Deck 15: Biosynthesis

Question 1

__________ 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

Answer 1

C

Question 2

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

Answer 2

A

Question 3

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

Answer 3

B

Question 4

What is/are the advantage(s) of the Calvin cycle being composed of multiple steps?

A) Energy flow is broken down into numerous reversible conversions.
B) Reversible conversions with near-zero $\Delta$ G values conserve more energy.
C) It provides substrates for sugar, amino acid, and nucleotide biosynthesis.
D) All of the above.
E) None of the above.

Question 5

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 6

How many turns of the Calvin cycle does it take to feed 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

This molecule links glycolysis with the TCA cycle, and it also serves as a precursor for many biosynthetic products:

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

Question 8

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 9

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 10

Substrates for biosynthesis of lipids and amino acids derive from the __________ pathways of glycolysis and the TCA cycle.

A) amphibolic
B) catabolic
C) anabolic
D) irreversible
E) none of the above

Question 11

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 12

The Calvin cycle is essentially __________.

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

Question 13

Most biomass on the biosphere has carbon fixed by chloroplasts and bacteria through __________.

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 14

The half-life of ¹⁴C is approximately __________.

A) 21 minutes
B) 14 days
C) two months
D) two years
E) 5,700 years

Question 15

Autotrophic bacteria and archaea use energy to produce cell building blocks solely from __________.

A) CO₂
B) N₂
C) a few mineral salts
D) all of the above
E) none of the above

Question 16

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 source of carbon, nitrogen, and other elements in anabolic pathways.
D) All of the above.
E) None of the above.

Question 17

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

Question 18

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 19

Rubisco catalyzes the reaction:

A) CO₂ + ribulose-1,5-bisphosphate $\rarr$ 2 phosphoglycerate
B) HCO+ 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 20

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 21

Gene expression of nitrogenase through NtrC is downregulated in high concentrations of:

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

Question 22

This molecule CANNOT freely cross biological membranes:

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

Question 23

Which pair is NOT matched correctly?

A) NtrC-regulates nitrogenase gene expression in response to NHconcentration
B) NtrB-phosphorylates NtrC when NHconcentration 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 24

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 25

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

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

Question 26

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

A) The priming reaction involves condensation of the C2-unit molecule acetyl-CoA with ACP.
B) A C3-intermediate (malonyl-CoA) is decarboxylated during chain elongation.
C) Fatty acid biosynthesis incorporates succinyl-CoA C4-units.
D) A and B are correct.
E) None of the above.

Question 27

The transfer of amino groups between two metabolites such as glutamate and glutamine with regeneration of their corresponding 2-oxoacids is called __________.

A) transamination
B) desaturation
C) glycosylation
D) hydrogenation
E) none of the above

Question 28

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 29

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 NH ?

A) 16
B) 24
C) 40
D) 80
E) none of the above

Question 30

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 31

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 32

What is denitrification?

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

Question 33

Which is the most complex amino acid specified by the genetic code?

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

Question 34

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 NHat ambient temperature
D) all of the above
E) none of the above

Question 35

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

A) 2
B) 3
C) 4
D) 5
E) 6

Question 36

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 37

The enzyme nitrogenase is inhibited by oxygen. In cyanobacteria, 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) spatial separation of nitrogen fixation (at night) and photosynthesis (during the day)
D) all of the above
E) none of the above

Question 38

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 (N $\equiv$ N).
C) Nitrogen forms must be fully reduced to NH₃/ NH.
D) All of the above.
E) None of the above.

Question 39

The amino acid biosynthetic trees 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 40

What are the molecules used in the extension reactions during polyketide biosynthesis?

A) acetyl-CoA units
B) malonyl-ACP units
C) coenzyme A
D) acyl-carrier protein
E) none of the above

Question 41

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

Question 42

Which of the following drugs is a nonribosomal-peptide antibiotic?

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

Question 43

It is thought that the Calvin cycle appeared after the divergence of the three kingdoms. What does support this hypothesis?

Question 44

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

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

How is fatty acid biosynthesis regulated in bacteria?

Question 47

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

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

Question 48

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

Question 49

Describe how genome scanning can be used to isolate unknown genes whose sequences are related to known genes in other organisms. Why might this be of use medically?

Question 50

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

Question 51

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 52

Which of the following is true of riboswitch regulation?

A) It is another name for RNAi.
B) It regulates the biosynthesis of tetrapyrroles.
C) It involves blocking RNA polymerase.
D) All of the above.
E) None of the above.

Question 53

The following is NOT 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 54

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 55

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 56

Which molecules use phosphoribosylpyrophosphate (PRPP) in their biosynthesis?

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

Question 57

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 58

Which of the following molecules provides a way to assimilate one carbon atom and one nitrogen atom into a structure?

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

Question 59

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

Question 60

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

Question 61

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

Question 62

Briefly describe the biosynthetic pathway for arginine.

Question 63

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

Question 64

What are nonribosomal peptide antibiotics? How are they synthesized?

Question 65

Why do some cyanobacterial heterocysts attract heterotrophic bacteria?

Question 66

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 67

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 68

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

Question 69

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 70

Briefly describe how NH is assimilated into biomass by bacteria.