You will be building a double-stranded DNA molecule, representing a short (20 base) sequence that could be found in a chromosome.  It will have a 3' --> 5' strand and a 5' --> 3' strand. Use two full 12-base-pair DNA models.  a) Upload a photo of a model once the first 6 nucleotides have been inserted to base pair with the two parent strands. b)Upload a photo of DNA polymerase I and Ligase in "action" removing the RNA primer nucleotides and making new phosphodiester bonds. c)Upload a photo of the final two DNA strands, after Termination, identifying the parent and daughter strands of each.

As shown, five DnaA boxes are found within the origin of replication in E. coli. Take a look at these five sequences carefully. A. Are the sequences of the five DnaA boxes very similar to each other? (Hint: Remember that DNA is double-stranded; think about these sequences in the forward and reverse directions.) B. What is the most common sequence for a DnaA box? In other words, what is the most common base in the first position, second position, and so on until the ninth position? The most common sequence is called the consensus sequence. C. The E. coli chromosome is about 4.6 million bp long. Based on random chance, is it likely that the consensus sequence for a DnaA box occurs elsewhere in the E. coli chromosome? If so, why aren’t there multiple origins of replication in E. coli?

Use the first picture for to answer the following questions.

A single DNA molecule contains two specific target sites separated by an intervening sequence. If site-specific recombination between these sites causes the intervening sequence to be released as a separate circular DNA molecule containing one target site, then the sites were oriented in                  A)   opposite directions causing excision.                      B)   the same direction causing excision.            C)   opposite directions causing integration.            D)   the same direction causing integration.            E)   the same direction causing inversion.

The figure below shows a molecule of DNA with its strands separated prior to DNA replication. The structure labeled “primer” on the figure below: A) will be used to construct the lagging strand B) is made of deoxyribonucleotides (DNA) C) reads 3’ to 5’ from left to right D) was made by DNA ligase

Which of the following statements about DNA polymerase I are true?   1) It requires both template DNA and a primer.   2) It can copy and join the ends of single-stranded circular DNA.   3) It uses only DNA as a template primer.   4) With respect to linear DNA, it copies only the 5′ end and then dissociates.   a) Only statements 1 and 3 are true.   b) Only statements 1 and 4 are true.   c) Only statements 1, 2, and 4 are true.   d) All of the listed statements are true.

Which of the following DNAs is most likely to contain the recognition sequence for a homodimeric DNA binding protein? (Note that only one strand of the DNA is shown - you will find it helpful to write down the sequence and the sequence of the opposite strand to answer this question.) a) 5’- G A G C G A T C G C T C - 3’ b) 5’- G A G C G A G A G C G A - 3’ c) 5’- G A G C G A A G C G A G - 3’

What do the enzymes topoisomerase I and topoisomerase II have in common? a) They both have nuclease activity. b) They both create double-strand DNA breaks. c) They both require ATP hydrolysis for their function. d) They both can create winding (tension) in an initially relaxed DNA molecule. e) All of the above.

Which is not a property of DNA polymerase? a) It requires a primer to begin synthesis b) It adds dNTPS only in a 5' to 3' direction c) It opens the two strands of template DNA at the repliction fork d) Its exonuclease activity is used in proofreading. 6. In an analysis of the composition of double-stranded DNA, which will always be found? a) A = G b) G=T c) A+T= G+ C d) A+ G C+T e) A = C 7._ DNA is synthesized through a process that is a) conservative b) semi-discontinuous c) bi-directional d) both a and b e) both b and c 8. The role of DNA ligase is to a) stabilize unwound DNA b) join Okazaki fragments together c) synthesize the RNA primer d) unwind the double helix e) hold the polymerase-for-extension in place at the replication fork 9.

Match the definition on the left with the term on the right Tightly hypercolled DNA that is not in use Loosely colled DNA that is currently being used a) Chromatin b) Chromosome