Discussion Questions

Biogeochemistry – Chapter 2

  1. Why is Fe the most prevalent transition metal in biological processes?
  1. Why is dioxygen rare in the Universe?
  1. Distinguish element abundance and element availability.
  1. Look at the charts of elemental abundances in Figs. II-3, -4, -5: why is there a gap in the middle?
  1. What makes Mo and W so unique among the 2nd and 3rd row transition metals?
  1. How did cyanobacteria shape the Earth’s biosphere as we know it?
  1. How do plant and bacterial photosynthesis differ?
  1. What is the basic (i.e. fundamental) equilibrium position of all Life?
  1. Discuss the results of dioxygen increase.
  1. What are some key roles of anaerobes?
  1. Distinguish methanogens, methanotrophs and acetotrophs.
  1. There are several symbiotic relationships between different organisms mentioned.   Describe one of these.
  1. Distinguish nitrogen fixation, (why is it called “fixed”?), nitrification, denitrification, assimilation, dissimilation.
  1. Can you point to human interference in otherwise stable biogeochemical cycles?
  1. DMSO, the smell of the sea and rain: what do these have in common?
  1. Summarize the relationship of metalloproteins and biogeochemistry.
  1.  It used to be the Russians.  Then it was certain orthodox Middle Eastern fanatics. Who should we really fear?

 

 

 

 

 

 

Electron Transfer Proteins – Chapter 10.1

  1. What are the requirements for fast and efficient lectron transfer between proteins?

  2. What metals exclusively are used in ET (electron transfer) proteins?

  3. What are the potential ranges for redox processes done by heme proteins, FeS proteins and blue copper proteins?

  4. What are the ways that the ET proteins can modulate the potentials of their redox centers? Have ready a couple of specific examples.

  5. Provide a couple of examples of how the crystal field of a metal is related to its redox properties.

  6. What is a HiPIP?

  7. In which biological domains are the different ferredoxins found?

  8. What axial ligation is used in ET hemes?

  9. Which of the four classes of copper proteins are ET proteins?

  10. What is similar about the FeS ET proteins and blue Cu ET proteins structures?

  11. Why are blue copper proteins blue? Explain process that causes color.

 

 

 

 

 

 

 

 

 

 

 

Electron Transfer Proteins – Chapter 10.3-4

  1. What is new in this book’s presentation of respiration?  What is confusing?
  2. What is the reaction that provides the energy to drive ATP formation in respiration?
  3. What is Eo’?
  4. What is the molecule essential for creating the H+ gradient?
  5. What are 2 requirements of chemiosmotic hypothesis?
  6. How many metals ae involved in respiration? 
  7. In what types of centers are these metals?
  8. What are the roles of these metals?
  9. How many proteins are involved?
  10. What are roles of these proteins?
  11. Explain all the components of Figure 10.3.5.
  12. Which metalloproteins have their own name?
  13. PS is separated into two processes: what are they and what is the role of each?
  14.  What is the “OEC”?
  15. How is the energy of light converted in chemical energy (in first step)?
  16. How many metals are involved in photosynthesis? 
  17. How many metals are involved in respiration? 
  18. Can you account for OEC electrons in Figure 10.3.15 (that compares OEC in PSII and CuB in respiration) and in Figure 10.4.6?
  19. What are the similarities and differences of respiration and photosynthesis?

 

 

 

 

 

Dioxygen in Biology - Chapter 11

section 1

1.What is the reduction scheme for molecular oxygen (inthe absence of enzyme catalysis)?

2. What are oxygen atom transfer reactions? Are they thermodynamically or kinetically unfavorable? Explain.

3. Why are free radical auto-oxidation pathways for OAT reactions not useful in biological systems?

4. Write out the flavin activation of dioxygen. Why is this reaction unique in biology? And, what is a flavin?????!!!!!!

5. What is inherently unstable about the presence of dioxygen in cells?

6. What are ROS? Make a list of them.

7. Make alist of biological antioxidants. Draw structures (where appropriate) and note mechanism of their operation.

8. Use MOT to explain why peroxide (O2)2- is so unstable. Can you explain how this relates to superoxide persistence and toxicity in cells?

9. Calculation #1: what is the reduction potential for O2/H2O at pH 2? at pH 10?

10. Calculation #2: convert the O2 spin flip energy, i.e. from triplet to singlet from kcal/mol (in text) to kJ/mo, to eV, and to cm-1.

 

 

section 2 - Superoxide Dismutases

1. What is the major source of superoxide in cells?

2. Write the balanced equation for the reaction catalyzed by SOD. Why is a caltalyst needed to do this reaction?

3. How many types of SOD are discussed in this section?

4. What are the roles of metal ions in these SOD enzymes?

5. What are the roles of the two metals in CuZnSOD? What are their coordination environments and how do these change during catalytic turnover?

 

 

 

 

section 3 - Peroxidases and Catalases

1. What is the difference between peroxidases and catalases?

2. What two limiting mechanisms are considered for breaking the O-O bond in peroxide? Which is used by these enzymes and why?

3. The heme in peroxidases is exactly like that in globins, yet these two proteins have different functions. What are these functions and how is the different reactivity controlled?

4. The text says: "the Fe3+/Fe2+ redox potential is lower in peroxidases compared to the globins." How is the Fe(3+/2+) potential adjusted in peroxidases? And, improve on the text's writing: how does the Fe(3+/2+) potential change in the peroxidases, that is, does it become more or less favorable?

5. How is the catalase active site unique?

6. In the mechanism for peroxidase, can you account for the electron movement among the various players in each step?

 

 

 

section 11. 4 - Oxygen Carriers

1. What are dioxygen-carrier proteins and what are the three types of dioxygen carriers?
2. What is cooperativity and what are the advantages of cooperative ligand binding vs. non-cooperative binding of O2?
3. Besides providing ligands to the metal center, what other roles do the dioxygen carrier proteins play?
4. What is "nested allostery" and what is its significance with respect to hemocyanin?
5. What is the role of water in the discrimination process between O2 and CO2 binding to mammalian Mb (monomeric Hemoglobin)?

6. What are the proximal and distal effects in modulation of ligand binding in proteins andhow do they affect O2 affinity?

7. What is similar in dioxygen binding by Hr and Hc ?

 

 

 

 

 

 

 

 

section 11. 5 - Oxygen Activating Enzymes

1. What is the first step in oxygen activation? What is the challenge of oxygen activation?

2. What are the three known types of O2 carriers and their corresponding oxygen-activating enzymes? Why are they important?

3. How does the active site of cytochrome P450 differ from that of hemoglobin? How does cytochrome P450 get its name?

4. What is the function of Cyt P450?

5. What is the catalytic mechanism for cytochrome P450? What are the proposed active species that may form upon the second electron to oxyP450, and what are some things discussed in the section regarding these proposed active species?

6. Tyrosinase and MMOH are enzymes that also have dinuclear active sites. What are the important consequences of introducing a second metal ion to an active site for oxygen activation?

7. How are tyrosinase and hemocyanin alike?

8. For the section regarding monooxygenase with a dicopper active site, describe some of the proposed mechanisms of O2 activation at a dicopper center and copper-dioxygen interactions. How are these dicopper complexes different from heme systems?

9. What i the most important Figure in section 11.5?

10. What are the common features of the proposed mechanisms for oxygen activation at the three distinct active sites discussed in Section XI.5.1?

 

 

section 11. 6 - Oxygen Reduction to Water

1) What are the basic facts on cytochrome c oxidase: its function, location, major players?

2) What are the two hemes and what is their role in cytochrome c oxidase?

3) What is the role of Cu(B) and Cu(A)?

4) What are the three steps to dioxygen reduction?

5) What do K and D pathways tell us about proton transfer?

6) Look at the respiratory chain diagram on p. 286. Which complex does cytochrome c oxidase correspond to and what is its function in respiration?

7) How does the effectivity of cytochrome c oxidase ATP formation compare to that in glycolysis?

8) What metals are found in cytochrome c oxidase?

 

 

 

section 12.1 - Hydrogen Metabolism

Here are our questions for chapter XII.1 :

1) What are the two main types of H2ases? What is common between the two types?

2) What is unusual about the metal environments at the catalytic sites of H2ases?

3) What kinds of organisms uses H2ases and for what purpose(s)?

4) How was EXAFS and XANES spectroscopies used in H2ase research?

 

 

section 12.2 - Carbon Metabolism

Here are our questions for chapter XII.2 :

1) Why is biological C1 reduction important for industrial chemistry?

2) How many different metallo-active sites are involved in C1 biocatalysis? List/draw them.

3) How many different redox cofactors are involved in C1 biocatalysis? List/draw them.

4) What familiar N-heterocycle makes an appearance? What is its role?

5) Identify all the organometallic species involved in sections 12.1 and 12.2.