The Replication of DNA

1.(a) Draw a schematic diagram of the primer:template junction, la eling the !" and #" ends of each of the strands. $ndicate where deo%&nucleotides are added during the process of DNA replication. ( ) Draw the reaction & which the deo%&nucleotides are added to a growing DNA strand during replication. 'hat happens to the p&rophosphate that is produced in this reaction( ). Descri e two wa&s & which DNA pol&merase ensures that the correct ase is added to the growing pol&nucleotide chain during replication, addressing what these mechanisms ha*e in common, and how the& differ. 'hat is the contri ution of these mechanisms toward the o*erall fidelit& of DNA replication( #. +riefl& summari,e the palm, thum , and finger domains of DNA pol&merase, and e%plain how the& contri ute to replication. 'hat is the role of the metal ions in the palm"s acti*it&( -. 'hat pre*ents ri onucleotides from eing incorporated into the growing DNA strand during replication of the genome( $n what aspect of replication are ri onucleotides used, and what ultimatel& happens to them( !. ./a,a/i disco*ered the fragments named after him & riefl& e%posing replicating DNA to radioacti*el&0la eled nucleotides, and then separating the la eled DNA fragments & si,e. 1sing this method, he identified two populations of fragments. Descri e what these two populations must ha*e loo/ed li/e. 'h& was it important to use a short e%posure to the radioacti*e la el rather than a longer one( 2. The si,e of ./a,a/i fragments differs in different organisms. 'hat might influence this si,e( 3ow might &ou test this possi ilit&( 4. 3ow is the DNA unwound at the replication for/( 'hat effect does this ha*e on the DNA upstream of the for/, and how does the cell deal with this effect( 5. Address how cooperati*e inding contri utes to 66+ function during DNA replication. 'hat is the ad*antage of such inding for 66+ acti*it&( 7. 6liding clamps are topologicall&0closed rings that can encircle the DNA dou le heli%. 3ow, then, are the& a le to get on and off the DNA( 'hat purpose is ser*ed & this stri/ing topolog&( 18 . 9ist at least fi*e distinct acti*ities pro*ided & proteins within the replisome. 'hat are some of the ad*antages of ha*ing multiple proteins wor/ing together to carr& out the *arious aspects of the replication process(

11 . Name three different initiators discussed in the chapter. 'hat features do the& ha*e in common, and how do the& differ( 1# . Descri e the *arious steps in*ol*ed in the initiation of replication in eu/ar&otes. 'hat proteins are in*ol*ed in each of the steps, and when in the cell c&cle does each of them occur( 3ow does their temporal segregation contri ute to the limitation of origin firing to at most once per cell c&cle( 1! . :%plain wh& the replication machiner& is incapa le of completel& replicating the ends of the chromosomes. 'hat is the practical effect of this( 3ow do eu/ar&otic cells get around this pro lem(