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MCB 229 Spring 2000 Study Guide 8

This study guide is intended for you to use while you are doing the assigned text reading. Quiz questions will be made with reference to topics in this study guide. Quiz #8, based on questions from this study guide, must be completed by midnight before the class on Thursday, Feb. 24. You will need to create your "myWebCT" account and visit the MCB 229 WebCT page in order to access this quiz.

1. Before you begin reading this material, take a moment to get an overview. The focus of this assignment is microbial autotrophs: organisms that use CO ₂ as their sole C-source. Since they don’t need organic materials (sugars, etc.) as a C-source, it’s a logical assumption that they can also make do without organic matter as an Energy source. In fact, there are two major groups of autotrophs: _______________, who get their energy from reduced inorganic molecules , and ________________, who get their energy from light.
2. I suggest reading pp. 193-195 first. Although the title is “The Photosynthetic Fixation of CO₂”, it applies to all autotrophs. The pathway is called the Calvin cycle (a.k.a. Calvin-Benson cycle, reductive pentose phosphate cycle). Where is this cycle localized in eukaryotes?____________ In cyanobacteria? _____________
3. Examine text and Fig. 10.4 to see the details of the Calvin cycle.
   (a) To what acceptor molecule is CO₂ added? ___________ (hint: see the blue box, “Carboxylation phase”)
   (b) What enzyme catalyzes the carboxylation reaction? ____________________ Note: This is the most abundant enzyme on planet earth!
   (c) What is the immediate product of the carboxylation reaction? _______________
   (d) In order to turn this product into reduced compounds such as sugars, what two additional reagents are necessary? _______________ and _______________ (hint: see the green box, “Reduction phase”).
4. The portions of the Calvin cycle in the purple box (“Regeneration phase”) look very confusing. It helps to understand what the purpose of this chemical dance is. For every 3 turns of the cycle (= 3 CO₂ molecules incorporated), it is possible to remove one 3-C reduced molecule as “product”. This creworked into amino acids, lipids, etc., for all the cell’s anabolic needs. All the other Calvin cycle intermediates must be recyled to generate more 5-C CO₂ acceptor molecules in order to be able to run the cycle again. So the challenge is to turn 3-C molecules into 5-C molecules. The Calvin cycle does this by an elaborate shuffle; two “3’s” are combined to make a “6”. A “6” is combined with a “3”, and the resulting 9 C-atoms reshuffled to a “4” and a “5”, and so forth. Try redrawing the purple diagram, replacing the molecular formulas with just the number of C-atoms in each molecule. You should note that overall logic: five 3-C molecules (15 total atoms) are rearranged to produce three 5-C molecules (same 15 total atoms).
5. It is customary to measure the Calvin cycle by what it “costs” to make one 6-C glucose molecule. How many turns of the cycle are necessary? _____ In addition to CO₂, what other molecules are necessary, and in what quantity? ___ molecules of _________; ___ molecules of _________ .
6. Pp. 179-182 describe one major group of autotrophs, the chemolithotrophs. How do they get their organic C? ___________ (the answer should be obvious; I’m just checking that you’re still awake!) List six possible molecules that can serve as their energy source: _____________ , _____________ , _____________ , _____________ , _____________ , _____________ .
7. Can chemolithotrophs ever use organic C as their carbon source? If so, do they then use organic C as their energy source?
8. Molecular hydrogen (H₂) is nature’s most perfect fuel. Not surprisingly, several bacterial genera have evolved the use of an enzyme, __________________ , in order to take advantage of H₂ as an energy source whenever it is around. What happens to H-atoms in such chemolithotrophs?
9. The nitrifying bacteria comprise two groups: the Nitrosomonas group, which use _____ as an energy source and produce _____ as waste, and the Nitrobacter group, which use ______ as an energy source and produce _____ as waste.
10. What is a major genus of sulfur oxidizing bacteria? __________ What waste product is produced by sulfur-oxidizing bacteria?_________ What impact does this have on the environment? (see Box 9.2)
11. Bacterial phototrophs (pp. 182-187) obtain energy from light. Their metabolism is often described in two stages: light reactions, in which they convert light energy into stored chemical energy, and dark reactions (= the Calvin cycle), in which they generate reduced organic molecules. There are two major groups of phototrophs, depending on whether they obtain electrons from water and produce oxygen (oxygenic) or obtain electrons from other sources and do not produce oxygen (anoxygenic). Which group(s) of bacteria are oxygenic? _________________ Which group(s) of bacteria are anoxygenic? _________________
12. What is the most common light-trapping pigment? __________________ What are common accessory pigments? ________________________________ Look at the structures of common pigments in Figs. 9.22 and 9.23 for recognition purposes.
13. What is an antenna? _______________ Roughly how many pigment molecules are in an antenna? _________________
14. The description of cyclic and noncyclic photophosphorylation is potentially confusing. This may help. Anoxygenic phototrophs (p. 185) have only one photosystem. When light reaches the reaction center, an electron is “excited” and released from bacteriochlorophyll to a higher energy state (see the upward arrows in Figs. 9.27 and 9.29). The electron now is passed from carrier to carrier (see downward arrows in same Figs.) until it reaches back to the initiating chlorophyll – it completes a cycle, so this is cyclic. This electron transport system is similar (but not identical) to the respiratory system – as electrons flow, protons are translocated to build up a protonmotive force. Add ATP synthase to the system and you can make ATP = photophosphorylation. Note that you don’t make NADPH directly from the cycle; how do anoxygenic phototrophs get their NADPH? ___________________ Why do they need NADPH? __________________ What waste product do they produce during this process? _________________
15. OK, now for noncyclic flow. Examine fig. 9.25. Note that there are two photosystems, called I and II. Start with PS I on the right. Light activates an electron, which is “excited” and released from bacteriochlorophyll to a higher energy state. It passes from carrier to carrier until it reaches NADP⁺. Here it combines (along with H⁺ ions) to form H atoms and generate reduced NADPH. Great, we’ve made NADPH! But the electrons have been removed, so how to get them back to the chlorophyll? Answer: use a second photosystem, PS II (left side of diagram). Once again, light energy excites and liberates electrons, and once again they are move from carrier to carrier in a membrane (this time they also translocate H+ ions, creating a proton gradient). Instead of going back where they started, these electrons flow to the reaction center of PS I, replacing electrons lost in the first excitation. So we’ve borrowed from Peter to pay Paul – now how can we repay Paul (e.g., where do we get electrons to replace those lost by the reaction center in PS II)? What’s the answer? ______________________
16. Which two groups of bacteria are anoxygenic phototrophs? _________________ and ________________ . How do they get their ATP? _____________________ How do they get their NADPH? ___________________________