Ch. 14

Question 1

Many prokaryotes can grow on C₁ compounds as their sole source of carbon. List some common C₁ compounds that support growth.

Answer 1

1. Carbon dioxide (CO₂)
2. Methane (CH₄)
3. Methanol (CH₂OH)
4. Methylamine (CH₃NH₂)

Question 2

A few strictly anaerobic prokaryotes that use carbon dioxide as a source of cell carbon also use it as an electron acceptor, reducing it to methane and deriving ATP from the process. These are the _____.

Answer 2

methanogens

Question 3

What are the 3 major autotrophic CO₂ fixation pathways in prokaryotes?

Answer 3

1. Calvin cycle
2. Acetyl-CoA pathway
3. Reductive TCA pathway

Question 4

The Calvin cycle makes _____ completely from _____.

Answer 4

1. PGALD
2. CO₂

Question 5

Where does the Calvin cycle take place in plants/algae vs. bacteria?

Answer 5

• Plants/algae: chloroplasts
• Bacteria: cytosol

Question 6

Summarize the Calvin cycle:
1. How many CO₂ molecules are reduced to PGALD?
2. How many electrons are required?
3. What provides the electrons? How many molecules of this are needed?

Answer 6

1. 3 CO₂ molecules
2. 12 electrons
3. 6 molecules of NAD(P)H

Question 7

For the Calvin cycle, NAD(P)H is not a sufficiently strong reductant to reduce CO₂ without an additional source of energy. How many ATPs are required for all the reductions?

Answer 7

6 ATPs (there are 6 reductions)

Question 8

What is the overall reaction of the Calvin cycle?

Answer 8

3CO₂ + 9 ATP + 6 NAD(P)H + 6H⁺ + 5H₂O –> PGALD + 9 ADP + 8 P_i + 6 NAD(P)⁺

Question 9

What are the 2 stages of the Calvin cycle?

Answer 9

1. Reductive carboxylation of RuBP to form PGALD
2. Consists of sugar rearrangements regenerating RuBP by using of the PGALD produced in Stage 1

Question 10

Explain what is happening in this diagram (Calvin cycle).

Answer 10

Question 11

What is the whole point of the sugar rearrangements of Stage 2?

Answer 11

To regenerate 3 RuBPs from 5 of the 6 PGALDs made in Stage 1

Question 12

What can the intermediates formed in the Calvin cycle be used for?

Answer 12

Can be used as precursors or used to make other precursors for biosynthesis

Question 13

Explain what is happening in this diagram (relationships between the Calvin cycle, glycolysis, and the PPP).

Answer 13

• Reaction 1: carboxylation of ribulose-1,5-bisphosphate is unique to the Calvin cycle
• Most of the other reactions also take place in glycolysis and the PPP
• The 12 reactions in the figure comprise the Calvin cycle
• The 3-phosphoglycerate enters glycolysis
• Reactions 2-6 take place during the reversal of glycolysis –> F-6-P
• F-6-P enters the PP at the sugar rearrangements (reaction 1)
• Calvin cycle diverges from PPP at reaction 8 (but produces the same intermediates/precursors)

Question 14

What are the 4 steps of the acetyl-CoA pathway? (In other words, how is acetyl-CoA made from CO₂ and H₂?)

Answer 14

1. Reduction of CO₂ to a methyl group (CH₃)
   - Methyl group transferred from THF to CODH
2. Reduction of a second molecule of CO₂ to a bound carbonyl group (CO)
   - Will become the carbonyl group of acetate
3. The bound methyl and carbonyl groups are condensed to form bound acetyl (CH₃CO)
4. The bound acetyl reacts with bound CoASH (CoAS) to form acetyl-CoA
   - Acetyl-CoA release from CODH

Question 15

Bacteria that use the acetyl-CoA pathway include:

Answer 15

• Methanogens
• Acetogenic bacteria
• Most autotrophic sulfate-reducing bacteria

Question 16

What is the fate of acetyl-CoA?

Answer 16

• Converted to acetate and excreted
  OR
• Assimilated into cell material (fatty acid synthesis)

Question 17

How does the acetyl-CoA pathway in methanogens (type of archaea) differ from the pathway in bacteria? (3 differences)

Answer 17

1. Co-factors
   - Carrier for the formyl is THMP instead of THF
2. Utilization of formate (CHOOH)
   - Instead of reducing free CO₂ to formate, they fix CO₂ onto a C₁ carrier called MFR and reduce it to formyl-MFR
3. Incorporation of acetyl-CoA
   - Convert it into PEP (feeds into incomplete TCA cycle –> gluconeogenesis)

Question 18

Explain what is happening in the figure (assimilation of acetyl-CoA into cell material in methanogens.

Answer 18

Question 19

Bacteria that use the reductive TCA cycle are:

Answer 19

1. Strict anaerobes: Desulfobacter and Chlorobium
2. Aerobe: Hydrogenobacter
3. Also present in archaea

Question 20

What is used to regenerate PEP (reductive TCA cycle)?

Answer 20

Acetyl-CoA

Question 21

What is the overall reaction of the reductive TCA cycle?

Answer 21

Synthesis of 1 mole of oxaloacetate and 4 moles of carbon dioxide

Question 22

To reverse the TCA cycle, 3 new enzymes are required. What are they and what TCA enzymes do they replace?

Answer 22

1. Fumarate reductase (succinate dehydrogenase)
2. α-Ketoglutarate synthase (α-Ketoglutarate dehydrogenase)
3. ATP-dependent citrate lyase (citrate synthase)

Question 23

What are methylotrophs?

Answer 23

Aerobic bacteria that can grow on compounds other than CO₂ that don’t have C-C bonds

Question 24

Methylotrophs oxidize _____ to _____.

Answer 24

1. C₁ compounds
2. CO₂

Question 25

What are the 3 pathways for formaldehyde incorporation in methylotrophs?

Answer 25

1. Serine-isocitrate lyase pathway
2. Ribulose-monophosphate cycle
3. Ethylmalonyl-CoA pathway for formaldehyde incorporation

Question 26

Summarize what happens in the carbon cycle.

Answer 26

• The methane produced by methanogens escapes into the aerobic atmosphere –> it is transformed back into CO₂ by aerobic methylotrophs
• CO₂ is reduced to organic carbon in the aerobic environments by photosynthetic eukaryotes and chemoautotrophic prokaryotes
• In anaerobic environments by, photosynthetic prokaryotes, acetogens, and methanogens

Question 27

In what type of anaerobic environments does methanogenesis occur?

Answer 27

• Swamps and marshes
• Mammalian rumen
• Termite intestines
• Anaerobic microenvironments in soil/lake muds/rice paddies