Biochemistry 8Th Edition Campbell Solutions Manual Full Chapter PDF
Biochemistry 8Th Edition Campbell Solutions Manual Full Chapter PDF
Biochemistry 8Th Edition Campbell Solutions Manual Full Chapter PDF
Solutions Manual
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Chapter 10
Biosynthesis of Nucleic Acids: Replication
SUMMARY
Section 10.1
Before cells divide, they must synthesize a new copy of DNA. This process is
called replication.
When DNA is used as a template to synthesize RNA, the process is called
transcription, and is the subject of the next chapter.
The RNA sequence of messenger RNA is used to direct the synthesis of proteins
in a process called translation.
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
the two cells has one of the original template strands and one of the new strands.
This process is called semiconservative replication.
When DNA molecules are replicated, the strands are separated at origins of
replications. Synthesis occurs in both directions from the origin along replication
forks.
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
synthesized discontinuously is called the lagging strand.
The pieces of DNA formed discontinuously are called Okazaki fragments and
they are later joined together by DNA Ligase.
The reaction of DNA synthesis involves the nucleophilic attack of the 3’-hydroxyl
of one nucleotide on the -phosphate of the incoming nucleoside triphosphate.
There are at least 5 DNA polymerases in E. coli, called Pol I through Pol V. Pol III
is the principal enzyme responsible for synthesis of new DNA, and it is a multiple
subunit enzyme.
DNA Polymerases I and II are involved in proofreading and repair processes.
All DNA synthesis requires an RNA primer.
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
for the positive supercoils that would form due to strand separation, and helicase
induces strand separation. Single-stranded binding proteins protect the single
stranded regions from nucleases.
Primase primes the synthesis of the lagging strand by the formation of primers,
and DNA ligase links pieces of newly formed DNA together.
The primer and the proteins at the replication fork are called the primosome
1
2 Chapter 10
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.
Due to proofreading and repair, the number of incorrect bases is reduced to one
in 109 to 1010.
Proofreading is the process where DNA Polymerase I removes incorrectly paired
bases immediately after they are added to the growing chain.
There are a variety of repair mechanisms that remove incorrect bases and
nucleotides and replace them with the correct ones.
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
the process is called homologous recombination. When very different nucleotide
sequences recombine, it is nonhomologous recombination.
Recombination does not occur randomly around a chromosome. There are some
areas of a chromosome, called hot spots, that are much more likely to show
recombination.
Recombination occurs by the breakage and reunion of DNA strands so that
physical exchange of DNA parts takes place. The mechanism was deduced in
1964 by Robin Holliday and is referred to as the Holliday Model
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.
Different proteins are used, and the system is more complex than it is in
prokaryotes. Replication is controlled so that it occurs only once during a cell-
division cycle, during the S phase.
There are at least 19 different DNA polymerases in eukaryotes, of which five
have been studied extensively -- , , , , and . Polymerase is the principal
synthesizer of DNA and is the equivalent of Pol III in prokaryotes.
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
versus lagging strands. This is exacerbated by inherent difficulties in picturing things in
three dimensions. Simple models using twisted strings are often helpful. The material on
DNA replication may be expected to take between one and two lectures. The additional
material on DNA repair will likely require most of a lecture period.
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
2. Directionality (5' —>3') of synthesis
3. Guarding against errors
B. Semiconservative replication
C. Bidirectional replication
III. DNA polymerase
A. Discontinuous synthesis of lagging strand
B. DNA polymerases from E. coli
1. Pol III core structure
2. Necessity of a primer
3. Proofreading functions
IV. Proteins required for replication
A. Unwinding of the double helix
1. DNA gyrase
2. helicase
3. SSB
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
D. Mismatch repair
E. Methylation as a way to distinguish strands
F. Base excision repair
G. Nucleotide-excision repair
H. Non-homologous DNA end-joining
VI. Recombination
A. Homologous vs nonhomologous
B. Location of crossing over
C. Holliday model
D. Proteins involved in recombination
VII. Eukaryotic DNA replication
A. Replicons
B. Cell cycle control
C. Eukaryotic DNA polymerases
D. The eukaryotic replication fork
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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
proteins directed by mRNA, which reflects the base sequence of DNA.
2. False. In retroviruses, the flow of information is RNA DNA.
3. DNA represents the permanent copy of genetic information, whereas RNA is
transient. The cell could survive production of some mutant proteins, but not DNA
mutation.
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
always package into light viral particles, and the heavy DNA would package into
heavy viral particles. This would lead to only two populations of phages after
infection. Their results showed, however, that there were intermediate
combinations that had DNA of different weights. This demonstrated that the
phage DNA was recombining.
Biosynthesis of Nucleic Acids: Replication 7
48. Similar to the experiment described in 47 above, using heavy isotopes
demonstrated the semi-conservative nature of replication. Intermediate weight
products of replication demonstrated that progeny DNA contains one parental
strand and one new strand.
49. Recombination occurs by the breakage and reunion of DNA strands so that
physical exchange of DNA parts takes place. The mechanism was deduced in
1964 by Robin Holliday and is referred to as the Holliday Model.
FOOTNOTES: