Chapter 10
Biosynthesis of Nucleic Acids: Replication
1
SUMMARY
Section 10.1
Before cells divide, they must synthesize a new copy of DNA. This process is
called replication.
Section 10.2
When a molecule of DNA is replicated, each of the two strands is used as a
template to create a complementary strand. When a cell divides into two, each of
Section 10.3
To achieve 5’ 3’ synthesis of DNA on two strands that are antiparallel, DNA
Polymerase synthesizes one strand continuously and the other discontinuously.
The strand synthesized continuously is called the leading strand and the one
Section 10.4
DNA replication is carried out by a multiprotein complex called the replisome.
Besides the DNA polymerases themselves, many other proteins are involved in
replication. DNA gyrase induces negative supercoils in the DNA to compensate
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Section 10.5
Bases would be paired incorrectly during DNA synthesis about once for every
104 to 105 base pairs unless there were a mechanism to increase fidelity.
Section 10.6
DNA recombination is a natural process in which genetic information is
rearranged to form new associations.
If the recombination involves a reaction between homologous sequences, then
Section 10.7
Replication in eukaryotes follows the same general outline as replication in
prokaryotes, with the most important difference being the presence of histone
proteins complexed to eukaryotic DNA.
LECTURE NOTES
Most students will have seen much of the material in this chapter in earlier
courses, particularly in beginning biology courses, but they are unlikely to have gone
into any of the molecular details. The most difficult aspect of DNA replication for
students to understand is frequently the distinct details of what is going on at the leading
Biosynthesis of Nucleic Acids: Replication 3
LECTURE OUTLINE
I. Flow of genetic information
A. Replication
B. Transcription
C. Translation
II. DNA replication
A. General considerations
1. Separation of strands
III. DNA polymerase
A. Discontinuous synthesis of lagging strand
B. DNA polymerases from E. coli
IV. Proteins required for replication
A. Unwinding of the double helix
B. Primase reaction
C. Synthesis and linking of new DNA strands
V. Proofreading and repair
A. Mutations as errors in replication
B. Nick translation
C. Common mutagens
VI. Recombination
A. Homologous vs nonhomologous
D. Proteins involved in recombination
VII. Eukaryotic DNA replication
A. Replicons
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ANSWERS TO PROBLEMS
10.1 The Flow of Genetic Information in the Cell
1. Replication is the production of new DNA from a DNA template. Transcription is
the production of RNA from a DNA template. Translation is the synthesis of
10.2 Replication of DNA
4. The semiconservative replication of DNA means that a newly formed DNA
molecule has one new strand and one strand from the original DNA. The
5. A replication fork is the site of formation of new DNA. The two strands of the
original DNA separate, and a new strand is formed on each original strand.
7. Separating the two strands of DNA requires unwinding the helix.
8. If the original Meselson–Stahl experiment had used longer pieces of DNA, the
9. Replication requires separating the strands of DNA. This cannot happen unless
the DNA is unwound.
10.3 DNA Polymerase
10. Most DNA-polymerase enzymes also have exonuclease activity.
11. DNA polymerase I is primarily a repair enzyme. DNA polymerase III is mainly
responsible for the synthesis of new DNA. See Table 10.1.
13. The reactants are deoxyribonucleotide triphosphates. They provide not only the
moiety to be inserted (the deoxyribonucleotide) but also the energy to drive the
reaction (dNTP inserted NMP + PPi, PPi 2Pi).
Biosynthesis of Nucleic Acids: Replication 5
16. The free 3′ end is needed as the site to which added nucleotides bond. A number
of antiviral drugs remove the 3′ end in some way.
17. The large negative ΔG° ensures that the back reaction of depolymerization does
not occur. Energy overkill is a common strategy when it is critically important that
10.4 Proteins Required for DNA Replication
20. All four deoxyribonucleoside triphosphates, template DNA, DNA polymerase, all
four ribonucleoside triphosphates, primase, helicase, single-strand binding
protein, DNA gyrase, DNA ligase.
21. DNA is synthesized from the 5′ end to the 3′ end, and the new strand is
22. DNA gyrase introduces a swivel point in advance of the replication fork. Primase
synthesizes the RNA primer. DNA ligase links small, newly formed strands to
produce longer ones.
23. In the replication process, the single-stranded portions of DNA are complexed to
specific proteins.
26. Specific enzymes exist to cut the DNA and give a supercoiled configuration at the
replication fork that allows replication to proceed.
27. Polymerase III does not insert a deoxyribonucleotide without checking to see that
the previous base is correct. It needs a previous base to check even if that base
the thumb is responsible for DNA binding.
29. Recently it was concluded that three Pol III enzymes are associated with the
replisome instead of two.
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10.5 Proofreading and Repair
32. When an incorrect nucleotide is introduced into a growing DNA chain as a result
of mismatched base pairing, DNA polymerase acts as a 3′-exonuclease,
removing the incorrect nucleotide. The same enzyme then incorporates the
correct nucleotide.
polymerase to incorporate the correct ones. DNA ligase seals the nick.
35. In DNA, cytosine spontaneously deaminates to uracil. The presence of the extra
methyl group is a clear indication that a thymine really belongs in that position,
not a cytosine that has been deaminated.
36. About 5000 books: 1010 characters/error × 1 book/(2 × 106 characters) = 5 × 103
books/error.
38. 1 second/1000 characters × 1010 characters/error × 107 seconds/error = 16.5
weeks/error nonstop.
39. Prokaryotes methylate their DNA soon after replication. This aids the process of
40. DNA is constantly being damaged by environmental factors and by spontaneous
mutations. If these mistakes accumulate, deleterious amino acid changes or
41. Prokaryotes have a last-resort mechanism for dealing with drastic DNA damage.
42. Non-homologous DNA End Joining (NHEJ) or recombination.
43. Ku70/80, DNA ligase IV, and several others.
44. It is error-prone as the repair proceeds without a template
45. It binds the broken ends of the DNA so replication can continue
10.6 Recombination
46. Recombination that involves a reaction between homologous sequences.
47. They used two different phages to infect bacteria. One of the phages had light
DNA and one had heavy DNA. Without recombination, the light DNA would
Biosynthesis of Nucleic Acids: Replication 7
48. Similar to the experiment described in 47 above, using heavy isotopes
49. Recombination occurs by the breakage and reunion of DNA strands so that
10.7 Eukaryotic DNA Replication
50. Eukaryotes usually have several origins of replication, whereas prokaryotes have
only one.
51. The general features of DNA replication are similar in prokaryotes and
52. Histones are proteins complexed to eukaryotic DNA. Their synthesis must take
53.
54. Eukaryotes have more DNA polymerases, which tend to be larger molecules.
Table 10.5.
55. Mechanisms exist to ensure that DNA synthesis takes place only once in the
56. If the telomerase enzyme were inactivated, DNA synthesis would eventually stop.
57. If histone synthesis took place faster than DNA synthesis, it would be highly
disadvantageous to invest the energy required for protein synthesis. The
histones would have no DNA with which to bind.
58. Replication licensing factors (RLFs) are proteins that bind to eukaryotic DNA.
They get their name from the fact that replication cannot proceed until they are
59. It is faster in prokaryotes. The DNA is smaller, and the lack of
compartmentalization within the cell facilitates the process. DNA replication in
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eukaryotes is linked to the cell cycle, and prokaryotic cells proliferate more
quickly than those of eukaryotes.
60. In reverse transcriptase action, the single RNA strand serves as a template for
61. Circular DNA does not have ends. This removes the necessity for maintaining
the 3′ template end on removal of the RNA primer. Telomeres and telomerase
are not needed with circular DNA.
62. The presence of a DNA polymerase that operates only in mitochondria is
63. The hypothesis that RNA was the original molecule of heredity, and was the first
64. Because finding that RNA can self-replicate leads credence to the RNA world
hypothesis and brings us a step closer to understanding how evolution began.