

Question 38

Industrial nitrogen fixation is achieved through the Haber process in which:

A) N₂ is reduced catalytically by H₂ at ambient temperature
B) N₂ is hydrogenated by CH₄ at extreme temperature and pressure
C) nitrate and nitrite are chemically converted to NH at ambient temperature
D) all of the above
E) none of the above

Question 39

Which of the following is NOT correct regarding nitrogen assimilation into biomass?

A) Different oxidation states of nitrogen require different amounts of reducing energy.
B) It is easy for living organisms to assimilate nitrogen due to its great stability.
C) Nitrogen forms must be fully reduced to NH₃.
D) All of the above.
E) None of the above.

Question 40

In the reductive TCA cycle, four or five ATPs are used to produce one oxaloacetate. How many molecules of CO₂ are fixed in this cycle?

A) two
B) three
C) four
D) five
E) six

Question 41

It is thought that the Calvin cycle appeared after the divergence of the three domains of life. What supports this hypothesis?

Question 42

Chorismate is used in a branched pathway to synthesize:

A) fatty acids
B) polyketide antibiotics
C) purines and pyrimidines
D) aromatic amino acids
E) tetrapyrroles

Question 43

Describe how modular enzymes function in polyketide biosynthesis. Why might this be of use medically?

Question 44

Briefly describe the reductive acetyl-CoA pathway. What is its relevance for methanogens?

Question 45

Which pair is NOT matched correctly?

A) coenzyme B₁₂-cobalt
B) chlorophyll a-magnesium
C) bacteriochlorophyll-magnesium
D) heme-iron
E) none of the above

Question 46

Which of the following drugs is a nonribosomal peptide antibiotic?

A) erythromycin
B) penicillin
C) tetracycline
D) vancomycin
E) ciprofloxacin

Question 47

The alternate origin of pyrrole rings in purple bacteria consists of:

A) the condensation of glycine and succinyl-CoA to produce 5-aminolevulinic acid
B) reduction of glutamate (in tRNA-glutamate), which is rearranged to 5-aminolevulinic acid
C) an unknown reaction
D) demetalation of coenzyme B₁₂
E) none of the above

Question 48

Which molecules use 5-phosphoribosyl-1-pyrophosphate (PRPP) in their biosynthesis?

A) amino acids
B) nucleotides
C) fatty acids
D) tetrapyrrole
E) nonribosomal peptide antibiotics

Question 49

Which of the following is the foundation of most biologically active tetrapyrrole derivatives?

A) chlorophyll
B) 5-aminolevulinic acid
C) uroporphyrinogen III
D) heme
E) cyanocobalamin

Question 50

What is the significance of finding polyketide-synthesis gene clusters in the metagenome of the sponge Discodermia dissoluta?

Question 51

How is fatty acid biosynthesis regulated in bacteria?

Question 52

Which of the following molecules provides a way to simultaneously assimilate one carbon atom and one nitrogen atom during purine biosynthesis?

A) acetyl-CoA
B) acetyl-ACP
C) malonyl-ACP
D) carbamoyl phosphate
E) NADPH

Question 53

Describe the 3-hydroxypropionate cycle; give examples of microorganisms that use this CO₂ fixation mechanism.

Question 54

What techniques and technical advances allowed Melvin Calvin to study carbon fixation? Why did he choose the unicellular alga Chlorella?

Question 55

Which of the following is true of tetrapyrrole biosynthesis?

A) It is regulated by nutritional and environmental needs.
B) It is regulated by riboswitches.
C) It is energetically expensive and therefore it only occurs when it is needed.
D) All of the above.
E) None of the above.

Question 56

How does the reductive or reverse TCA cycle differ from the regular TCA cycle?

Question 57

Variations of the tetrapyrrole ring structure enable coordination to different __________ ions.

A) halogen
B) metal
C) organometallic
D) all of the above
E) none of the above

Question 58

Which of the following is correct regarding the biosynthesis of purines and pyrimidines?

A) 5-phosphoribosyl-1-pyrophosphate (PRPP) is a precursor to both purines and pyrimidines.
B) The pyrimidine ring is synthesized first, and then linked to 5-phosphoribosyl-1-pyrophosphate.
C) The purine ring is built around the C1 of 5-phosphoribosyl-1-pyrophosphate.
D) All of the above.
E) None of the above.

Question 59

What are polyalkanoates and what are bacterially produced polyalkanoates used for? Why are they of ecological and medical interest?

Question 60

What technique was used to demonstrate that gene expression of the CO₂-concentrating mechanism (CCM) transporters is induced by low levels of CO₂? Briefly explain the basis of the technique.

Question 61

Tryptophan is among the so-called essential amino acids for humans, as we cannot produce it ourselves. Briefly describe tryptophan biosynthesis in bacteria. Why is it so energetically expensive to synthesize this aromatic amino acid?

Question 62

Briefly describe how NH₄⁺ is assimilated into biomass by bacteria.

Question 63

The bacterial enzyme nitrogenase performs the reduction of N₂ gas using a large amount of energy and reducing power. Describe the nitrogen reduction steps during nitrogenase activity and write the overall reaction.

Question 64

What is the health risk of having nitrates in drinking water? What conditions favor the accumulation of nitrates and nitrites in bodies of water?

Question 65

Discuss nutritional and environmental influences on the synthesis of tetrapyrroles in bacteria.

Question 66

How do ammonium and oxygen regulate the expression of nitrogen fixation genes?

Question 67

Briefly describe the biosynthetic pathway for arginine.

Question 68

Describe the dual roles of the arginine repressor in the regulation of intracellular arginine levels.

Question 69

How do cyanobacteria benefit from their heterocysts attracting heterotrophic bacteria?

Question 70

What are nonribosomal peptide antibiotics? How are they synthesized?