<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Because the DNA double helix is very stable, __ and __ are required to separate them in vitro <b><o:p></o:p></b>
<!--[if !supportLists]--><b>b.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->Two proteins that do this in vivo are __ and __, which are needed to open up the double helix to provide a template <b><o:p></o:p></b>
</question>
base pairs are locked in place
high temperatures
DNA helicase and single-strand DNA-binding proteins

<question>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->DNA helicases: first isolated as proteins that __; use __ to propel themselves rapidly along a DNA single strand; they __<b><o:p></o:p></b>
<!--[if !supportLists]--><b>1.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->There are helicase that can unwind in t eh __ or __; but, a helicase moving 5’ to 3’ on the lagging strand is more common<b><o:p></o:p></b>
</question>
hydrolyze ATP when they are bound to single strands of DNA
ATP hydrolysis
pry the helix apart
5’à3’ direction or the 3’à 5’ direction

<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">  </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->__ bind tightly and cooperatively to exposed single-stranded DNA without __; aid helicases by __, thereby preventing the formation of the __ that readily form in single-strand DNA, which can __
<answer>
Single-strand DNA-binding (SSB) proteins (aka: helix-destabilizing proteins)

covering the bases

stabilizing the single strand and straightening out the regions of single-stranded DNA on the lagging strand template

short hairpin helices

impede the DNA synthesis catalyzed by DNA polymerase
</answer>

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->The tendency to __ allows DNA pol (that just finished making an Okazaki fragment) to be __<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->However, it is more difficult for the polymerase to __. <b><o:p></o:p></b>
<!--[if !supportLists]--><b>1.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->To combat this, there is a __ that keeps polymerase firmly on the DNA when it is moving, but release it as soon as the polymerase runs into a double-stranded region of DNA<b><o:p></o:p></b>
</question>
dissociate from a DNA molecule
recycled
synthesize the long DNA strands produced at a replication fork and rapidly dissociate
sliding clamp protein

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->The Sliding clamp forms a __. One side binds to the __, and the whole ring slides __<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->The assembly of the clamp around the DNA requires __ by a special protein complex, the __, which __ as it loads the clamp on to a __ <b><o:p></o:p></b>
</question>
ring around the DNA double helix
back of the DNA polymerase
freely along the DNA as the polymerase moves
ATP hydrolysis
clamp loader
hydrolyzes ATP
primer-template junction

<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->On the leading strand, the moving DNA pol is __ and __. The DNA pol on the lagging strand remains attached until __, at which point it dissociates from the template. It then uses a __. <b><o:p></o:p></b>
<answer>
bound to the clamp and remains associated for a while

reaching the 5’ end of the preceding fragment

new clamp
</answer>

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Most proteins involved in replication are part of a large multienzyme complex that rapidly synthesizes DNA. The complex remains __and the DNA is __.<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->__ opens the DNA helix <b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                            </span>ii.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->Two __ work at the fork on each strand<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                          </span>iii.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->__: provides the RNA proimers<b><o:p></o:p></b>
</question>
stationary 
threaded through it
DNA helicase
DNA pols
DNA primase

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->This complex facilitates the __ each time an __ is synthesized: the __ and the __ are kept in place as a part of the protein machine even when they detach from their DNA template. It also __. <b><o:p></o:p></b>
<!--[if !supportLists]--><b>b.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->__ increase the rate of spontaneous mutation. One such mutant makes a defective form of the__ that is a part of the DNA polymerase enzyme<b><o:p></o:p></b>
</question>
<answer>
loading of the polymerase clamp
Okazaki fragment
clamp loader
lagging strand DNA polymerase molecule
increae efficiency

Mutator genes
 3’-to-5’ proofreading exonuclease
</answer>

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->One proofreading system that removes replication errors made by the polymerase that were missed by __ is the __, which detects the potential for distortion in the DNA helix from the __.<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->The system must be able to __, where the replication error occurred.<b><o:p></o:p></b>
</question>
proofreading exonucleases
strand-directed mismatch repair system
misfit between noncomplementary base pairs
distinguish and remove the mismatched nucleotide only on the newly synthesized strand

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->The __ used by the mismatch proofreading system in E. coli depends on __of __ in DNA. <b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->__ are added to all A residues in the sequence GATC, but not until after A has been incorporated. <b><o:p></o:p></b>
<!--[if !supportLists]--><b>1.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->As a result, the only GATC sequences that have not been methylated yet are in the __. The recognition of these __ allows the new DNA strands to be transiently distinguished from old ones<b><o:p></o:p></b>
</question>
strand-distinction mechanism
methlation 
selected A residues
Methyl groups
new strands just behind a replication fork.
unmethylated GATCs

<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->The three step process involves __, __, and __.
recognition of a mismatch, excision of the segment of DNA containing the mismatch from the newly synthesized strand, and resynthesis of the excised segment using the old strand as a template.

<question>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->There is a similar mechanism in umans that helps with predispositions to certain types of cancer, which is due to a __<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->Because most of us __, we are protected<b><o:p></o:p></b>
<span>In eucaryotes, to distinguish from the parental strand at the site of a mismatch, __is not needed</span>
</question>
<answer>
defective copy of a mismatch repair gene

inherit two good copies of each gene that encodes a mismatch proofreading protein

methlation
</answer>

<question>
<!--[if !supportLists]--><b>1.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Instead, newly synthesized lagging-strand DNA contains __; and, these __ provide a signal that directs the __<b><o:p></o:p></b>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->This idea requires that the newly synthesized DNA on the leading strand be transiently __.<b><o:p></o:p></b>
</question>
nicks (before they are sealed by DNA ligase)
nicks (single-strand breaks
mismatch proofreading system to the appropriate strand
nicked

<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Because DNA gets tangled during unwinding and too much energy is required to prevent it, a __is formed in the helix by proteins known as __, which adds itself __ to a __, thereby breaking a __. This is reversible and the phosphodiester bond reforms when the protein leaves<b><o:p></o:p></b>
swivel 
DNA topoisomerases
covalently to a DNA backbone phosphate
phosphodiester bond in a DNA strand

<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->Topoisomerase I: __<b><o:p></o:p></b>
produces a transient single-strand break (or nick), which allows the two sections of DNA helix on either side of the nick to rotate freely relative to each other, using the phosphodiester bond in the strand opposite the nick as a swivel point

<question>
<!--[if !supportLists]--><b>1.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Any __in the DNA helix will drive this rotation in the direction that relieves the tension<b><o:p></o:p></b>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->As a result, DNA replication can occur with the __—the part just ahead of the fork<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                                                                                                      </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->Because the __ that joins the __ to a __ retains the energy of the cleaved __, resealing is rapid and does not require additional energy input<b><o:p></o:p></b>
<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                                                                                                    </span>ii.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->In this respect, the rejoining mechanism differs from that catalyzed by the enzyme DNA ligase<b><o:p></o:p></b>
</question>
tension 
rotation of only a short length of helix
covalent linkage
DNA topoisomerase protein
DNA phosphate
phosphodiester bond

<!--[if !supportLists]--><b><span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">                                                              </span>i.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->Topoisomerase II: __<b><o:p></o:p></b>
forms a covalent linkage to both strands of the DNA helix at the same time, making a transient double-strand break in the helix

<question>
<!--[if !supportLists]--><b>1.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->These enzymes are activated by sites on chromosomes where __<b><o:p></o:p></b>
<!--[if !supportLists]--><b>2.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Once one binds to such a crossing site, the protein uses __ to perform the following set of reactions efficiently:<b><o:p></o:p></b>
<!--[if !supportLists]--><b>a.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->It __ to create a __<b><o:p></o:p></b>
<!--[if !supportLists]--><b>b.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">      </span></b><!--[endif]-->It causes the second, nearby double helix to __<b><o:p></o:p></b>
<!--[if !supportLists]--><b>c.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->It then reseals the break and dissociates from the DNA<b><o:p></o:p></b>
<!--[if !supportLists]--><b>3.<span style="font-weight:normal; font-stretch:normal; font-size:7pt; font-family:'Times New Roman';">       </span></b><!--[endif]-->Topoisomerase II can separate __<b><o:p></o:p></b>
</question>
two double helices cross over each other
ATP hydrolysis
breaks one double helix reversibly
DNA “gate”
pass through this break
two interlocked DNA circles