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The recombinases cleave theDNA at specific points and ligate the strandsto new partners. This type of recombination isfound in virtually all cells, and its many functionsinclude DNA integration and regulation of geneexpression. In vertebrates, a programmed recombination reaction related to site-specific recombination is used to join immunoglobulin gene segmentsto form immunoglobulin genes during B-lymphocyte differentiation. Some small segments of DNA,called transposons, are capable of moving from onepoint in a chromosome to another point in the sameor another chromosome.
These elements are foundin virtually all cells.854Part IV Information PathwaysFurther ReadingGeneralKornberg, A. & Baker, T.A. (1991) DNA Replication, 2nd edn, W.H. Freeman and Company, NewYork.An excellent primary source.Kucherlapati, R. & Smith, G.R. (eds) (1988) Genetic Recombination, American Society of Microbiology, Washington, DC.Excellent reviews on a wide assortment of recombination topics.Richardson, C.C. & Lehman, I.R. (eds) (1990) Molecular Mechanisms in DNA Replication and Recombination, Alan R.
Liss, Inc., New York.A collection of a papers from a major symposium onthe topic.ReplicationBramhill, D. & Kornberg, A. (1988) A model forinitiation at origins of DNA replication. Cell 54,915-918.Burgers, P.M.J. (1989) Eukaryotic DNA polymerases a and 8: conserved properties and interactions, from yeast to mammalian cells. Prog. Nucleic Acid Res.
Mol. Biol. 37, 235-280.Sancar, A. & Sancar, G.B. (1988) DNA repair enzymes. Annu. Rev. Biochem. 57, 29-67.RecombinationBerg, D.E. & Howe, M.M. (eds) (1989) MobileDNA, American Society for Microbiology, Washington, DC.Reviews covering many topics related to transposition.Cox, M.M. & Lehman, I.R. (1987) Enzymes of genetic recombination.
Annu. Rev. Biochem. 56, 229262.Craig, N.L. (1988) The mechanism of conservativesite-specific recombination. Annu. Rev. Genet. 22,77-105.Landy, A. (1989) Dynamic, structural, and regulatory aspects of A site-specific recombination. Annu.Rev. Biochem. 58, 913-949.A thorough description of the protein-DNA complexes involved in this reaction.Mizuuchi, K.
(1992) Transpositional recombination: insights from Mu and other elements. Annu.Rev. Biochem. 61, 1011-1051.Campbell, J. (1988) Eukaryotic DNA replication:yeast bares its ARSs. Trends Biochem. Sci. 13, 212217.Radding, CM. (1991) Helical interactions in homologous pairing and strand exchange driven byRecA protein. J. Biol. Chem.
266, 5355-5358.A good, short summary.Echols, H. & Goodman, M.F. (1991) Fidelity mechanisms in DNA replication. Annu. Rev. Biochem.60, 477-511.Roca, A.I. & Cox, M.M. (1990) The RecA protein:structure and function. Crit. Rev. Biochem. Mol.Biol.
25, 415-456.Marians, K.J. (1992) Prokaryotic DNA replication.Annu. Rev. Biochem. 61, 673-719.Taylor, A.F. (1992) Movement and resolution ofHolliday junctions by enzymes from E. coli. Cell69, 1063-1065.McHenry, C.S. (1991) DNA polymerase III holoenzyme. J. Biol. Chem.
266, 19127-19130.Radman, M. & Wagner, R. (1988) The high fidelityof DNA duplication. Sci. Am. 259 (August), 40-46.Wang, T.S.-F. (1991) Eukaryotic DNA polymerases.Annu. Rev. Biochem. 60, 513-552.RepairFriedberg, E.C. (1985) DNA Repair, W.H. Freeman and Company, New York.Modrich, P. (1991) Mechanisms and biological effects of mismatch repair. Annu. Rev. Genet.
25,Problems1. Conclusions from the Meselson-Stahl Experiment The Meselson-Stahl experiment provedthat DNA undergoes semiconservative replicationin E. coli. In the "dispersive" model of DNA replication, the parent DNA strands are cleaved intopieces of random size and are then joined withpieces of the newly replicated DNA to yield daughter duplexes in which, in the Meselson-Stahl experiment, both strands would contain random segments of both heavy and light DNA. Explain howthe results of the Meselson-Stahl experimentruled out such a model.2. Number of Turns in the E. coli ChromosomeHow many turns must be unwound during replication of the E. coli chromosome? The chromosomecontains about 4.7 x 106 base pairs.3.
Replication Time in E. coli From the data inthis chapter, how long would it take to replicatethe E. coli chromosome at 37 °C, if two replicationforks start from the origin? Under some conditionsE. coli cells can divide every 20 min. Can you suggest how this is possible?4. Base Composition of DNAs Made from SingleStranded Templates Determine the base composition you might expect in the total DNA synthesizedby DNA polymerase on templates provided by anequimolar mixture of the two complementarystrands of circular bacteriophage </>X174 DNA. Thebase composition of one strand is A, 24.7%; G,24.1%; C, 18.5%; and T, 32.7%.
What assumption isnecessary to answer this problem?5. Okazaki Fragments In the replication of theE. coli chromosome, about how many Okazakifragments would be formed? What factors guarantee that the numerous Okazaki fragments are assembled in the correct order in the new DNA?6. Leading and Lagging Strands List and compare the precursors and enzymes needed to makethe leading versus lagging strands during DNAreplication in E. coli.7. Fidelity of Replication of DNA What factorsparticipate in ensuring the fidelity of replicationduring the synthesis of the leading strand of a newDNA? Would you expect the lagging strand to bemade with the same fidelity as the leading strand?Give reasons for your answers.8.
DNA Repair Mechanisms Vertebrate and plantcells often methylate cytosine in DNA to form5-methylcytosine (see Fig. 12-5a). In these samecells, there is a specialized repair system that recognizes G-T mismatches and repairs them toG=C base pairs. Rationalize this repair system interms of the presence of 5-methylcytosine in theDNA.9. Holliday Intermediates How are the Hollidayintermediates formed in homologous genetic recombination and in site-specific recombination different?10. DNA Recombination A circular DNA moleculeis converted to two smaller circles by an enzyme orenzymes in a crude cellular extract.
What types ofrecombination could account for this reaction, andwhat else must you know to determine which typeit is?C H A P T E RRNA MetabolismThe expression of the genetic information contained in a segment ofDNA always involves the generation of a molecule of RNA. At firstglance, a strand of RNA may seem quite similar to a strand of DNA,differing only in the hydroxyl group at the 2' position and the substitution of uracil for thymine.
As we will see, however, these small differences confer on RNA the potential for much greater structural diversity than DNA, a diversity that allows RNA to assume a variety ofcellular functions. RNA molecules not only carry and express geneticinformation, they can also act as catalysts.RNA is the only macromolecule known to have both informationaland catalytic functions, leading to much speculation that it may havebeen the essential chemical intermediate in the development of life onthis planet.
The discovery of catalytic RNAs has changed the very definition of the word "enzyme." Many RNAs are also complexed with proteins, forming complicated biochemical machines with a wide varietyof functions.With the exception of the RNA genomes of certain viruses, all RNAmolecules are derived from information permanently stored in DNA.In a process called transcription, an enzyme system converts thegenetic information of a segment of DNA into an RNA strand with abase sequence complementary to one of the DNA strands.
Three majorkinds of RNA are produced. Messenger RNA (mRNA) carries thesequences that encode the amino acid sequence of one or more polypeptides specified by a gene or set of genes in the chromosomes. TransferRNA (tRNA) is an adapter that reads the information encoded in themRNA and transfers the appropriate amino acid to the growing polypeptide chain during protein synthesis. Ribosomal RNA (rRNA)molecules associate with proteins to form the intricate protein synthetic machine, the ribosome. In addition, there are many specializedRNAs with regulatory or catalytic functions.Replication and transcription differ in one important respect.
During replication the entire chromosome is copied to yield daughterDNAs identical to the parent DNA, whereas transcription is selective:only particular genes or groups of genes are transcribed at any onetime. The transcription of DNA can therefore be regulated so that onlygenetic information needed by the cell at a particular moment is transcribed. Specific regulatory sequences indicate the beginning and endof the segments of DNA to be transcribed, as well as which DNA strandis to be used as template. Regulation also involves a variety of proteinsthat will be described in more detail in Chapter 27.856Chapter 25 RNA MetabolismIn this chapter we begin by describing the synthesis of RNA on aDNA template, a process similar in many respects to DNA synthesis.We then turn to postsynthetic processing and turnover of RNA molecules.
Many of the specialized functions of RNA will be encountered inthis discussion of the posttranscriptional reactions. Indeed, the substrates for RNA enzymes are generally other RNA molecules. We conclude the chapter with an examination of systems in which RNA ratherthan DNA serves as a template for the transfer of genetic information.Here, the information pathways are expanded and come full circle, andtemplate-directed nucleic acid synthesis is revealed as a process withstandard rules that apply regardless of whether the template or product is RNA or DNA.
This biological interconversion of DNA and RNAas information carriers leads finally to a discussion of the origin ofbiological information.DNA-Dependent Synthesis of RNAWe can most usefully begin our discussion of RNA synthesis by comparing it with DNA replication as described in Chapter 24. Transcription is very similar to replication in terms of chemical mechanism,polarity (direction of synthesis), and use of a template.
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