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MCB 229 Spring 2000 Study Guide 10 Prof. Terry
Covers Lecture for March 9

This study guide is intended for you to use while you are doing the assigned text reading. Quiz questions will be made with reference to topics in this study guide. Quiz #10, based on questions from this study guide, must be completed by midnight before the class on Thursday, March 9. You will need to create your "myWebCT" account and visit the MCB 229 WebCT page in order to access this quiz.

Chapter 11 (p. 212-225). DNA and RNA.
  1. Note: some of this information will be review of material you've had in Biology 107 and perhaps other MCB courses. If this material is new to you and you did not take Biology 107, you may find it profitable to review that material: go to <http://www.sp.uconn.edu/~bi107vc/fa99/terry/DNA.html>.
  2. What is a purine? A pyrimidine? A nucleoside? A nucleotide? To what do the numbers 1', 2', ...., 5' refer? What is the difference between ribose and deoxyribose? See Fig. 11.1 and relevant text.
  3. What nucleotide components make up the backbone of a DNA strand? Which components are involved in base pairing? What are the two complementary base pairs, and how many H-bonds are involved in each? What does it mean to say that the two strands of DNA are antiparallel? How does the structure of DNA differ from the structure of RNA?
  4. In prokaryotes, what is the shape of a DNA molecule? _____ Is the DNA complexed with histones? _____ Is it complexed with other proteins? ______ Is it supercoiled? _____ Is it organized in nucleosomes? _____ Does DNA synthesis begin at a single site or at multiple sites? _____
  5. In eukaryotes, what is the shape of a DNA molecule? _____ Is the DNA complexed with histones? _____ Is it complexed with other proteins? ______ Is it supercoiled? _____ Is it organized in nucleosomes? _____ Does DNA synthesis begin at a single site or at multiple sites? _____
  6. Define each of the following terms: Transcription, Translation, Replication, Replicon.
  7. One DNA strand has the following sequence:
       3'-ACCGATTACAG-5'.          3'-ACCGATTACAG-5'.
    (a) _______________________    (b) _______________________
    (a) If this strand is replicated, what is the product? (b) If this strand is transcribed, what is the product?
  8. What is a replicating fork, and what process is always in process when such forks are seen? Do bacterial cells replicate their circular chromosomes unidirectionally or bidirectionally? What is a theta structure and when would you expect to see one?
  9. Rolling circle replication (see Fig. 11.9) does not occur during chromosomal replication, but is found during ___________________ .
  10. DNA replication requires a number of enzymes. What role does each of the following enzymes play? See Figures 11.2, 11.3, and text.
    DNA polymerase I:
    DNA polymerase III:
    Helicases
    Topoisomerases (ex: DNA gyrase):
    Single-stranded DNA binding proteins:
    DNA-dependent RNA primase:
    DNA ligase
    Pyrophosphatase
  11. What is a lagging strand? A leading strand? An Okazaki fragment?
  12. What is the error frequency for DNA replication: (a) per base replicated? One in _____; (b) per gene per generation? One in ______ .
  13. What enzyme(s) is(are) involved in proofreading newly synthesized DNA to correct errors?
  14. What is the rate of DNA replication in bacteria? _________ base pairs/sec. In eukaryotes? _________ base pairs/sec.
  15. In bacteria: What enzyme is required for RNA synthesis (transcription)? _____________ How many subunits does this enzyme have? _____ What is the difference between the core enzyme and the sigma factor?
  16. In bacteria: What is a promoter, and where would you find one? What is a Pribnow box, and what is the "signature" base sequence for such "boxes"?
  17. Your text has an error on page 222: "RNA polymerase copies only the template or sense strand". This should read: "RNA polymerase copies only the template or antisense strand". This error is a common one in many texts, and at first seems counterintuitive, so let me explain the logic. When scientific publications report DNA sequence information, they only show one strand (since the other strand could always be predicted by base-pairing rules, it would be wasteful to show both). Which strand should you illustrate? At first glance, it seems logical to write down the template strand, from which RNA sequence is encoded. After all, that's the most important DNA strand, right? If this were the case, you would publish:
    3'-AAGATTACGGAC-5' (DNA template); and this strand would encode the m-RNA sequence:
    5'-UUCUAAUGCCUG-3' (RNA message).

    But actually this isn't very helpful. It's not easy to look at the DNA sequence as written and see the coding information. Furthermore, since the two strands are antiparallel, you'd have to read the DNA strand backwards, from R to L, to figure out the predicted amino acid sequence.

    A much better choice is to publish the non-template DNA strand, which is almost identical to the RNA message, with the substitution of U for T. Because this DNA strand reveals the predicted amino acid sequence directly, and in the correct L to R order, it is called the "sense" strand (but it is not the template strand!). For example:
    5'-TTCTAATGCCTC-3' (DNA sense strand)
    5'-UUCUAAUGCCUG-3' (RNA message). Note that the two sequences are identical, except for the substitution of U for T.

    If I give you the following DNA sense strand, what is the RNA message strand?
    5'-AAAGAGCCCTAATTACCGA-3'(DNA sense strand)
    ______________________________
  18. In bacteria: What signal(s) is(are) recognized to terminate the transcription process?
  19. In eukaryotes: how many RNA polymerases are used? ____ Roughly how many subunits are present? ____ Is this different from the situation in bacteria? ______
  20. Note that transcription in eukaryotes is much more complicated than in bacteria. I don't expect you to know the details as listed on p. 223, except as indicated by specific questions here. Suffice it to say that each eukaryotic gene is regulated not only by having its own promoter but by requiring other proteins to activate the process.
  21. What is an intron? An exon? Are these found in bacteria in general? Are they found in any special groups of bacteria?
  22. What is a ribozyme? Give an example.