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Chap. 4 Problem 2
The two strands of the double-helical plasmid DNA separate (melt,
denature) at 90˚C. During cooling down to 25˚C, the strands come
back together. However, because the single-stranded DNA
sequencing primer is in great excess, it hybridizes preferentially to
its complementary region of the plasmid. This prevents the two
complementary strands of the plasmid DNA from reannealing at the
region where the primer binds. DNA polymerases used in sequencing
bind to the 3’-OH group of the primer and extend it in the
sequencing reactions. DNA sequencing is covered in Chap. 5.
Chap. 4 Problem 4
Prokaryotic mRNAs are ready to be
translated immediately after they
are transcribed. Prokaryotic mRNAs
often are polycistronic, and contain
coding sequences for multiple genes
that are under the control of a
common promoter. Eukaryotic
mRNAs typically encode only a single
protein. They further are
extensively post-transcriptionally
modified by capping, intron splicing,
and polyadenylation reactions (Fig.
4.15).
Chap. 4 Problem 6
An operon is a collection of tandemly linked genes that are
transcribed in a single polycistronic mRNA. In the E. coli trp operon,
the five gene products all work together in the biosynthesis pathway
for the amino acid tryptophan. It is advantageous to link genes
together in an operon, so that only one promoter must be regulated
to coordinate expression of the related genes. In eukaryotes, the trp
genes are transcribed separately (Fig. 4.13b). Thus, multiple
promoters must be coordinately regulated to achieve the goal of
balanced expression.
Chap. 4 Problem 8
DNA polymerases synthesize DNA
strands in a 5’  3’ direction while
moving 3’  5’ relative to a
template strand. While one strand
(the leading strand) can be
synthesized continuously as the
replication fork advances, the
other strand (the lagging strand)
must be synthesized discontinuously
in segments (Okazaki fragments)
due to the polarity of DNA
polymerase chain elongation.
Synthesis of the lagging strand
occurs from primers laid down on
the template strand as it is
exposed by movement of the fork.
(See Fig. 4.30)
Chap. 4 Problem 15
a.
If DNA were unwound by helicases for replication, but stabilizing
ssDNA binding proteins such as RPA were mutated and could not
bind to the ssDNA, then replication would cease due to
reformation of dsDNA.
b. If a mRNA molecule formed a hairpin loop on itself at the AUG
start site, then the AUG start codon could not be located by the
ribosomal initiation complex. Translation of the mRNA would be
blocked.
c.
If a cell were unable to produce functional tRNAiMet, then
translation of most mRNAs would be blocked at the initiation
step. tRNAiMet is the only tRNA that can be used to initiate
translation.