C2005/F2401 '09 -- Recitation Problems #7

1. (From exam #2 of '03) A. A cell is making one new Okazaki fragment. The cell contains all the necessary enzymes and substrates.

        A. Then a U could be located (at the 5’ end of) (at the 3’ end of) (at either end of) (in the middle of) (at none of these places in) the fragment, AND

        B. Synthesis of the entire Okazaki fragment should involve the use of (ligase) (primase) (pyrophosphatase) (DNA polymerase) (regular RNA polymerase) (none of these). Circle all that apply and explain your reasoning.

2.  (From Exam #2 of '02)    A DNA sequence is given below. The dotted line (.........)  indicates a long chain of bases; the sequence doesn't matter for this problem. All the questions below refer to the sequence shown. If no explanation is asked for, none was needed on the exam, but be sure you can explain all your answers.
 

    A.  Fill in the blank with the appropriate base sequence and label all the ends.
 

    B. Suppose transcription starts at one end of the molecule shown and goes left to right.

        B-1. The template strand(s) should be (the bottom) (the top strand) (sections of both strands) (all of both strands) (neither) (can’t predict)

        B-2. The base on the 5’ end of the product made will be (C) (U) (T) (A) (G) (more than one of these – you’ll make more than type of product).

        B-3. If the RNA made here is a messenger RNA, which strand of the DNA is the "sense" strand? (top) (bottom) (can't predict).

    C.  Suppose you are replicating the DNA shown in a test tube, using the normal enzymes of replication. There is one replication fork, going left to right.

        C-1. The lagging strand will be complementary to (the top strand) (the bottom strand) (sections of both) (neither) (can’t predict), AND

        C-2. You should get an Okazaki fragment including the sequence (GACCT) (TCCAG) (AGGTC) (CTGGA) (none of these), AND

        C-3. This Okazaki fragment will be (the first) (the last) (neither first or last) (either the first or the last) to be made. 
Explain briefly. (Or better yet, draw a diagram and label all ends and directions of synthesis.)
 

    D.  Suppose you want to amplify the molecule shown using PCR. You have the following primers: 

        (a) 5’ AGGTC 3’   (b) 3’ AGGTC 5’   These primers are unrealistically short for exam purposes.

        D-1. You could use (a) (b) (either one) (neither) (can’t tell from information given) as one of the primers to amplify the molecule shown using PCR. Explain your choice briefly.
   D-2. If you use the correct primers to amplify the DNA shown, discontinuous synthesis should occur when making the complement to (the top strand) (the bottom strand) (all of both strands) (parts of both strands) (neither strand (can't predict).

    E. In part B, it says transcription goes left to right. In part C, it says the replication fork goes left to right. Suppose that you can do it that way in a test tube, but that in a real bacterium, the directions are the other way around – both transcription and replication go right to left for the section shown. If the directions are reversed, then

        E-1. The product(s) of transcription should be (the same) (different) (beats me).

        E-2. Tthe products(s) of replication should be (the same) (different) (can’t predict). Explain briefly.