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MCB 229 Spring 2000 Study Guide 12 Prof. Terry
Covers Lecture for March 16

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 #12, based on questions from this study guide, must be completed by midnight before the class on Thursday, March 16. You will need to create your "myWebCT" account and visit the MCB 229 WebCT page in order to access this quiz.

Chapter 12 (p. 237-250)
  1. This chapter presents a lot of examples of different types of regulatory mechanisms. It is easy to get lost in the details. Broadly speaking, there are three major categories of regulatory mechanisms:
    • regulation by channeling
    • regulation of enzyme activity.
    • regulation of enzyme synthesis
    For each of these, what effect does the regulatory system have? How quickly (if at all), can the cell "change gears" when conditions change? Metabolic channeling is not nearly as important in bacteria as it is in eukaryotes, and we will skip over it.
  2. What is an allosteric enzyme? What are the two types of sites present in all such enzymes? Note that allosteric enzymes are constructed differently: some respond to effector binding by increasing activity; others respond by decreasing activity. (As an analogy, realize that engineers could in principle design two types of floor pedals; one type speeds up the engine as you push down the petal – as in your car; the other type would slow down the engine as you pushed down the petal. No cars of the latter type have been built, for obvious reasons, but in the world of enzymes both analogous types exist.)
  3. A good number of enzymes exist in two forms: active and inactive. Converting from one form to the other requires addition (or removal) of a modification group, a chemical "tag". Phosphate is a common modification group; enzymes that add phosphate to other enzymes are called kinases.
  4. How does feedback inhibition work? In a biosynthetic pathway A -> B -> C -> D -> E, which molecule is most likely to be the feedback inhibitor? Why?
  5. What is an isozyme? Under what conditions would you expect to find isozymes?
  6. We examined the "TATA..." sequence as part of the consensus sequence for the E. coli promoter. Is this the "universal" promoter for E. coli (i.e., is this the –10 sequence that all sigma factors recognize)? What is meant by sigma70? By sigmaF? By sigma28? When would each of these be expressed?
  7. What is repression? What is induction?
  8. What is the difference between constitutive, inducible, and repressible genes? Give an example of each.
  9. Distinguish negative and positive control, and give an example of each.
  10. Where does a repressor protein bind in a bacterial operon? how does it affect the activity of RNA polymerase?
  11. What is lactose? What are the products of lactose hydrolysis? What enzyme is required for this hydrolysis?
  12. Diagram the structure of the lac operon. What is the role of each of the following regions of this operon: p site, o site, Z gene, Y gene. Why is this called an operon?
  13. Diagram the mRNA made from the lac operon. How many AUG (start) codons are found in this RNA?
  14. In the lac operon, under what conditions will the enzymes be synthesized? Under what conditions will they be repressed?
  15. How does positive control differ from negative control?
  16. The "classic" example of positive control in E. coli is catabolite repression. What is the function of the Catabolite Activator Protein (CAP)? What role does cyclic AMP play in regulation? What fate would you predict for a cell that mutated so it could not make c-AMP? What fate would you predict for a cell that mutated so it always made high levels of c-AMP? Describe some different genes regulated by catabolite repression. Why is this an example of “global” regulation?
  17. What is diauxic growth? How is it related to catabolite repression? What advantage might this mechanism provide for a bacterium?
  18. Most bacterial mRNAs are translated as they are being transcribed – coupled transcription/translation. There are some well-characterized exceptions, however, and attenuation of genes for the synthesis of tryptophan is the best-studied example. Under what environmental conditions does it make sense that tryptophan mRNA would stop being made? Examine Fig. 12.18 and text to see how attenuation works.
  19. Skim the material on antisense RNA and control of cell cycle; neat stuff, but I won't test you on this.