Q1. Explain the Calvin cycle process that produces a full molecule of glucose and regenerates the ribulose bisphosphate molecule.

Background

Topic: Calvin Cycle (Photosynthetic Carbon Fixation)

This question tests your understanding of the Calvin cycle, which is the primary pathway for carbon fixation in photosynthetic organisms. It involves the conversion of CO2 into glucose and the regeneration of ribulose bisphosphate (RuBP).

Key Terms and Formulas:

• Ribulose bisphosphate (RuBP): The molecule that accepts CO2 in the cycle.

• Glucose: The end product of the cycle after two turns.

• ATP and NADPH: Energy carriers used in the cycle.

• Key formula:

Step-by-Step Guidance

1. Describe the three main phases: carbon fixation, reduction, and regeneration.

2. Explain how CO2 is incorporated into RuBP by the enzyme Rubisco, forming 3-phosphoglycerate (3-PGA).

3. Discuss how ATP and NADPH are used to convert 3-PGA into glyceraldehyde-3-phosphate (G3P).

4. Show how two G3P molecules are combined to form one glucose molecule after multiple turns of the cycle.

5. Outline the steps involved in regenerating RuBP from G3P, using ATP.

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Q2. Under what circumstances does oxygenic photophosphorylation use noncyclic photophosphorylation and when does it use cyclic photophosphorylation? Also, describe what occurs during each process.

Background

Topic: Photosynthetic Electron Transport

This question tests your understanding of the two types of photophosphorylation in oxygenic photosynthesis: cyclic and noncyclic, and the conditions under which each occurs.

Key Terms and Formulas:

• Noncyclic photophosphorylation: Involves both Photosystem II and I, produces ATP and NADPH, releases O2.

• Cyclic photophosphorylation: Involves only Photosystem I, produces ATP but not NADPH or O2.

• Key formula: (water splitting in noncyclic)

Step-by-Step Guidance

1. Identify the role of Photosystem II and Photosystem I in noncyclic photophosphorylation.

2. Explain how electrons flow from water to NADP+ in noncyclic, producing O2 and NADPH.

3. Describe the conditions (e.g., high NADP+ demand) that favor noncyclic photophosphorylation.

4. Discuss how cyclic photophosphorylation occurs when NADPH is abundant and more ATP is needed.

5. Outline the electron flow in cyclic photophosphorylation (electrons return to Photosystem I), resulting in ATP production only.

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Q3. Why does an organism that is able to respire both aerobically and anaerobically preferentially undergo aerobic respiration?

Background

Topic: Aerobic vs. Anaerobic Respiration

This question tests your understanding of the energetic differences between aerobic and anaerobic respiration and why organisms prefer aerobic conditions.

Key Terms and Formulas:

• Aerobic respiration: Uses O2 as the terminal electron acceptor, yields more ATP.

• Anaerobic respiration: Uses other electron acceptors (e.g., nitrate, sulfate), yields less ATP.

• Key formula:

Step-by-Step Guidance

1. Compare the energy yield (ATP) of aerobic vs. anaerobic respiration.

2. Explain the role of oxygen as a highly efficient electron acceptor.

3. Discuss how the redox potential of O2 allows for maximum energy extraction from substrates.

4. Describe the ecological and physiological reasons for preferential aerobic respiration.

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Q4. How do Cyanobacteria impact the ecology of both aquatic and terrestrial environments on Earth?

Background

Topic: Cyanobacteria and Ecosystem Function

This question tests your knowledge of the ecological roles of Cyanobacteria, including their contributions to primary production and nitrogen fixation.

Key Terms and Formulas:

• Primary production: Synthesis of organic compounds from CO2.

• Nitrogen fixation: Conversion of atmospheric N2 to ammonia.

• Key formula:

Step-by-Step Guidance

1. Describe the role of Cyanobacteria in photosynthesis and oxygen production.

2. Explain their ability to fix nitrogen and its importance for nutrient cycling.

3. Discuss their impact on aquatic ecosystems (e.g., algal blooms, primary production).

4. Describe their role in soil fertility and terrestrial ecosystems.

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Q5. Based on your knowledge of microbial transformations of inorganic nitrogen species, what impact would you predict extensive tilling to have on the fate of ammonium-based nitrogen fertilizer?

Background

Topic: Nitrogen Cycle and Soil Microbiology

This question tests your understanding of how soil oxygenation affects microbial nitrogen transformations, especially nitrification and loss of nitrogen from soil.

Key Terms and Formulas:

• Nitrification: Conversion of NH4+ to NO3- by microbes.

• Denitrification: Reduction of NO3- to N2 gas.

• Key formula: (nitrification)

Step-by-Step Guidance

1. Explain how tilling increases soil oxygen levels.

2. Describe how increased oxygen promotes nitrification by aerobic bacteria.

3. Discuss the mobility of nitrate and its tendency to leach from soil.

4. Predict the fate of ammonium-based fertilizer under extensive tilling.

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Q6. What metabolism would be favored when there is a lack of electron acceptors?

Background

Topic: Metabolic Pathways and Electron Acceptors

This question tests your understanding of how cells adapt their metabolism when external electron acceptors are unavailable.

Key Terms and Formulas:

• Fermentation: Metabolic process that does not require external electron acceptors.

• Substrate-level phosphorylation: ATP generation in fermentation.

• Key formula:

Step-by-Step Guidance

1. Identify the role of electron acceptors in respiration.

2. Explain why fermentation is favored when electron acceptors are absent.

3. Describe how ATP is produced via substrate-level phosphorylation in fermentation.

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Q7. Escherichia coli can grow in glucose broth both aerobically and anaerobically. When grown aerobically, these bacteria divide every 20 minutes. However, when grown anaerobically they require about 100 minutes to divide. What may account for this difference in growth rate?

Background

Topic: Microbial Growth Rates and Metabolism

This question tests your understanding of how energy yield affects microbial growth rates under different conditions.

Key Terms and Formulas:

• Aerobic respiration: High ATP yield.

• Anaerobic respiration: Lower ATP yield.

• Key formula:

Step-by-Step Guidance

1. Compare the ATP yield of aerobic and anaerobic respiration.

2. Explain how ATP availability affects cell division and growth rate.

3. Discuss the metabolic pathways used under each condition.

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Q8. What is the Glyoxylate shunt or cycle and what is it important for?

Background

Topic: Glyoxylate Cycle and Metabolic Adaptation

This question tests your understanding of the glyoxylate cycle, which allows organisms to convert fatty acids into carbohydrates.

Key Terms and Formulas:

• Glyoxylate cycle: Modified TCA cycle.

• Key enzymes: Isocitrate lyase, malate synthase.

• Key formula:

Step-by-Step Guidance

1. Describe the steps of the glyoxylate cycle and its key enzymes.

2. Explain how the cycle bypasses decarboxylation steps of the TCA cycle.

3. Discuss its importance for growth on acetate or fatty acids.

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Q9. Differentiate between exergonic and endergonic in terms of free-energy calculations.

Background

Topic: Thermodynamics in Biochemistry

This question tests your understanding of the concepts of exergonic and endergonic reactions based on Gibbs free energy.

Key Terms and Formulas:

• Exergonic: Releases energy, .

• Endergonic: Requires energy input, .

• Key formula:

Step-by-Step Guidance

1. Define exergonic and endergonic reactions in terms of .

2. Explain how negative indicates spontaneous reactions.

3. Discuss the implications for cellular metabolism.

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Q10. Describe in as much detail as possible what Nitrogen fixation is and what the key products of this process are.

Background

Topic: Nitrogen Fixation

This question tests your understanding of the biochemical process of nitrogen fixation and its ecological significance.

Key Terms and Formulas:

• Nitrogenase: Enzyme complex responsible for fixation.

• Key formula:

Step-by-Step Guidance

1. Describe the role of nitrogenase in breaking the triple bond of N2.

2. Explain the energy requirements and electron donors for the process.

3. List the key products: ammonia (NH3) and hydrogen (H2).

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Q11. Define anaplerotic reactions and give one example of such. See Q8 as example.

Background

Topic: Anaplerotic Reactions in Metabolism

This question tests your understanding of reactions that replenish TCA cycle intermediates.

Key Terms and Formulas:

• Anaplerotic: Reactions that refill metabolic cycle intermediates.

• Key formula: (via pyruvate carboxylase)

Step-by-Step Guidance

1. Define anaplerotic reactions and their importance.

2. Provide an example, such as pyruvate carboxylation.

3. Explain how these reactions maintain TCA cycle function.

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Q12. What does this equation define? Give names and values where known for each term in the equation. What would negative or positive values of the equation imply for chemical reactions? ∆G°′ = [−nF] ∙ [∆E′o ]

Background

Topic: Bioenergetics and Redox Reactions

This question tests your understanding of the relationship between free energy change and redox potential.

Key Terms and Formulas:

• : Standard free energy change.

• : Number of electrons transferred.

• : Faraday constant (96,485 C/mol).

• : Standard reduction potential difference.

• Key formula:

Step-by-Step Guidance

1. Identify each term in the equation and its significance.

2. Explain how relates to electron transfer.

3. Discuss the meaning of negative and positive values.

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Q13. Calculate the ∆G°′ for each of the above reactions. What type of reactions are these?

Background

Topic: Redox Reactions and Bioenergetics

This question tests your ability to calculate free energy changes for redox reactions using the redox tower.

Key Terms and Formulas:

• : Standard free energy change.

• : Standard reduction potential difference.

• Key formula:

Step-by-Step Guidance

1. Identify the electron donors and acceptors for each reaction.

2. Determine from the redox tower for each pair.

3. Set up the calculation for using the formula.

4. Do not perform the final calculation yet; prepare the values for the next step.

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Q14. What does the Great Plate Count Anomaly refer to and how would the microbial ecologist trying to describe an ecosystem circumvent this problem?

Background

Topic: Microbial Ecology and Cultivation

This question tests your understanding of the limitations of culturing microbes and alternative methods for ecosystem analysis.

Key Terms and Formulas:

• Great Plate Count Anomaly: Discrepancy between microscopic and culture-based counts.

• Alternative methods: Molecular techniques, direct microscopy.

Step-by-Step Guidance

1. Define the Great Plate Count Anomaly.

2. Explain why most microbes are not culturable on standard media.

3. Describe alternative approaches for ecosystem analysis.

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Q15. In class you were introduced to three types of photosynthesis carried out by phototrophic bacteria. What are the major differences between these three and what groups of microbes carry out which form? Be sure to distinguish between electron donation and acceptance, energy production and photosystem type.

Background

Topic: Bacterial Photosynthesis Diversity

This question tests your understanding of the different types of photosynthesis in bacteria, including oxygenic and anoxygenic forms.

Key Terms and Formulas:

• Oxygenic photosynthesis: Uses water as electron donor, produces O2.

• Anoxygenic photosynthesis: Uses other donors (e.g., H2S), does not produce O2.

• Photosystem types: I and II.

Step-by-Step Guidance

1. List the three types: oxygenic, anoxygenic (purple bacteria), anoxygenic (green bacteria).

2. Describe the electron donors and acceptors for each type.

3. Explain the energy production and photosystem differences.

4. Identify the microbial groups associated with each type.

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Q16. In one sentence describe the above process and fill in each numbered label

Background

Topic: Photosynthetic Electron Transport Chain

This question tests your ability to identify and describe the components of the photosynthetic electron transport chain.

Key Terms and Formulas:

• Photosystem II, Photosystem I, electron carriers, ATP synthase.

• Key formula:

Step-by-Step Guidance

1. Briefly describe the overall process (light-driven electron transport).

2. Identify each numbered label based on the diagram.

3. Explain the function of each component in the chain.

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Q17. Distinguish between Dissimilative Sulfur reducers and dissimilative sulfur oxidizers

Background

Topic: Sulfur Metabolism in Microbes

This question tests your understanding of microbial sulfur transformations and their ecological roles.

Key Terms and Formulas:

• Dissimilative sulfur reduction: Reduction of sulfate to sulfide for energy.

• Dissimilative sulfur oxidation: Oxidation of sulfide to sulfate for energy.

• Key formula: (reduction), (oxidation)

Step-by-Step Guidance

1. Define dissimilative sulfur reduction and its products.

2. Define dissimilative sulfur oxidation and its products.

3. Explain the ecological significance of each process.

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