Lodish H. - Molecular Cell Biology (5ed, Freeman, 2003) (794361), страница 62
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What are Watson-Crick base pairs? Why are theyimportant?2. TATA box–binding protein binds to the minor grooveof DNA, resulting in the bending of the DNA helix (seeFigure 4-5). What property of DNA allows the TATAbox–binding protein to recognize the DNA helix?3. Preparing plasmid (double-stranded, circular) DNA forsequencing involves annealing a complementary, short,single-stranded oligonucleotide DNA primer to one strand ofthe plasmid template. This is routinely accomplished by heating the plasmid DNA and primer to 90 C and then slowlybringing the temperature down to 25 C. Why does this protocol work?4. What difference between RNA and DNA helps to explain the greater stability of DNA? What implications doesthis have for the function of DNA?5. What are the major differences in the synthesis andstructure of prokaryotic and eukaryotic mRNAs?6. While investigating the function of a specific growth factor receptor gene from humans, it was found that two typesof proteins are synthesized from this gene.
A larger proteincontaining a membrane-spanning domain functions to recognize growth factors at the cell surface, stimulating a specific downstream signaling pathway. In contrast, a related,smaller protein is secreted from the cell and functions to bindavailable growth factor circulating in the blood, thus inhibiting the downstream signaling pathway. Speculate onhow the cell synthesizes these disparate proteins.7. Describe the molecular events that occur at the lacoperon when E. coli cells are shifted from a glucose-containingmedium to a lactose-containing medium.8. The concentration of free phosphate affects transcription of some E.
coli genes. Describe the mechanism for this.9. Contrast how selection of the translational start site occurs on bacterial, eukaryotic, and poliovirus mRNAs.10. What is the evidence that the 23S rRNA in the largerRNA subunit has a peptidyl transferase activity?11. How would a mutation in the poly(A)-binding proteinI gene affect translation? How would an electron micrographof polyribosomes from such a mutant differ from the normal pattern?12. What characteristic of DNA results in the requirementthat some DNA synthesis is discontinuous? How areOkazaki fragments and DNA ligase utilized by the cell?13.
What gene is unique to retroviruses? Why is the proteinencoded by this gene absolutely necessary for maintainingthe retroviral life cycle, but not that of other viruses?A N A LY Z E T H E DATANASA has identified a new microbe present on Mars and requests that you determine the genetic code of this organism.To accomplish this goal, you isolate an extract from this microbe that contains all the components necessary for proteinsynthesis except mRNA. Synthetic mRNAs are added to thisextract and the resulting polypeptides are analyzed:Synthetic mRNAResulting PolypeptidesAAAAAAAAAAAAAAAALysine-Lysine-Lysine etc.CACACACACACACACAThreonine-HistidineThreonine-Histidine etc.AACAACAACAACAACAThreonine-ThreonineThreonine etc.Glutamine-GlutamineGlutamine etc.Asparagine-AsparagineAsparagine etc.ReferencesFrom these data, what specifics can you conclude about themicrobe’s genetic code? What is the sequence of the anticodonloop of a tRNA carrying a threonine? If you found that thismicrobe contained 61 different tRNAs, what could youspeculate about the fidelity of translation in this organism?REFERENCESStructure of Nucleic AcidsDickerson, R.
E. 1983. The DNA helix and how it is read. Sci.Am. 249:94–111.Doudna, J. A., and T. R. Cech. 2002. The chemical repertoireof natural ribozymes. Nature 418:222–228.Kornberg, A., and T. A. Baker. 1992. DNA Replication, 2d ed.W. H. Freeman and Company, chap. 1. A good summary of the principles of DNA structure.Wang, J. C. 1980. Superhelical DNA. Trends Biochem. Sci.5:219–221.Transcription of Protein-Coding Genes and Formationof Functional mRNABrenner, S., F. Jacob, and M. Meselson.
1961. An unstable intermediate carrying information from genes to ribosomes for proteinsynthesis. Nature 190:576–581.Young, B. A., T. M. Gruber, and C. A. Gross. 2002. Views oftranscription initiation. Cell 109:417–420.Control of Gene Expression in ProkaryotesBell, C. E., and M. Lewis. 2001. The Lac repressor: a secondgeneration of structural and functional studies. Curr. Opin. Struc.Biol. 11:19–25.Busby, S., and R.
H. Ebright. 1999. Transcription activation bycatabolite activator protein (CAP). J. Mol. Biol. 293:199–213.Darst, S. A. 2001. Bacterial RNA polymerase. Curr. Opin. Struc.Biol. 11:155–162.Muller-Hill, B. 1998. Some repressors of bacterial transcription.Curr. Opin.
Microbiol. 1:145–151.The Three Roles of RNA in TranslationAlexander, R. W., and P. Schimmel. 2001. Domain-domain communication in aminoacyl-tRNA synthetases. Prog. Nucleic Acid Res.Mol. Biol. 69:317–349.Bjork, G. R., et al. 1987. Transfer RNA modification. Ann. Rev.Biochem. 56:263–287.Garrett, R. A., et al., eds. 2000. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions.
ASM Press.Hatfield, D. L., and V. N. Gladyshev. 2002. How selenium hasaltered our understanding of the genetic code. Mol. Cell Biol.22:3565–3576.Hoagland, M. B., et al. 1958. A soluble ribonucleic acid intermediate in protein synthesis. J. Biol. Chem. 231:241–257.Holley, R. W., et al. 1965. Structure of a ribonucleic acid.
Science 147:1462–1465.145Ibba, M., and D. Soll. 2001.The renaissance of aminoacyl-tRNAsynthesis. EMBO Rep. 2:382–387.Khorana, G. H., et al. 1966. Polynucleotide synthesis and thegenetic code. Cold Spring Harbor Symp. Quant. Biol. 31:39–49.Maguire, B. A., and R. A. Zimmermann. 2001. The ribosomein focus. Cell 104:813–816.Nirenberg, M., et al. 1966. The RNA code in protein synthesis.Cold Spring Harbor Symp. Quant. Biol. 31:11–24.Ramakrishnan, V. 2002.
Ribosome structure and the mechanismof translation. Cell 108:557–572.Rich, A., and S.-H. Kim. 1978. The three-dimensional structureof transfer RNA. Sci. Am. 240(1):52–62 (offprint 1377).Stepwise Synthesis of Proteins on RibosomesGingras, A. C., R. Raught, and N. Sonenberg. 1999. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Ann. Rev. Biochem. 68:913–963.Green, R.
2000. Ribosomal translocation: EF-G turns the crank.Curr. Biol. 10:R369–R373.Hellen, C. U., and P. Sarnow. 2001. Internal ribosome entry sitesin eukaryotic mRNA molecules. Genet. Devel. 15:1593–1612.Kisselev, L. L., and R. H. Buckingham. 2000. Translational termination comes of age. Trends Biochem.
Sci. 25:561–566.Kozak, M. 1999. Initiation of translation in prokaryotes andeukaryotes. Gene 234:187–208.Noller, H. F., et al. 2002. Translocation of tRNA during proteinsynthesis. FEBS Lett. 514:11–16.Pestova, T. V., et al. 2001. Molecular mechanisms of translationinitiation in eukaryotes. Proc. Nat’l. Acad. Sci. USA 98:7029–7036.Poole, E., and W. Tate.
2000. Release factors and their role asdecoding proteins: specificity and fidelity for termination of proteinsynthesis. Biochim. Biophys. Acta 1493:1–11.Ramakrishnan, V. 2002. Ribosome structure and the mechanismof translation. Cell 108:557–572.Sonenberg, N., J. W. B. Hershey, and M. B.
Mathews, eds. 2000.Translational Control of Gene Expression. Cold Spring Harbor Laboratory Press.DNA ReplicationBullock, P. A. 1997. The initiation of simian virus 40 DNA replication in vitro. Crit. Rev. Biochem. Mol. Biol. 32:503–568.Kornberg, A., and T. A. Baker. 1992. DNA Replication, 2d ed.W. H.
Freeman and CompanyWaga, S., and B. Stillman. 1998. The DNA replication fork ineukaryotic cells. Ann. Rev. Biochem. 67:721–751.Viruses: Parasites of the Cellular Genetic SystemFlint, S. J., et al. 2000. Principles of Virology: Molecular Biology, Pathogenesis, and Control. ASM Press.Hull, R. 2002.
Mathews’ Plant Virology. Academic Press.Knipe, D. M., and P. M. Howley, eds. 2001. Fields Virology. Lippincott Williams & Wilkins.Kornberg, A., and T. A. Baker. 1992. DNA Replication, 2d ed.W. H. Freeman and Company. Good summary of bacteriophagemolecular biology.5BIOMEMBRANESAND CELLARCHITECTUREAtomic force microscopy reveals sphyingomyelin rafts (orange)protruding from a dioleoylphosphatidylcholine background(black) in a mica-supported lipid bilayer.
Placental alkalinephosphatase (yellow peaks), a glycosylphosphatidylinositolanchored protein, is shown to be almost exclusively raftassociated. [From D. E. Saslowsky et al., 2002, J. Biol. Chem.277:26966–26970.]Prokaryotes, which represent the simplest and smallestcells, about 1–2 m in length, are surrounded by aplasma membrane but contain no internal membranelimited subcompartments (see Figure 1-2a). Although DNA isconcentrated in the center of these unicellular organisms, mostenzymes and metabolites are thought to diffuse freely withinthe single internal aqueous compartment. Certain metabolicreactions, including protein synthesis and anaerobic glycolysis,take place there; others, such as the replication of DNA andthe production of ATP, take place at the plasma membrane.In the larger cells of eukaryotes, however, the rates ofchemical reactions would be limited by the diffusion of smallmolecules if a cell were not partitioned into smaller subcompartments termed organelles.
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