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MCB 229 Spring 2000 Study Guide 9 Prof. Terry
Covers Lecture for March 7

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 #9, based on questions from this study guide, must be completed by midnight before the class on Tuesday, March 7. You will need to create your "myWebCT" account and visit the MCB 229 WebCT page in order to access this quiz.

Chapter 10 (p. 191-193; 196-203; 206-208)
  1. Some pathways such as the Embden-Meyerhof pathway can occur in both directions, either catabolically (breaking glucose down), or anabolically (building glucose up). Are the same enzymes used for both directions? ___ Yes ____ Most are shared, but a few are different ___ All are different
  2. What redox carrier is used mainly by catabolic reactions? ________ What redox carrier is used mainly for anabolic reactions? ________
  3. What is meant by "substrate-level phosphorylation"?
  4. Of what value are phosphatase enzymes to bacteria? (Think! Remember that cells need CHNOPS)
  5. Sulfur is one of the CHNOPS requirements – what is it used for (be specific)? If the only sulfur source available is sulfate ion, what do microbes have to do to convert this into a usable form?
  6. What is the basic difference between assimilatory and a dissimilatory reduction of sulfate, SO4=? What is the end product of each reduction? What happens to each of these end products? This is a very important distinction – it will recur several times in these readings.
  7. Pay special attention to nitrogen metabolism. Write out the structural formulas for the following compounds to be sure you are familiar with them: nitrogen gas, nitrate, nitrite, and ammonia.
  8. Organisms obtain their nitrogen by one of three basic routes: (1) ____________________, (2) _____________________ or (3) _____________________
  9. What reaction does the enzyme glutamate dehydrogenase carry out? Write this reaction out to include the structure of alpha-ketoglutarate and glutamic acid (you can find their structures on p. 198). Note that alpha-ketoglutarate is a TCA cycle compound and will be produced in appreciable quantity when organisms are growing on sugars or fats; this reaction is often the major reaction for converting ammonia into an organic –NH2 group.
  10. Once amino groups have been created, how are they transferred to create other compounds? What class of enzymes is involved?
  11. What is assimilatory nitrate reduction? What is the starting point? What is the ending compound? What additional components are required? What metal is required for this process? What enzymes are involved?
  12. Nitrogen accounts for ____ % of the atmosphere, yet it is generally unavailable for living organisms. Certain bacteria are able to convert N2 into NH3, a process called _______________________. What enzyme carries out this process? ___________ What additional materials are required? ______________ What metal(s) is(are) required for this process?___________
  13. Synthesis of amino acids is the most common metabolic activity for most cells, since amino acids are the precursors of proteins. I don't expect you to learn the pathways for synthesis of all 20 amino acids, only to know the general features. Study Fig. 10.17, which shows how amino acids branch out of the Embden-Meyerhof and TCA cycle. There are 3 "parent compounds" in central metabolism that serve as the starting point for synthesis of most (15) of the amino acids; what are they? (1) ____________ , (2) ____________ , (3) ____________ . Note also that the parent compound for aromatic amino acids (phenylalanine, tyrosine, tryptophan) is _____________ , derived from the pentose phosphate pathway.
  14. The need for "anaplerotic reactions" (or "refilling reactions") arises because pathways like TCA cycle are used for both anabolic and catabolic reactions. For example, if a cell is using glucose as its sole C-source, it must catabolize some glucose to make ATP, but it must also use some glucose to make amino acids and proteins (which require the ATP just made). For example, it's possible that for every 100 molecules of glucose, when we get down to the TCA cycle, 50 are going to be removed, e.g., by converting alpha-ketoglutarate into glutamic acid (and thence to other amino acids). That leaves only 50 molecules to continue around the TCA cycle to produce oxaloacetate, which means that for the next 100 molecules of glucose being broken down to pyruvate and acetyl CoA, the TCA cycle doesn't have enough oxaloacetate to handle them. And the situation gets worse with every turn of the cycle! What's a poor bacterium to do? They use an "anaplerotic reaction" to add some extra molecules into the TCA cycle. What is this reaction called? ___________________ It can occur in two variant forms: both produce oxaloacetate, but they use different enzymes and different substrates. What are the two starting materials? _______ and ________.
  15. Note that the glyoxylate cycle (Fig. 10.20) presents another way for cells to "refill" TCA cycle intermediates. This pathway is only used when cells are growing on _____________ as a carbon source, in which case glycolysis is not used and the anaplerotic reaction described in the previous question cannot be used.
  16. Skim the discussion of purines, pyrimidines, nucleotides, and lipid synthesis. You're not responsible for this material.
  17. Briefly look at the section on peptidoglycan synthesis on pp. 206-208. Note that the amino sugars NAG and NAM are bound to a carrier molecule. Next, _____________ (how many?) amino acids are added. Then the nascent chain is transferred to a different carrier, ______________ , that can cross the cell membrane. Next, NAG is added, the complete subunit is translocated across the membrane, and finally the subunit is incorporated into the cell wall by the process of ____________, in which a peptide bond links the peptides.

Chapter 40 (p. 832-839)
  1. What is meant by a producer? A consumer? A decomposer? Are all producers phototrophs? Where are non-photosynthetic producers found?
  2. What is a hydrothermal vent? Where can you find them?
  3. What is meant by "mineralization"? What is a "microenvironment"? Look at Fig. 40.5 for an example of how a microenvironment can be created at the confluence of two gradients. This situation occurs commonly in nature.
  4. What is an oligotrophic environment? How do bacteria adapt to such environments?
  5. Biogeochemical cycling refers to the frequent interconversions of elements into different organic and inorganic components. Let's follow the fate of one oxygen atom, in an O2 molecule you just breathed in, for example. It circulates into your liver and is turned into H2O during respiration. A few hours from now it is been flushed out towards the Willimantic River. En route, it gets inside an E. coli in the sewage plant and, during a hydrolysis reaction, becomes an –OH group on an amino acid. The bacterium is eaten by a single-celled protist and the amino acid becomes part of a protein. The protist is eaten by a water bug, and the protein is digested in the gut, during which the oxygen atom is again released as water. The water molecule drifts down to Long Island sound, where it gets inside a photosynthetic diatom. Photosynthesis occurs and the oxygen is released into the air as O2. It travels for several years before being breathed in by another animal. And so forth.... This kind of story can be written for each atom of every element. We will consider only 3 cycles: carbon, nitrogen, and sulfur.
  6. Carbon cycle: study fig. 40.7. Note that there both aerobic and anaerobic processes; and that different processes occur in these 2 compartments. I recommend studying the cycle, closing your book, and trying to recreate the cycle from memory and logic.
  7. Sulfur cycle: study fig. 40.8, which is unfortunately not especially clear. Note the difference between assimilatory and dissimilatory sulfate reduction. Which occurs only anaerobically? I recommend also looking at my animation, linked from the lecture notes on this topic: <http://www.sp.uconn.edu/~terry/229sp00/lectures/Scycleanim.html> I recommend studying the cycle, closing your book, and trying to recreate the cycle from memory and logic.
  8. Nitrogen cycle: study Fig. 40.9. I also recommend also looking at my animation, linked from the lecture notes on this topic: <http://www.sp.uconn.edu/~terry/229sp00/lectures/Ncycleanim.html> What is meant by the terms: nitrification? Denitrification? Assimilatory nitrate reduction? Dissimilatory nitrate reduction? Which processes are carried out by chemolitotrophs? By anaerobic respirers? I recommend studying the cycle, closing your book, and trying to recreate the cycle from memory and logic.
  9. You're not responsible for the rest of the material in this chapter. If you have a moment, skim the contents so you know what's here and where to find it. If you have more than a moment, read on, especially the material on cycling of iron and other metals. This is interesting stuff. This chapter may be useful if you write the second extra credit paper on microbes and environment.