Page 56 - Genetics_From_Genes_to_Genomes_6th_FULL_Part2

Problems 215

material in bacteria and in DNA-containing viruses. DNA banded at a density intermediate between that of
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Some viruses do not contain DNA but have RNA in- pure N DNA and pure N DNA following equilib-
side the phage particle. An example is the tobacco rium density centrifugation. When they allowed the
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mosaic virus (TMV) that infects tobacco plants, caus- bacteria to replicate one additional time in N me-
ing lesions in the leaves. dium, they observed that half of the DNA remained at
Two different variants of TMV exist that have the intermediate density, while the other half banded at
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different forms of a particular protein in the virus parti- the density of pure N DNA. What would they have
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cle that can be distinguished. It is possible to reconsti- seen after an additional generation of growth in N
tute TMV in vitro (in the test tube) by mixing purified medium? After two additional generations?
proteins and RNA. The reconstituted virus can then be 18. If you expose human tissue culture cells (for example,
used to infect the host plant cells and produce a new HeLa cells) to H-thymidine just as they enter S
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generation of viruses. Design an experiment to show phase, then wash this material off the cells and let
that RNA, rather than protein, acts as the hereditary them go through a second S phase before looking at
material in TMV. the chromosomes, how would you expect the H to be
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15. The CAP protein is shown bound to DNA in Fig. 6.15. distributed over a pair of homologous chromosomes?
CAP binds a specific sequence of base pairs in DNA (Ignore the effect recombination could have on this
(N = any base): outcome.) Would the radioactivity be in (a) one chro-
matid of one homolog, (b) both chromatids of one ho-
5′ TGTGANNNNNNTCACA 3′ molog, (c) one chromatid each of both homologs,
3′ ACACTNNNNNNAGTGT 5′
(d) both chromatids of both homologs, or (e) some
a. In a long double-stranded DNA molecule with ran- other pattern? Choose the correct answer and explain
dom base sequence and an equal number of A–T your reasoning. (This problem extends the analysis
and G–C base pairs, how many different kinds of begun in Solved Problem III.)
DNA sequences could be bound by CAP? 19. Draw a replication bubble with both replication forks
b. In the same DNA molecule, how frequently would and label the origin of replication, the leading strands,
a CAP binding site of any type be present? Of a lagging strands, and the 5′and 3′ ends of all strands
particular type? shown in your diagram.
c. CAP protein binds DNA as dimer; two identical 20. a. Do any strands of nucleic acid exist in nature in
CAP protein subunits bound to each other bind which part of the strand is DNA and part is RNA?
DNA. Can you detect a special feature of the DNA If so, describe when such strands of nucleic acid
site that CAP binds that suggests that two identical are synthesized. Is the RNA component at the 5′
protein subunits bind the DNA? (Hint: Try reading end or at the 3′ end?
the sequence in the 5′-to-3′ direction on each strand.) b. RNA primers in Okazaki fragments are usually very
d. CAP protein binds to the major groove of DNA. short, less than 10 nucleotides and sometimes as
Do you expect that DNA helicase is required for short at 2 nucleotides in length. What does this fact
CAP to bind DNA? tell you about the processivity of the primase
enzyme—that is, the relative ability of the enzyme
Section 6.4 to continue polymerization as opposed to dissociating
16. In Meselson and Stahl’s density shift experiments (di- from the template and from the molecule being
synthesized? Which enzyme is likely to have a greater
agrammed in Fig. 6.20), describe the results you processivity, primase or DNA polymerase III?
would expect in each of the following situations:
a. Conservative replication after two rounds of DNA 21. As Fig. 6.21 shows, DNA polymerase cleaves the
high-energy bonds between phosphate groups in nu-
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synthesis on N. cleotide triphosphates (nucleotides in which three
b. Semiconservative replication after three rounds phosphate groups are attached to the 5′ carbon atom
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of DNA synthesis on N. of the deoxyribose sugar). The enzyme uses this en-
c. Dispersive replication after three rounds of DNA ergy to catalyze the formation of a phosphodiester
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synthesis on N. bond when incorporating new nucleotides into the
d. Conservative replication after three rounds of DNA growing chain.
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synthesis on N. a. How does this information explain why DNA chains
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17. When Meselson and Stahl grew E. coli in N medium grow during replication in the 5′-to-3′ direction?
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for many generations and then transferred the cells to N b. The action of the enzyme DNA ligase in joining
medium for one generation, they found that the bacterial Okazaki fragments together is shown in Fig. 6.23.