Deck 15: Biosynthesis

Question 1

Rubisco catalyzes which of the following reactions?

Answer 1

A

Question 2

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

A) cyanobacteria
B) purple phototrophs
C) lithotrophs
D) heterotrophs
E) methanogens

Answer 2

D

Question 3

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

Answer 3

B

Question 4

Which of the following statements concerning glyceraldehyde-3-phosphate is FALSE?

A) One G3P is produced by everything three turns of the cycle.
B) Two molecules of G3P condense to form a six-carbon sugar.
C) One more G3P condenses with a sugar to form a larger molecule used for biosynthesis.
D) PGA is reduced to G3P after the PGA moves out of the carboxysome.
E) G3P is reoxidized to carbon dioxide so that the cycle continues.

Question 5

The enzyme that carries out this reaction shown in the diagram below is ________, and the end product is ________.

A) 3-phosphoglycerate synthetase; added to another carbon dioxide
B) 3-phosphoglycerate synthetase; reduced to glyceraldehyde-3-phosphate
C) nitrogenase; reduced to glyceraldehyde-3-phosphate
D) Rubisco; reduced to glyceraldehyde-3-phosphate
E) Rubisco; added to another carbon dioxide

Question 6

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) polymerase chain reaction
E) high-performance liquid chromatography

Question 7

Which of the following are unique in that they fix CO₂ as their sole carbon source?

A) organotrophs and iron oxidizers
B) photoheterotrophs and chemiolithotrophs
C) photoautotrophs and lithotrophs
D) heterotrophs and methanogens
E) methanogens and photoheterotrophs

Question 8

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 9

All microorganisms require all of the following for biosynthetic purposes EXCEPT

A) phosphorous.
B) reduction.
C) energy.
D) carbon.
E) nitrogen gas.

Question 10

An association between two Antarctic microorganisms is pictured below. It provides an interaction that supplies ________, made by the ________, to the ________.

A) amino acids; diatom; bacterium
B) fixed nitrogen; diatom; bacterium
C) fixed nitrogen; bacterium; diatom
D) vitamin B12; diatom; bacterium
E) vitamin B12; bacterium; diatom

Question 11

Two strains of E. coli were developed, each of which overproduced an amino acid, either histidine or tryptophan. When grown together in medium with adequate amino acids, they grew but did not associate with each other. When these strains were grown together in medium without histidine and tryptophan, they grew and formed ________ in order to ________.

A) carboxysomes; share the excess of the two amino acids
B) carboxysomes; provide ATP to each other to make the missing amino acids
C) nanotubes; share the excess of the two amino acids
D) nanotubes; provide ATP to each other to make the missing amino acids
E) heterocysts; share the excess of the two amino acids

Question 12

What methods do microorganisms NOT use to minimize energy for biosynthesis?

A) inhibiting or killing competitors by making antimicrobials
B) loss of genes encoding enzymes for a nutrient that can be provided by the environment
C) regulation of gene expression so that molecules are not made if available
D) allosteric control of biosynthetic enzyme activity
E) transport of ATP from the environment into the cell to drive biosynthesis

Question 13

The ________ pathway is utilized for carbon fixation in chloroplasts and cyanobacteria.

A) acetyl-CoA
B) reverse tricarboxylic acid cycle
C) 3-hydroxypropionate cycle
D) reductive pentose phosphate cycle
E) Krebs cycle

Question 14

The structures marked with arrows in the photo below are ________ and are used to ________.

A) polyhydroxyalkanoates; sequester reactions using bicarbonate or carbon dioxide and Rubisco
B) polyhydroxyalkanoates; store carbon for energy
C) carboxysomes; store carbon for energy
D) carboxysomes; sequester reactions using bicarbonate or carbon dioxide and Rubisco
E) heterocysts; sequester reactions using bicarbonate or carbon dioxide and Rubisco

Question 15

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) being near the surface of a pond where more oxygen is available
E) possession of a variety of chlorophylls to absorb a wide range of wavelengths of light

Question 16

The catalytic site of Rubisco is located in

A) the large subunit.
B) the small subunit.
C) a cavity that forms between an LSU and an SSU.
D) the chloroplast.
E) the chlorosome.

Question 17

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 18

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) mass spectroscopy

Question 19

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) a pathway to synthesize fatty acids but not sugars.
E) a pathway that is used only when light is present.

Question 20

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) 5

Question 21

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) Temperature has no effect.

Question 22

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 23

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; only GTP is used

Question 24

Many of the antibiotics and other pharmaceutical agents isolated from Streptomyces species are

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

Question 25

Denitrification is the

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) removal of nitro groups from organic molecules.
E) removal of amino groups from organic molecules.

Question 26

The most ancient CO₂ fixation pathway in methanogens is the

A) reverse TCA cycle.
B) 3-hydroxypropionate cycle.
C) Calvin cycle.
D) reductive acetyl-CoA pathway.
E) Krebs cycle.

Question 27

The cell diagrammed below provides an overview of some regulation of the Calvin cycle. Which of the following is NOT involved in this regulation?

Question 28

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

A) catabolic
B) anaplerotic
C) decarboxylation
D) dehydrogenation
E) co-factor induced

Question 29

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) NADPH

Question 30

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 carboxylated during chain elongation to yield an even number of carbons.
C) Fatty acid biosynthesis incorporates succinyl-CoA.
D) Fatty acids do not have an even number of carbons.
E) It is now easier to add double bonds.

Question 31

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) Only bacteria and archaea can assimilate elemental nitrogen.
E) It is expensive, requiring reducing energy and ATP.

Question 32

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) the reactions are thermodynamically impossible.
E) large amounts of ATP are generated.

Question 33

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 uses up TCA intermediates for anabolic pathways.
C) Reverse TCA regenerates succinyl-CoA, which may enter gluconeogenesis.
D) A large amount of ATP is generated.
E) All reactions take place in a carboxysome.

Question 34

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 s -54
E) NifHDKTY-components of nitrogenase

Question 35

The enzyme nitrogenase is inhibited by oxygen. Which of the following does NOT protect nitrogenase from oxygen?

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) growth under aerobic conditions
E) growth under anaerobic conditions

Question 36

Industrial nitrogen fixation is achieved through the Haber process

A) in which N2 is reduced catalytically by H2 at ambient temperature.
B) in which N2 is hydrogenated by CH4 at extreme temperature and pressure.
C) in which nitrate and nitrite are chemically converted to NH at ambient temperature.
D) which requires little energy.
E) which is carried out by purified enzymes in a reactor.

Question 37

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

A) reverse TCA cycle.
B) 3-hydroxypropionate cycle.
C) Calvin cycle.
D) reductive acetyl-CoA pathway.
E) glyoxylate bypass.

Question 38

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

A) NADH
B) NADPH
C) ferredoxin
D) H2
E) O2

Question 39

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 40

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 41

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

Question 42

Which of 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) Both purines and pyrimidines use inosine monophosphate as a precursor.
E) Both purines and pyrimidines are built by adding carbon components to ribose 5-phosphate.

Question 43

Nitrogenase is diagrammed below. This particular enzyme is shown in the format just before it begins a cycle of nitrogen reduction. This goal is accomplished in four steps. What is the first step?

A) N2 gas binds to the active site on the FeMo protein.
B) NADPH binds to the active site in order to reduce it prior to N2 binding.
C) Two e - are transferred to the Fe protein and then to the FeMo protein, which are used to reduce H+ to H2 prior to N2 binding.
D) The preexisitng NH4+ is removed prior to N2 binding.
E) Fe and Mo are bound to the active sites and then released prior to the next cycle.

Question 44

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 45

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 46

Briefly discuss how carbon molecules of different sizes can be made for biosynthesis. What else is needed and how is it obtained?

Question 47

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

Question 48

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

Question 49

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

Question 50

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 51

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 52

Which of the following is NOT a tetrapyrrole?

A) cytochrome
B) chlorophyll
C) vitamin B12
D) tryptophan
E) hemoglobin

Question 53

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

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

Question 54

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 55

Which amino acid is NOT one of the first amino acids produced by ancient cells?

A) glutamate
B) tyrosine
C) glycine
D) valine
E) asparate

Question 56

Which of the following molecules CANNOT freely cross biological membranes?

A) O2
B) CO2
C) NH4+
D) N2
E) H2O

Question 57

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) 2-oxoglutarate aminase (2-OA); glutamine
E) 2-oxoglutarate dehydrogenase (2-ODH); glutamine

Question 58

Which of the following does NOT serve as an intermediate in the biosynthesis of amino acids?

A) citrate
B) 2-oxoglutarate
C) pyruvate
D) 3-phosphoglycerate
E) pentose phosphate

Question 59

Which of the following drugs is a nonribosomal peptide antibiotic?

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

Question 60

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

Question 61

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

Question 62

Certain amino acids are more energetically expensive than others (tryptophan versus glutamate). Thus, when proteins are moved to the cell surface, extended outside the surface, or secreted out of the cell, there is a potential harm. Why is this potentially harmful, and what adaptations do bacteria have for this potential loss? Give an example.

Question 63

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 64

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

Question 65

What are nonribosomal peptide antibiotics? How are they synthesized?

Question 66

How do cyanobacteria benefit from their heterocysts attracting heterotrophic bacteria?

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

How is fatty acid biosynthesis regulated in bacteria?

Question 69

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 70

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

Question 71

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

Question 72

Discuss evidence that supports the idea that glutamate, aspartate, alanine, glycine, and valine were the first amino acids produced by ancient cells.

Question 73

Briefly describe the biosynthetic pathway for arginine.